In 1998 a study of facial symmetry and beauty was experimented on by  Gillian Rhodes  called "Facial symmetry and the perception of beauty". [ 11 ]  In the experiment, images of human faces were digitally manipulated to show various amounts of symmetry. People were asked to rate the faces, and found that the faces with the most symmetry were the most attractive.


Developmental homeostasis is present not only in humans, but in animals as well. The choosing of symmetrical features over asymmetrical features have been observed in birds, lizards, Araneae, and even insects. For example,  barn swallow  females have been reported to prefer males whose long outer feathers are the same length on each side. Symmetrical males gain a reproductive advantage because of the female mate choice. [ 1 ]


Another example is the behavior exhibited in the damselfly  Lestes viridis , where males with more symmetrical hindwings were mated with more than their unmated rivals with asymmetrical hindwings. [ 1 ]  These examples show that individuals with high quality features are able to reproduce their large and symmetrical traits, while individuals who have lower quality features suffer costs to produce their asymmetrical traits. [ 12 ]


One species that chooses their mates based on body symmetry is the brush-legged wolf spider. Males who have larger tufts on one leg than the other (asymmetrical) tend to be smaller and have poorer fitness than the males who have symmetrical tufts. During courtship, the males wave their hair foreleg tufts, and symmetrical males are chosen over asymmetrical males by the females. [ 1 ]


A  diallel cross  is a mating scheme used by  plant  and  animal  breeders, as well as  geneticists , to investigate the genetic underpinnings of quantitative traits. [ 1 ] [ 2 ]


In a full diallel, all parents are crossed to make hybrids in all possible combinations. Variations include half diallels with and without parents, omitting reciprocal crosses. [ 3 ]  Full diallels require twice as many crosses and entries in experiments, but allow for testing for  maternal and paternal  effects. [ 4 ]  If such "reciprocal" effects are assumed to be negligible, then a half diallel without reciprocals can be effective.


Common analysis methods utilize  general linear models  to identify  heterotic groups , [ 5 ]  estimate  general  or  specific combining ability , [ 6 ] [ 7 ]  interactions with testing environments and years, or estimates of additive, dominant, and epistatic genetic effects [ 8 ] [ 9 ]  and genetic correlations. [ 10 ]


There are four main types of diallel mating design:


Distal promoter  elements are  regulatory DNA sequences  that can be many kilobases distant from the  gene  that they regulate. [ 1 ]


They can either be  enhancers  (increasing expression) or  silencers  (decreasing expression). They act by binding  activator  or  repressor  proteins ( transcription factors ) and the intervening DNA bends such that the bound proteins contact the  core promoter  and  RNA polymerase . [ 1 ]


T-cell development and activation is controlled by complementary placement of proximal and distal  lck  promoters. The generated environment of a Lck-PROX mice when approached with proximal promoter demonstrates maximal  lck  protein and normal thymic development, while distal promoters lead to deficient  lck  protein and unnormal thymic levels.  [ 2 ]


Further research at the late stage of thymocyte development reveals that distal Lck promoter with driven Cre will result in the distal  lck  gene promoter to drive Cre expression to be limited within innate-like T cells. There is a cell type specific function in innate-like T cells based on the distal  lck  promoter - driven Cre. [ 3 ]


Multiple studies have discovered abnormalities in distal promoters within cancer cells. For example, an overactive distal promoter located about 1 kilobase away from the MUC5B gene contributes to atypical expression of this gene in gastric cancer cells. [ 4 ]  Similarly, a few polymorphisms in the RUNX3 distal promoter alter the promoter's function, increasing the activity of the NF-κB transcription factor and the expression of the IL1B gene. These polymorphisms have been correlated with increased vulnerability to intestinal gastric cancer. [ 5 ]


Another cancer- related gene is EGLN2, which is located in the chromosome (19q13.2 region). This gene encodes an enzyme that can recognize conserved prolyl residues and hydroxylates it in a α-subunit of hypoxia inducible factor (HIF). The functional polymorphism is a 4bp insertion/deletion within the distal promoters, which can affect the expression of EGLN2. [ 6 ]


Distal promoters in RNA polymerase II bind at enhancer elements and may act as a marker for active regulatory sequences.  [ 7 ]


Distyly  is a type of  heterostyly  in which a plant demonstrates  reciprocal herkogamy . This breeding system is characterized by two separate flower morphs, where individual plants produce flowers that either have long styles and short stamens (L-morph flowers), or that have short styles and long stamens (S-morph flowers). [ 1 ]   However, distyly can refer to any plant that shows some degree of  self-incompatibility  and has two morphs if at least one of the following characteristics is true; there is a difference in  style  length,  filament  length,  pollen  size or shape, or the surface of the  stigma . [ 2 ]  Specifically these plants exhibit intra-morph self-incompatibility, flowers of the same style morph are incompatible. [ 3 ]  Distylous species that do not exhibit true self-incompatibility generally show a bias towards inter-morph crosses - meaning they exhibit higher success rates when reproducing with an individual of the opposite morph. [ 4 ]


The first scientific account of distyly can be found in Stephan Bejthe's Caroli book  Clusii Atrebatis Rariorum aliquot stirpium   [ 5 ] .   Bejthe describes the two floral morphs of  Primula veris.   Charles Darwin  popularized distyly with his account of it in his book  The Different Forms of Flowers on Plants of the Same Species . [ 6 ]  Darwin's book represents the first account of intramorphic self-incompatibility in distylous plants and focuses on garden experiments in which he looks at seed set of different distylous  Primula . Darwin names the two floral morphs S- and L-morph, moving away from the  vernacular  names, Pin (for L-morph) and Thrum (for S-morph), which he states were initially assigned by florist.


Distylous species have been identified in 28 families of Angiosperm, likely evolving independently in each family. [ 7 ]  This means, the system has evolved at least 28 times, though it has been suggested the system has evolved multiple times within some families. [ 7 ]  Since distyly has evolved more than once, it is considered a case of  convergent evolution . [ 7 ]


Reciprocal herkogamy likely evolved to prevent the pollen of the same flower from landing on its own stigma. This in turn promotes outcrossing.


In a study of  Primula veris  it was found that pin flowers exhibit higher rates of self-pollination and capture more pollen than the thrum morph. [ 8 ]  Different  pollinators  show varying levels of success while pollinating the different  Primula  morphs, the head or proboscis length of a pollinator is positively correlated to the uptake of pollen from long styled flowers and negatively correlated for pollen uptake on short styled flowers. [ 9 ]  The opposite is true for pollinators with smaller heads, such as bees, they uptake more pollen from short styled morphs than long styled ones. [ 9 ]  The differentiation in pollinators allows the plants to reduce levels of intra-morph pollination.


There are two main hypothetical models for the order in which the traits of distyly evolved, the 'selfing avoidance model'  [ 10 ]  and the 'pollen transfer model'. [ 11 ]


A  supergene , called the self-incompatibility (or S - ) locus, is responsible for the occurrence of distyly. [ 7 ]  The  S -locus is composed of three tightly linked genes ( S -genes) which  segregate  as a single unit. [ 7 ]


Traditionally it was hypothesized that one  S- gene controls all female aspects of distyly, one gene that controls the male morphological aspects, and one gene that determines the male  mating type . [ 12 ]  While this hypothesis appears to be true in  Turnera , [ 13 ]  it is not true in   Primula   [ 14 ]  nor  Linum . [ 15 ]   The S-morph is  hemizygous  for the  S- locus and the L-morph does not have an  allelic  counterpart  [ 7 ] .  The hemizygotic nature of the  S- locus has been shown in  Primula   [ 14 ]   ,   Gelsemium , [ 16 ]   Linum   [ 17 ] [ 15 ] ,  Fagopyrum   [ 18 ] [ 19 ] ,   Turnera, [ 13 ]   Nymphoides [ 20 ]  and  Chrysojasminum . [ 21 ]


The presence of the  S- locus results in changes to  gene expression  between the two floral morphs, as has been demonstrated using  transcriptomic analyses  of  Lithospermum multiflorum   [ 22 ]   ,  Primula veris , [ 23 ]   Primula oreodoxa   [ 24 ] ,  Primula vulgaris   [ 25 ]  and  Turnera subulata [ 26 ] , and  Forsythia suspensa . [ 27 ]


In  Chrysojasminum , the  S -locus is composed of two  S -genes,  BZR1  and  GA2ox . [ 21 ]   GA2ox is hypothetically involved in establishing self-incompatibility. [ 21 ]


The S - morph of  Fagopyrum  contains ~2.8 Mb hemizygous region which likely represents the  S -locus as it contains  S-ELF4  which establishes female morphology and mating type. [ 18 ] [ 19 ]


In  Gelsemium , the  S -locus is composed of four genes,  GeCYP ,  GeFRS6 , and  GeGA3OX  are hemizygous and  TAF2  appears to be allelic with a truncated copy in the L-morph. [ 16 ]   GeCYP  appears to share a last common ancestor (or  ortholog ) with the  Primula S -gene  CYP T .   It is currently hypothesized that the for  S -genes in  Gelsemium  were inherited as a group rather than separately. [ 16 ]  This is the only known case of the  S -genes being inherited as a group rather than individually.


In  Linum  the  S -locus is composed of nine genes, two are  LtTSS1  and  LtWDR-44  the other seven are unnamed and are of unknown function. [ 15 ]   LtTSS1  is hypothesized to regulate style length in the S-morph. [ 17 ]   Synonymous substitution  analysis of three of the  S -genes suggest the  S -locus in  Linum  evolved in a step by step manner, though only three of the nine genes were analyzed. [ 15 ]


The  S -locus of  Nymphoides  contains three genes  NinS1 ,  NinKHZ2 , and  NinBAS1. [ 20 ]   NinBAS1  is only expressed in the style and is hypothetical involved in regulation of brassinosteroids,  NinS1  is only expressed in the stamen,  NinKHZ2  is expressed in both stamen and style. [ 20 ]  Similar to other  S -loci, the  Nymphoides S -locus appears to have evolved via stepwise duplication events. [ 20 ]


In  Primula  the  S- locus is composed of five genes,  CYP T (or  CYP734A50 ),  GLO T  (or  GLOBOSA2 ) , KFB T , PUM T ,  and  CCM T .  The supergene evolved in a step-by-step manner, meaning each  S- gene duplicated and move to the pre- S -locus independently of the others. [ 28 ] [ 29 ]  Synonymous substitution analysis of the  S -genes suggest the oldest  S -gene in  Primula  is likely  KFB T  which likely duplicated about 104 million years ago, followed by  CYP T (42.7 MYA), GLO T  (37.4 MYA),  CCM T (10.3 MYA). [ 29 ]  It is unknown when  PUM T  evolved as it does not have a  paralog  within the  Primula  genome.


Of the five  S -genes, two have been characterized.  CYP T ,  a  cytochrome P450  family member, is the female morphology [ 30 ]  and it is the female self-incompatibility gene, [ 31 ]  meaning it promotes rejection of self pollen.  CYP T   is likely producing these phenotypes via inactivation of  brassinosteroids . [ 30 ] [ 31 ]  Inactivation of brassinosteroids in the S-morph by  CYP T  results in repression of cell elongation in the style by repressing expression of  PIN5 , ultimately producing the short pistil phenotype. [ 30 ] [ 32 ]   GLO T  , a  MADS-BOX  family member, [ 33 ]   i s the male morphology gene as it promotes  corolla tube  growth under the stamen. [ 28 ]  It is unknown how the other three  S -genes are contributing to distyly in  Primula.


In  Turnera  the  S -locus is composed of three genes,  BAHD, SPH1,  and  YUC6. [ 13 ]   BAHD  is likely an  acyltransferase  involved in inactivation of brassinosteroids; [ 34 ]  it is both the female morphology [ 34 ]  and female self-incompatibility gene. [ 35 ]   YUC6  is likely involved in  auxin  biosynthesis based on homology; it is the male self-incompatibility gene and establishes pollen size dimorphisms. [ 36 ]   SPH1  is likely involved in filament elongation based on short filament mutant analysis. [ 13 ]


A  diversity panel  is a collection of genetic material or individual samples taken from a diverse  population  of a certain  species . The idea is to illustrate the genetic and phenotypic diversity of the species.


Diversity panels exist for human populations, mouse and other  organisms .


Researchers in the area of  genetics  often use diversity panels in order to reveal genotypes that are linked to certain  traits , such as in  QTL mapping  with  Genome-wide association study .
Those study analyze the  Gene–environment interaction  underneath simple and complex traits. [ 1 ]


In  genetics ,  DNase I hypersensitive sites  ( DHSs ) are regions of  chromatin  that are sensitive to cleavage by the  DNase I  enzyme.  In these specific regions of the genome, chromatin has lost its condensed structure, exposing the DNA and making it accessible. This raises the availability of DNA to degradation by enzymes, such as DNase I. These accessible chromatin zones are functionally related to  transcriptional activity , since this remodeled state is necessary for the binding of proteins such as  transcription factors .


Since the discovery of DHSs 30 years ago, they have been used as markers of regulatory DNA regions.  These regions have been shown to map many types of  cis-regulatory elements  including promoters, enhancers, insulators, silencers and locus control regions. A high-throughput measure of these regions is available through  DNase-Seq . [ 2 ]


The  ENCODE  project proposes to map all of the DHSs in the  human genome  with the intention of cataloging human regulatory DNA.


DHSs mark transcriptionally active regions of the genome, where there will be cellular selectivity.  So, they used 125 different human cell types.  This way, using the massive sequencing technique, they obtained the DHSs profiles of every cellular type.  Through an analysis of the data, they identified almost 2.9 million distinct DHSs.  34% were specific to each cell type, and only a small minority (3,692) were detected in all cell types.  Also, it was confirmed that only 5% of DHSs were found in TSS (Transcriptional Start Site) regions.  The remaining 95% represented distal DHSs, divided in a uniform way between intronic and intergenic regions.  The data gives an idea of the great complexity regulating the genetic expression in the human genome and the quantity of elements that control this regulation.


The high-resolution mapping of DHSs in the model plant  Arabidopsis thaliana  has been reported. Total 38,290 and 41,193 DHSs in leaf and flower tissues have been identified, respectively. [ 3 ]


The study of DHS profiles combined with other techniques allows analysis of regulatory DNA in humans:


The data obtained were validated with the chromosome conformation capture carbon copy (5C) technique.  This technique is based in the physical association that exists between the promoter and the enhancers, determining the regions of chromatin that enter in contact in the promoter/enhancer connections.


It was confirmed that the majority of promoters were related with more than one enhancer, which indicates the existence of a complicated network of regulation for the immense majority of genes.  Surprisingly, they also found that approximately half of the enhancers were found to be associated with more than one promoter.  This discovery shows that the human cis-regulatory system is much more complicated than initially thought.


The number of distal cis-regulatory elements connected to a promoter is related to the quantitative average of the regulation complexity of a gene.  In this way, it was determined that human genes with more interactions with distal DHSs, and with at least one more complex regulation, corresponded with those genes with functions in the immune system.  This indicates that the complex of cellular and environmental signals processed by the immune system is directly encoded in the cis-regulatory architecture of its constituent genes.


Domestication islands  refers to regions within DNA that do not change despite gene flow between wild and domesticated species. [ 1 ]


In 2005, a study of  genomic DNA  within species of mosquitoes found that there were "speciation islands" of genes that remain differentiated despite considerable gene flow, and are therefore expected to contain the genes responsible for reproductive isolation between species. [ 2 ]  In the following years, there was criticism of this proposal and that there might be other explanations, including  nucleotide  diversity within species [ 3 ]  or reduced diversity. [ 4 ]  This debate continues.


In 2007, a study of the  genomic DNA  differences of wild compared to domesticated species of beans found that there was a large fraction of the genome of the common bean that appears to have been subjected to the effects of selection during  domestication . Domestication appears to have affected not only the target genes, but also a large portion of the genome around these genes. These "domestication islands" have probably experienced a higher level of isolation between the wild and the domesticated forms in comparison with the rest of the genome, probably because of linkage to the loci selected during domestication. [ 1 ]


In 2015, a study looked at the  genome  sequences of pigs, and found that the assumption of  reproductive isolation and strong domestication bottlenecks were incompatible with the data. The domestication process is believed to have begun through human intervention, involving a small number of individuals and relying on reproductive isolation between wild and domesticated forms. Although there has been genetic exchange between domestic and wild pigs, the genomes of domestic pigs show significant signs of selection at genetic loci influencing behavior and physical characteristics. The conclusion was that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created "islands of domestication" in the genome. [ 5 ]


Domestication syndrome  refers to two sets of  phenotypic  traits that are common to either  domesticated plants [ 1 ] [ 2 ]  or  domesticated animals . [ 3 ]


Domesticated animals tend to be smaller and less aggressive than their wild counterparts; they may also have floppy ears, variations to coat color, a smaller brain, and a shorter muzzle. Other traits may include changes in the endocrine system and an extended breeding cycle. [ 3 ] [ 4 ] [ 5 ]  These animal traits have been claimed to emerge across the different species in response to selection for tameness, which was purportedly demonstrated in a  famous Russian fox breeding experiment , [ 6 ] [ 7 ] [ 8 ]  though this claim has been disputed. [ 9 ] [ 10 ]


Other research [ 3 ]  suggested that pleiotropic change in   neural crest  cell regulating genes was the common cause of shared traits seen in many domesticated animal species. However, several recent publications have either questioned this neural crest cell explanation [ 4 ] [ 11 ] [ 10 ]  or cast doubt on the existence of domestication syndrome itself. [ 9 ]  One recent publication [ 10 ]  points out that shared selective regime changes following transition from wild to domestic environments are a more likely cause of any convergent traits. In addition, the sheer number, diversity, and phenotypic importance of neural crest cell-derived vertebrate features means that changes in genes associated with them are almost inevitable in response to any significant selective change. [ 10 ]


The process of  plant domestication  has produced changes in  shattering /fruit  abscission , shorter height, larger  grain  or fruit size, easier  threshing ,  synchronous flowering , and increased yield, as well as changes in color, taste, and texture. [ 12 ]


Charles Darwin 's study of  The Variation of Animals and Plants Under Domestication  in 1868 identified various behavioral, morphological, and physiological traits that are shared by domestic animals, but not by their wild ancestors. These shared traits became known as "the domestication syndrome", [ 3 ]  a term originally used to describe common changes in domesticated grains. [ 1 ] [ 2 ]  In animals, these traits include tameness, docility, floppy ears, altered tails, novel coat colors and patterns, reduced brain size, reduced body mass and smaller teeth. [ 3 ] [ 4 ] [ 5 ]  Other traits include changes in craniofacial morphology, alterations to the endocrine system, and changes to the female estrous cycles including the ability to breed all year-round. [ 3 ] [ 5 ] [ 14 ]


A recent hypothesis suggests that  neural crest  cell behaviour may be modified by domestication, which then leads to those traits that are common across many domesticated animal species. [ 3 ] [ 15 ] [ 16 ]  This hypothesis has claimed support from many gene-based studies; e.g., [ 17 ] [ 18 ]  However, recent publications have disputed this support; pointing out that observed change in neural crest related genes only reveals change in neural crest-derived features. [ 4 ] [ 11 ]  In effect, it is not evidence of linked trait changes in different species due to pleiotropic neural crest mechanisms as claimed by the neural crest cell hypothesis. [ 3 ]  For example, all of the craniofacial skeleton is derived from the neural crest, so any animal population that experiences evolutionary change in craniofacial features will show changes in genes associated with the neural crest. The number and importance of neural crest cell features in all vertebrates means change in these features is almost inevitable under the major selective regime shifts experienced by animals making the wild to domestic transition. [ 10 ]


Many similar traits – both in animals and plants – are produced by  orthologs ; however, whether this is true for domestication traits or merely for wild forms is less clear. Especially in the case of plant  crops , doubt has been cast because some domestication traits have been found to result from unrelated  loci . [ 19 ]


In 2018, a study identified 429 genes that differed between modern dogs and modern wolves. As the differences in these genes could also be found in ancient dog fossils, these were regarded as being the result of the initial domestication and not from recent breed formation. These genes are linked to  neural crest  and  central nervous system  development. These genes affect  embryogenesis  and can confer tameness, smaller jaws, floppy ears, and diminished craniofacial development, which distinguish domesticated dogs from wolves and are considered to reflect domestication syndrome. The study concluded that during early dog domestication, the initial selection was for behavior. This trait is influenced by those genes which act in the neural crest, which led to the phenotypes observed in modern dogs. [ 18 ]


The 2023  parasite-mediated domestication  hypothesis suggests that  endoparasites  such as  helminths  and  protozoa  could have mediated the domestication of mammals. Domestication involves taming, which has an endocrine component; and parasites can modify endocrine activity and  microRNAs . Genes for resistance to parasites might be linked to those for the domestication syndrome; it is predicted that domestic animals are less resistant to parasites than their wild relatives. [ 20 ] [ 21 ]


A dog's cranium is 15% smaller than an equally heavy wolf's, and the dog is less aggressive and more playful. Other species pairs show similar differences.  Bonobos , like  chimpanzees , are a close genetic cousin to humans, but unlike the chimpanzees, bonobos are not aggressive and do not participate in lethal inter-group aggression or kill within their own group. The most distinctive features of a bonobo are its cranium, which is 15% smaller than a chimpanzee's, and its less aggressive and more playful behavior. These, and other, features led to the proposal that bonobos are a 'self-domesticated' ape. [ 22 ] [ 23 ]  In other examples, the  guinea pig 's cranium is 13% smaller than its wild cousin the  cavy , and domestic fowl show a similar reduction to their wild cousins. In a famous Russian farm fox experiment, foxes selectively bred for reduced aggression appeared to show other traits associated with domestication syndrome. This prompted the claim that domestication syndrome was caused by selection for tameness. The foxes were not selectively bred for smaller craniums and teeth, floppy ears, or skills at using human gestures, but these traits were demonstrated in the friendly foxes. Natural selection favors those that are the most successful at reproducing, not the most aggressive. Selection against aggression made possible the ability to cooperate and communicate among foxes, dogs and bonobos. [ 22 ] : 114  [ 24 ]  The more docile animals have been found to have less testosterone than their more aggressive counterparts, and testosterone controls aggression and brain size. [ 25 ]  The further away a dog breed is genetically from wolves, the larger the relative brain size is. [ 26 ]


The domestication syndrome was reported to have appeared in the  domesticated silver fox  cultivated by  Dmitry Belyayev 's breeding experiment. [ 27 ]  However, in 2015 canine researcher  Raymond Coppinger  found historical evidence that Belyayev's foxes originated in  fox farms  on  Prince Edward Island  and had been bred there for  fur farming  since the 1800s, and that the traits demonstrated by Belyayev had occurred in the foxes prior to the breeding experiment. [ 28 ]  A 2019 opinion paper by Lord and colleagues argued that the results of the "Russian farm fox experiment" were overstated, [ 13 ]  although the pre-domesticated origins of these Russian foxes were already a matter of scientific record. [ 8 ]


In 2020, Wright et al. [ 29 ]  argued Lord et al.'s critique refuted only a narrow and unrealistic definition of domestication syndrome because their criteria assumed it must be caused by genetic pleiotropy, and arises in response to 'selection for tameness'--as was claimed by Belyaev, [ 6 ]  Trut, [ 7 ]  and the proposers of the neural crest hypothesis. [ 3 ] [ 16 ]  In the same year, Zeder [ 30 ]  pointed out that it makes no sense to deny the existence of domestication syndrome on the basis that domestication syndrome traits were present in the pre-domesticated founding foxes.


The hypothesis that neural crest genes underlie some of the phenotypic differences between domestic and wild horses and dogs is supported by the functional enrichment of  candidate genes  under selection. [ 27 ]  But, the observation of changed neural crest cell genes between wild and domestic populations need only reveal changes to features derived from neural crest, it does not support the claim of a common underlying genetic architecture that causes all of the domestication syndrome traits in all of the different animal species. [ 11 ]


Gleeson and Wilson [ 10 ]  synthesised this debate and showed that animal domestication syndrome is not caused by selection for tameness, or by neural crest cell genetic pleiotropy. However, it could result from shared selective regime changes (which they termed 'reproductive disruption') leading to similarly shared trait changes across different species--in effect, a series of partial trait convergences. They proposed four primary selective pathways that are commonly altered by the shift to a domestic selective context, and would often lead to similar shifts in different populations. These pathways are:


Because the 'Reproductive Disruption' [ 10 ]  hypothesis explains domestication syndrome as a result of changed selective regimes, it can encompass multiple genetic or physiological ways that similar traits might emerge in the different domesticated species. For example, tamer behaviour might be caused by reduced adrenal reactivity, [ 31 ]  by increased oxytocin production, [ 32 ]  or by a combination of these or other mechanisms, across the different populations and species.


The same concept appears in the  plant domestication  process which produces  crops , but with its own set of syndrome traits. In cereals, these include little to no  shattering [ 12 ] /fruit  abscission , [ 19 ]  shorter height (thus decreased  lodging ), larger  grain [ 12 ]  or fruit [ 19 ]  size, easier  threshing ,  synchronous flowering , altered timing of  flowering , increased grain weight, [ 12 ]   glutinousness  (stickiness, not  gluten  protein content), [ 19 ] [ 12 ]  increased  fruit /grain number, altered color compounds, taste, and texture,  daylength  independence,  determinate growth , lesser/no  vernalization , less  seed dormancy . [ 19 ]


Control of the syndrome traits in cereals is by:


Many of these are mutations in  regulatory genes , especially  transcription factors , which is likely why they work so well in domestication: They are not new, and are relatively ready to have their magnitudes altered. In annual grains,  loss of function  and  altered expression  are by far the most common, and thus are the most interesting goals of  mutation breeding , while  copy number variation  and  chromosomal rearrangements  are far less common. [ 12 ]


A  doubled haploid  (DH) is a genotype formed when  haploid  cells undergo chromosome doubling. Artificial production of doubled haploids is important in  plant breeding .


Haploid cells are produced from  pollen  or  egg  cells or from other cells of the  gametophyte , then by induced or spontaneous chromosome doubling, a doubled haploid cell is produced, which can be grown into a doubled haploid plant. If the original plant was  diploid , the haploid cells are  monoploid , and the term  doubled monoploid  may be used for the doubled haploids. Haploid organisms derived from  tetraploids  or  hexaploids  are sometimes called  dihaploids  (and the doubled dihaploids are, respectively, tetraploid or hexaploid).


Conventional  inbreeding  procedures take six generations to achieve approximately complete  homozygosity , whereas doubled haploidy achieves it in one generation. [ 1 ]  Dihaploid plants derived from tetraploid crop plants may be important for breeding programs that involve diploid wild relatives of the crops.


The first report of the haploid plant was published by Blakeslee  et al.  (1922) in  Datura stramonium . Subsequently, haploids were reported in many other species. Guha and Maheshwari (1964) developed an  anther  culture technique for the production of haploids in the laboratory. Haploid production by wide crossing was reported in  barley  (Kasha and Kao, 1970) and  tobacco  (Burk  et al. , 1979). Tobacco,  rapeseed , and barley are the most responsive species for doubled haploid production. Doubled haploid methodologies have now been applied to over 250 species. [ 2 ]


Doubled haploids can be produced  in vivo  or  in vitro . Haploid embryos are produced  in vivo  by  parthenogenesis ,  pseudogamy , or chromosome elimination after wide crossing. The haploid embryo is rescued, cultured, and chromosome-doubling produces doubled haploids. The  in vitro  methods include  gynogenesis  ( ovary  and flower culture) and  androgenesis  (anther and microspore culture). [ 3 ]  Androgenesis is the preferred method. Another method of producing the haploids is wide crossing. In barley, haploids can be produced by wide crossing with the related species  Hordeum bulbosum ; fertilization is affected, but during the early stages of seed development the  H. bulbosum  chromosomes are eliminated leaving a haploid embryo. In tobacco ( Nicotiana tabacum ), wide crossing with  Nicotiana africana  is widely used. When  N. africana  is used to pollinate  N. tabacum , 0.25 to 1.42 percent of the  progeny  survive and can readily be identified as either  F1 hybrids  or maternal haploids. Although these percentages appear small, the vast yield of tiny seeds and the early death of most seedlings provide significant numbers of viable hybrids and haploids in relatively small soil containers. This method of interspecific pollination serves as a practical way of producing seed-derived haploids of  N. tabacum , either as an alternative method or complementary method to anther culture.


In DH method only two types of genotypes occur for a pair of alleles, A and a, with the frequency of ½ AA and ½  aa, while in diploid method three genotypes occur with the frequency of ¼ AA, ½ Aa, ¼ aa. Thus, if AA is desirable genotype, the probability of obtaining this genotype is higher in haploid method than in diploid method. If n loci are segregating, the probability of getting the desirable genotype is (1/2)n by the haploid method and (1/4)n by the diploid method. Hence the efficiency of the haploid method is high when the number of genes concerned is large.


Studies were conducted comparing DH method and other conventional breeding methods and it was concluded that adoption of doubled haploidy does not lead to any bias of genotypes in populations, and random DHs were even found to be compatible to selected line produced by conventional pedigree method. [ 4 ]


Most of the economic traits are controlled by genes with small but cumulative effects. Although the potential of DH populations in quantitative genetics has been understood for some time, it was the advent of molecular marker maps that provided the impetus for their use in identifying loci controlling quantitative traits. As the  quantitative trait loci  (QTL) effects are small and highly influenced by environmental factors, accurate  phenotyping  with replicated trials is needed. This is possible with doubled haploidy organisms because of their true breeding nature and because they can conveniently be produced in large numbers. Using DH populations, 130 quantitative traits have been mapped in nine crop species. [ 5 ]  In total, 56 DH populations were used for QTL detection. [ 2 ]


In  backcross conversion , genes are introgressed from a donor  cultivar  or related species into a recipient elite line through repeated  backcrossing . A problem in this procedure is being able to identify the lines carrying the trait of interest at each generation. The problem is particularly acute if the trait of interest is recessive, as it will be present only in a heterozygous condition after each backcross. The development of molecular markers provides an easier method of selection based on the genotype (marker) rather than the phenotype. Combined with doubled haploidy it becomes more effective. In marker assisted backcross conversion, a recipient parent is crossed with a donor line and the hybrid (F1) backcrossed to the recipient. The resulting generation (BC1) is backcrossed and the process repeated until the desired genotypes are produced. The combination of doubled haploidy and molecular marker provides the short cut. In the backcross generation one itself, a genotype with the character of interest can be selected and converted into homozygous doubled-haploid genotype. [ 6 ]  Chen  et al.  (1994) used marker assisted backcross conversion with doubled haploidy of BC1 individuals to select stripe rust resistant lines in barley.


In  bulked segregant analysis , a population is screened for a trait of interest and the genotypes at the two extreme ends form two bulks. Then the two bulks are tested for the presence or absence of molecular markers. Since the bulks are supposed to contrast in the alleles that contribute positive and negative effects, any marker polymorphism between the two bulks indicates the linkage between the marker and trait of interest. BSA is dependent on accurate phenotyping and the DH population has particular advantage in that they are true breeding and can be tested repeatedly. DH populations are commonly used in bulked segregant analysis, which is a popular method in marker assisted breeding. [ 7 ]  This method has been applied mostly to rapeseed and barley.


Genetic maps are very important to understand the structure and organization of genomes from which evolution patterns and  syntenic  relationships between species can be deduced. Genetic maps also provide a framework for the mapping of genes of interest and estimating the magnitude of their effects and aid our understanding of genotype/phenotype associations. DH populations have become standard resources in genetic mapping for species in which DHs are readily available. Doubled haploid populations are ideal for genetic mapping. It is possible to produce a genetic map within two years of the initial cross regardless of the species. Map construction is relatively easy using a DH population derived from a hybrid of two homozygous parents as the expected segregation ratio is simple,  i.e.  1:1. DH populations have now been used to produce genetic maps of barley, rapeseed, rice, wheat, and pepper. DH populations played a major role in facilitating the generation of the molecular marker maps in eight crop species. [ 2 ]


Genetic ratios and mutation rates can be read directly from haploid populations. A small doubled haploid (DH) population was used to demonstrate that a dwarfing gene in barley is located chromosome 5H. [ 8 ]  In another study the segregation of a range of markers has been analyzed in barley. [ 9 ]


Although QTL analysis has generated a vast amount of information on gene locations and the magnitude of effects on many traits, the identification of the genes involved has remained elusive. This is due to poor resolution of QTL analysis. The solution for this problem would be production of recombinant chromosome substitution line, [ 10 ]  or stepped aligned recombinant inbred lines. [ 11 ]  Here, backcrossing is carried out until a desired level of recombination has occurred and genetic markers are used to detect desired recombinant chromosome substitution lines in the target region, which can be fixed by doubled haploidy. [ 12 ]  In rice, molecular markers have been found to be linked with major genes and QTLs for resistance to rice blast, bacterial blight, and  sheath blight  in a map produced from DH population. [ 13 ]


Traditional breeding methods are slow and take 10–15 years for cultivar development. Another disadvantage is inefficiency of selection in early generations because of  heterozygosity .
These two disadvantages can be over come by DHs, and more elite crosses can be evaluated and selected within less time.


Uniformity is a general requirement of cultivated line in most species, which can be easily obtained through DH production. [ 14 ]  There are various ways in which DHs can be used in cultivar production. The DH lines themselves can be released as cultivars, they may be used as parents in hybrid cultivar production or more indirectly in the creation of breeders lines and in germplasm conservation. Barley has over 100 direct DH cultivars. [ 6 ]  According to published information there are currently around 300 DH derived cultivars in 12 species worldwide.


The relevance of DHs to plant breeding has increased markedly in recent years owing to the development of protocols for 25 species. [ 2 ]  Doubled haploidy already plays an important role in hybrid cultivar production of vegetables, and the potential for ornamental production is being vigorously examined. DHs are also being developed in the medicinal herb  Valeriana officinalis  to select lines with high pharmacological activity. Another interesting development is that fertile homozygous DH lines can be produced in species that have self-incompatibility systems. [ 15 ]


The ability to produce homozygous lines after a single round recombination saves a lot of time for the plant breeders. Studies conclude that random DH’s are comparable to the selected lines in pedigree inbreeding. [ 16 ]  The other advantages include development of large number of homozygous lines, efficient genetic analysis and development of markers for useful traits in much less time. More specific benefits include the possibility of seed propagation as an alternative to vegetative multiplication in ornamentals, and in species such as trees in which long life cycles and inbreeding depression preclude traditional breeding methods, doubled haploidy provides new alternatives.


The main disadvantage with the DH population is that selection cannot be imposed on the population. But in conventional breeding selection can be practised for several generations: thereby desirable characters can be improved in the population.


In haploids produced from anther culture, it is observed that some plants are aneuploids and some are mixed haploid-diploid types. Another disadvantage associated with the double haploidy is the cost involved in establishing tissue culture and growth facilities. The over-usage of doubled haploidy may reduce genetic variation in breeding germplasm. Hence one has to take several factors into consideration before deploying doubled haploidy in breeding programmes.


Technological advances have now provided DH protocols for most plant genera. The number of species amenable to doubled haploidy has reached a staggering 250 in just a few decades. Response efficiency has also improved with gradual removal of species from recalcitrant category. Hence it will provide greater efficiency of plant breeding.


In  biochemistry , in the  biological  context of  organisms '  regulation of gene expression  and production of  gene products ,  downregulation  is the process by which a  cell  decreases the production and quantities of its  cellular components , such as  RNA  and  proteins , in response to an external stimulus. The complementary process that involves increase in quantities of cellular components is called  upregulation. [ 1 ]


An example of downregulation is the cellular decrease in the expression of a specific  receptor  in response to its increased activation by a molecule, such as a  hormone  or  neurotransmitter , which reduces the cell's sensitivity to the molecule. This is an example of a locally acting ( negative feedback ) mechanism.


An example of upregulation is the response of  liver  cells exposed to such  xenobiotic  molecules as  dioxin . In this situation, the cells increase their production of  cytochrome P450 enzymes , which in turn increases degradation of these dioxin molecules.


Downregulation or upregulation of an RNA or protein may also arise by an  epigenetic  alteration. Such an epigenetic alteration can cause expression of the RNA or protein to no longer respond to an external stimulus. This occurs, for instance, during  drug addiction  or  progression to cancer .


All living cells have the ability to receive and process signals that originate outside their membranes, which they do by means of proteins called  receptors , often located at the cell's surface imbedded in the plasma membrane. When such signals interact with a receptor, they effectively direct the cell to do something, such as dividing, dying, or allowing substances to be created, or to enter or exit the cell. A cell's ability to respond to a chemical message depends on the presence of receptors tuned to that message. The more receptors a cell has that are tuned to the message, the more the cell will respond to it.


Receptors are created, or expressed, from instructions in the DNA of the cell, and they can be increased, or upregulated, when the signal is weak, or decreased, or downregulated, when it is strong. [ citation needed ]  Their level can also be up or down regulated by modulation of systems that degrade receptors when they are no longer required by the cell.


Downregulation of receptors can also occur when receptors have been chronically exposed to an excessive amount of a ligand, either from  endogenous  mediators or from  exogenous  drugs. This results in  ligand -induced desensitization or internalization of that receptor. This is typically seen in animal hormone receptors. Upregulation of receptors, on the other hand, can result in super-sensitized cells, especially after repeated exposure to an antagonistic drug or prolonged absence of the ligand.


Some  receptor agonists  may cause downregulation of their respective receptors, while most  receptor antagonists  temporarily upregulate their respective receptors. The disequilibrium caused by these changes often causes  withdrawal  when the long-term use of a  drug  is discontinued.


Upregulation and downregulation can also happen as a response to  toxins  or  hormones . An example of upregulation in  pregnancy  is hormones that cause cells in the  uterus  to become more sensitive to  oxytocin .


Elevated levels of the hormone  insulin  in the blood trigger downregulation of the associated receptors. [ 2 ]  When insulin binds to its receptors on the surface of a cell, the hormone receptor complex undergoes  endocytosis  and is subsequently attacked by intracellular  lysosomal   enzymes . [ 3 ]  The internalization of the insulin molecules provides a pathway for degradation of the hormone, as well as for regulation of the number of sites that are available for binding on the cell surface. [ 4 ]  At high plasma concentrations, the number of surface receptors for insulin is gradually reduced by the accelerated rate of receptor internalization and degradation brought about by increased hormonal binding. [ 5 ] [ page needed ]  The rate of  synthesis  of new receptors within the  endoplasmic reticulum  and their insertion in the plasma membrane do not keep pace with their rate of destruction. Over time, this self-induced loss of target cell receptors for insulin reduces the target cell's sensitivity to the elevated hormone concentration. [ 5 ]


This process is illustrated by the  insulin  receptor sites on target cells, e.g. liver cells, in a person with type 2  diabetes . [ 6 ]  Due to the elevated levels of blood  glucose  in an individual, the  β-cells  ( islets of Langerhans ) in the  pancreas  must release more insulin than normal to meet the demand and return the blood to  homeostatic  levels. [ 7 ]  The near-constant increase in blood insulin levels results from an effort to match the increase in blood glucose, which will cause receptor sites on the liver cells to downregulate and decrease the number of receptors for insulin, increasing the subject's resistance by decreasing sensitivity to this hormone. [ citation needed ]  There is also a hepatic decrease in sensitivity to  insulin . This can be seen in the continuing  gluconeogenesis  in the liver even when blood glucose levels are elevated. This is the more common process of  insulin resistance , which leads to adult-onset diabetes. [ 8 ]


Another example can be seen in  diabetes insipidus , in which the kidneys become insensitive to  arginine vasopressin .


Family-based, adoption, and twin studies have indicated that there is a strong (50%) heritable component to vulnerability to substance abuse addiction. [ 9 ]


Especially among genetically vulnerable individuals, repeated exposure to a drug of abuse in adolescence or adulthood causes addiction by inducing stable downregulation or upregulation in expression of specific genes and  microRNAs  through  epigenetic alterations . [ 10 ]  Such downregulation or upregulation has been shown to occur in the brain's reward regions, such as the  nucleus accumbens . [ 10 ]


DNA damage appears to be the primary underlying cause of cancer. [ 11 ]  DNA damage can also increase  epigenetic  alterations due to errors during DNA repair. [ 12 ] [ 13 ]  Such mutations and epigenetic alterations can give rise to  cancer  (see  malignant neoplasms ). [ 12 ] [ 13 ] [ verification needed ]  Investigation of epigenetic down- or upregulation of repaired DNA genes as possibly central to progression of cancer has been regularly undertaken since 2000. [ 14 ]


Epigenetic downregulation of the DNA repair gene  MGMT  occurs in 93% of bladder cancers, [ 15 ]  88% of stomach cancers, 74% of thyroid cancers, 40–90% of colorectal cancers, and 50% of brain cancers. [ citation needed ]  Similarly, epigenetic downregulation of  LIG4  occurs in 82% of colorectal cancers and epigenetic downregulation of  NEIL1  occurs in 62% of  head and neck cancers  and in 42% of  non-small-cell lung cancers .


Epigenetic upregulation of the DNA repair genes  PARP1  and  FEN1  occurs in numerous cancers (see  Regulation of transcription in cancer ).  PARP1  and  FEN1  are essential genes in the error-prone and mutagenic DNA repair pathway  microhomology-mediated end joining . If this pathway is upregulated, the excess mutations it causes can lead to cancer.  PARP1  is over-expressed in tyrosine kinase-activated leukemias, [ 16 ]  in neuroblastoma, [ 17 ]  in testicular and other germ cell tumors, [ 18 ]  and in Ewing's sarcoma. [ 19 ]   FEN1  is upregulated in the majority of cancers of the breast, prostate, stomach, neuroblastomas, pancreas, and lung. [ 20 ]   [ citation needed ]


The " drifty gene hypothesis " [ 1 ]  was proposed by the British biologist  John Speakman  as an alternative to the  thrifty gene hypothesis  originally proposed by James V Neel in 1962. [ 2 ]


Speakman's critique of the thrifty gene hypothesis is based on an analysis of the pattern and level of mortality during  famines . Despite much anecdotal evidence used to suggest that famines cause substantial mortality, Speakman suggests that where real data are available famines actually involve rather low levels of mortality and there is no evidence that fat people survive famines better than lean people. In fact, mortality actually falls mostly on groups such as the very young and very old where differential mortality in relation to body composition is highly unlikely. [ 3 ] [ 4 ]


Moreover, there is some confusion among proponents of the thrifty gene hypothesis about how long famines have played a role in evolution. On the one hand some proponents suggest famines have been an "ever present" threat dating back to the dawn of  Australopithecines  about 4–6 million years ago, while others indicate that famines may actually only have been important since the  invention of agriculture , because crop failures would exert devastating effects on our ancestors. Speakman argues that either scenario poses difficulties. If we have been under intense selection for the past 6 million years then simple calculations of the spread of favorable alleles under positive selection, known since the 1920s, indicate that we should all be obese and diabetic, which we clearly are not [ original research? ] . However, if selection has only been acting for the past 15,000 years then there has been insufficient time for thrifty genes to spread at all. [ dubious  –  discuss ]


It is argued instead that the modern distribution of the obese phenotype likely comes about because of  genetic drift  in the genes encoding the regulation system controlling an upper limit on our body fatness. Hence the name "drifty" genes, to contrast the positively selected "thrifty genes". Such drift may have started because around 2 million years ago when ancestral humans effectively removed the risk of  predation , which was probably a key factor maintaining the upper boundary of the regulation system.


The drifty gene hypothesis was presented as part of a presidential debate at the 2007 Obesity Society meeting in New Orleans, with the counter-arguments favoring the thrifty gene hypothesis presented by British nutritionist Andrew Prentice. The main thrust of Prentice's argument against the drifty gene idea is that Speakman's critique of the thrifty gene hypothesis ignores the huge impact that famines have on fertility. It is argued by Prentice that while famine may actually have only been a force driving evolution of thrifty genes for the past 15,000 years or so, because famines exert effects on both survival and fertility the selection pressure may have been sufficient even over such a short timescale to generate the current phenotype distribution of BMI. This critique was published back-to-back with the original 'drifty gene' paper in the International Journal of Obesity in November 2008. [ 5 ]


Prentice et al [ 5 ]  predicted that the emerging molecular genetics field would ultimately provide a way to test between the adaptive 'thrifty gene' idea and the non-adaptive 'drifty gene' idea because it would be possible to find signatures of positive selection in the human genome, at genes that are linked to both obesity and type 2 diabetes, if the 'thrifty gene' hypothesis is correct. Two comprehensive studies have been performed seeking such signatures of selection. Ayub et al (2015) [ 6 ]  searched for signatures of positive selection at 65 genes linked to type 2 diabetes, and Wang and Speakman (2016) [ 7 ]  searched for signatures of selection at 115 genes linked to obesity. In both cases there was no evidence for such selection signatures at a higher rate than in random genes selected for matched GC content and recombination rate. These two papers provide strong evidence against the thrifty gene idea, and indeed against any adaptive explanation which relies on selection during our recent evolutionary history, but instead provide strong support the 'drifty gene' interpretation. [ citation needed ]


The concept of a biological  species  as a group of organisms capable of interbreeding to produce viable offspring dates back to at least the 18th century, although it is often associated today with  Ernst Mayr .  Species of the fruit-fly  Drosophila  are one of the most commonly used organisms in evolutionary research, and have been used to test many theories related to the evolution of species.  The  genus   Drosophila  comprises numerous species that have varying degrees of premating and postmating isolation (including hybrid sterility) between them.  These species are useful for testing hypotheses of the reproductive mechanisms underlying  speciation .


Working in the early 20th century  T.H. Morgan , was the first to use  Drosophila  to explore heredity.  Primarily on the basis of work with  D. melanogaster , Morgan and his colleagues C.B. Bridges, A.H. Sturtevant, and H.J. Mueller developed a chromosome theory of heredity, for which Morgan was awarded a Nobel Prize in 1933.  Their experiments consisted of cross-breeding  Drosophila  mutants and documenting offspring.  Another highly regarded figure in  Drosophila  research was Theodosius  Dobzhansky , who invented the use of genetic markers and used them to study  hybrid   sterility  between  Drosophila pseudoobscura  and  Drosophila persimilis . [ 1 ]  This experimental method has been used for many years.


The  genome  of  D. melanogaster , has been sequenced and studied in fine detail.  It is now known that  Drosophila  has 6 chromosomes—an X/Y pair and four  autosomal  chromosomes.  The genome comprises about 139.5 million base pairs.  There are about 15,000 genes.


Gender is determined in  Drosophila  not by the presence or absence of the Y chromosome as in mammals, but by the ratio of X chromosomes to autosomes.


In the off-spring of crosses between  Drosophila simulans  and its island derivative  Drosophila mauritiana,  female hybrids are fertile but male hybrids are sterile.  Recent studies have shown that a critical gene for gender determination in  Drosophila  known as the sex-lethal gene is highly misregulated in  D. melanogaster  and  D. simulans  hybrids, compared with the degree of misregulation of non-sex biased genes studied.  The sex-lethal gene is often abnormally expressed in male hybrids from  D. melanogaster  mothers as a result of re-localization of the male-specific complex to the X chromosome, which contributes to the male sterility.  Abnormalities in sperm array were found in very few individuals during their larval stage, meaning that disruptions in  spermatogenesis  most likely occur during later stages in life. [ citation needed ]


Experiments involving crosses between  D. pseudoananassae  and  D. bipectinata ,  D. pseudoananassae  and  D. parabipectinata , and  D. pseudoananassae  and  D. malerkotliana  have further shown that the Y chromosome has a role in hybrid male sterility.  The possible interactions of Y chromosome are X-Y, Y-autosome and Y-cytoplasm. [ 2 ]   The sterile males carry a set of conspecific autosomes to the Y chromosome, which results in fertility because of the Y-dominant autosome interactions.  Therefore, Y-autosome interactions are ruled out in this type of hybrid sterility.


Since cytoplasmic factors can be compatible between these species, [ citation needed ]  such factors are also dismissed as the cause of sterility.


However, in  Drosophila paulistorum  there is information suggesting that if Y chromosome and cytoplasm are from different parents, the male is usually sterile. [ 3 ]  X-Y interactions are the most likely cause of sterility in male hybrids.  It has been shown that interbreeding organisms that have more genetic compatibilities have less disruption of  spermatogenesis  and normal sized testes, while species who are less genetically compatible have a higher disruption in spermatogenesis and generally have atrophied testes. [ citation needed ]


Another possible cause of sterility among species in which presence or absence of one or the other sex chromosome determines gender, is if one sex chromosome of one species has recessive alleles interacting with autosomal alleles of the mating species.  This could cause the heterogametic sex chromosome in the hybrid to be inviable or sterile, but homogametic sex chromosome will be fertile. [ 4 ]  Consequently, in species where presence or absence of a Y chromosome determines gender, for instance, individuals carrying XY chromosomes (males) will be sterile and those carrying XX (females) will be fertile.  This is closely related to  Haldane's rule .


It has also been shown that microbial infections of invertebrates can cause modification of the gender and fertility of host's off-spring. For instance, infections of nematodes or of arthropods, including  Drosophila , species of the rickettsial bacteria  Wolbachia  can produce a male-specific sterility, which is congenital by means of transmission through the female line.


Experiments have led scientists to believe that many observations recorded in laboratories neglect existing  polymorphism  factors in hybrid sterility due to crossing parents from non-isofemale lines, as well as possibly underestimating actual degrees of sterility caused by inaccurate measures of  motility . [ citation needed ]  Failure to account for potential polymorphism could lead to misinterpretation of the scale on which hybrid sterility occurs.


Dynamical genetics  is a subfield of  molecular biology  and  genetics  that studies phenomena in which physiological  protein complexes  alter  DNA . The study of such mechanisms is important because they promote useful functions, for example the  immune system recombination  (on the  individual scale ) and  chromosomal crossover  (on the  evolutionary  scale). Furthermore, when such mechanisms malfunction, diseases such as  neurodegenerative disorders  are caused.


Typical examples of dynamical genetics subjects are:


In  Xenopus laevis , the specification of the three germ layers ( endoderm ,  mesoderm  and  ectoderm ) occurs at the  blastula  stage. [ 1 ]  Great efforts have been made to determine the factors that specify the endoderm and mesoderm. On the other hand, only a few examples of genes that are required for  ectoderm  specification have been described in the last decade. The first molecule identified to be required for the specification of ectoderm was the ubiquitin ligase  Ectodermin  (Ecto, TIF1-γ, TRIM33); later, it was found that the deubiquitinating enzyme,  FAM/USP9x , is able to overcome the effects of ubiquitination made by Ectodermin in Smad4 (Dupont et al., 2009). Two transcription factors have been proposed to control gene expression of ectodermal specific genes:  POU91/Oct3/4 [ 2 ]  and  FoxIe1/Xema . [ 3 ] [ 4 ]  A new factor specific for the ectoderm,  XFDL156 , has shown to be essential for suppression of mesoderm differentiation from pluripotent cells. [ 5 ]


The protein Ectodermin, firstly identified in  Xenopus  embryos, promotes ectodermal fate and suppresses the mesoderm formation mediated by the signaling of  Transforming Growth Factor β (TGFβ)  and  Bone Morphogenic Proteins  (BMP), members of the TGFβ-superfamily. [ 6 ]  When the TGFβ ligands bind to TGFβ receptors, they cause the activation of the signal transducers R-Smads ( Smad2 ,  Smad3 ). Smad4 forms a complex with activated R-Smads and activates transcription of specific genes in response to TGFβ signal. The BMP pathway transmits its signals in a similar way but through other types of R-Smads ( Smad1 ,  Smad5  and  Smad8 ). The transcription factor Smad4 is the only common mediator shared between both TGFβ and the BMP pathways. [ 7 ]  During ectoderm specification, the function of Smad4 is regulated by ubiquitination and deubiquitination made by ectodermin and FAM, respectively. The ubiquitination state of Smad4 will determine if it is able to respond to signals derived from TGFβ and BMP. [ 6 ] [ 8 ]  The equilibrium of the activity, localization and timing of TGFβ and BMP transducers, Smad4, FAM and of Ectodermin should be achieved in order to be able to modulate the gene expression of genes required for germ layer formation.


A  cDNA  library from the blastula stage of a frog embryo was cloned into RNA expression plasmids to generate synthetic mRNA. The mRNA was then injected into several  Xenopus  embryos at a four-cell stage and looked in early  blastula  embryos for an expansion of the region of the ectodermal marker Sox2 and diminution of the expression of the mesodermal marker  Xbra . Ectodermin was one out of 50 clones to present this phenotype when injected into embryos. [ 6 ]  The identification of FAM was done through a  siRNA  screen to find  deubiquitinases  that regulate the response to TGFβ.


Ectodermin mRNA is maternally deposited in the animal pole of the egg. In the early blastula stage of the embryo, Ectodermin mRNA and protein forms a gradient that goes from the animal pole (highest concentration) down to the marginal zone (lowest concentration) to prevent TGFβ and  nodal signals  that induce mesoderm originating from the vegetal pole. Ectodermin mRNA is enriched in the dorsal side of the embryo, and at the end of this stage the expression gradually disappears. [ 6 ]  Smad4 is ubiquitinated by Ectodermin in the nucleus and exported to the cytoplasm where it can be deubiquitinated by FAM; this way Smad4 can be recycled and be functional again. Although there is no expression profile of FAM in early embryos in  Xenopus , in the zebra fish, FAM homolog is expressed ubiquitously at a two-cell stage but as development proceeds then its only expressed in the cephalic central nervous system. [ 9 ]


Ectodermin is a ubiquitin E3 ligase that inhibits the TGFβ and the BMP signaling pathways by inhibition of Smad4 via ubiquitination of Lysine 519 and also though direct binding to phospho-Smad2. [ 6 ] [ 8 ]  Injection of Ecto mRNA in the marginal zone leads to an expansion of the early ectodermal marker, Sox2, and a reduction of mesodermal markers (Xbra, Eomes, Vent-1, Mix-1 and Mixer). The opposite happens in knockdown experiments of Ectodermin by using a morpholino strategy; embryos become more sensitive to Activin response, they show an increase and expansion of the expression of mesodermal specific genes and down-regulate the expression of neural plate and epidermis marker (Sox2 and cytokeratin respectively). In line with a RING-finger dependent ubiquitin-ligase activity of Ectodermin, an Ecto RING-finger mutant (C97A/C100A) is inactive in gain-of-function. [ 6 ]  Gain-of-function of FAM increases the responses from BMP and TGFβ and its loss-of-function by mutation in a critical residue for its activity caused inhibition of TGFβ response.


The molecular function of human ectodermin to act as a negative regulator of Smad4 suggests that this specific function is conserved among the vertebrate lineage. [ 6 ]  The sequence identity between FAM homologs is higher than 90% when comparing the homologs of  Xenopus , zebrafish, mouse, and human, suggesting that this might also be conserved among other organisms. [ 9 ]  Indeed, knockout gene inactivation in mouse embryos showed that the function of ectodermin as inhibitor of TGF-beta signaling is conserved. [ 10 ]  Embryos lacking of ectodermin show defective development of the anterior visceral endoderm (AVE), which is the first tissue that is induced by TGF-beta signals in mouse embryos; in accordance with loss of an inhibitor, ectodermin-/- embryos showed enlarged AVE induction. As the AVE is a natural source of secreted TGF-beta antagonists, this primary AVE expansion caused secondarily, at later stages, an inhibition of extracellular TGF-beta ligands, resulting in embryos lacking of mesoderm development. This model was confirmed by the finding that ectodermin-/- embryos were rescued to wild type (normal AVE, normal mesoderm development) by lowering the genetic dosage of the main TGF-beta ligand of the embryo, Nodal. Further supporting a role as TGF-beta inhibitor, tissue-selective deletion of ectodermin from the epiblast (from which the mesoderm, but not the AVE, derive) left the AVE untouched but caused this time an expansion of anterior mesodermal fates, indicative of increased responsiveness to TGF-beta signals. Collectively, these data confirmed with genetic tools a cell-autonomous role for ectodermin as inhibitor of Smad4 responses previously identified in Xenopus embryos and human cell lines.


During early in development in  Xenopus , the transcription factor FoxI1e/Xema activates epidermal differentiation and represses endoderm and mesoderm specific genes in animal caps (Suri et al., 2005).  It is suggested that FoxI1e is active before the ectoderm differentiates into epidermis and the central nervous system.


Mir et al., 2005 identified FoxI1e (Xema) by selecting genes that were down-regulated under mesoderm-inducing signals in the ectoderm compared to vegetal region of an early  blastula  embryo. Also, high expression of this gene was observed in animal caps in embryos that lack VegT compared to wild type.


FoxI1e mRNA is expressed zygotically (stage 8.5) and reaches higher level of expression early in gastrulation and maintains that level in neurula, tailbud until early tadpole stages. [ 4 ]  FoxI1e has a peculiar mosaic expression pattern, it is expressed first in the dorsal ectoderm and while gastrula progresses, the expression goes through the ventral side and its expression is down-regulated in the dorsal side when the neural plate is forming. [ 11 ]  FoxI1e is dependent on BMP signals in the neurula stage, limiting the localization of FoxI1e to the ventral side of the ectoderm.


FoxI1e/Xema belongs to the FoxI1 class of fork head transcription factor family, known to participate in mesoderm formation, eye development [ 12 ]  and ventral head specification. [ 13 ]  It has been proposed that Notch and/or  NODAL , expressed in the vegetal/mesoderm region of the early  blastula  embryo, could potentially be the inhibitors of FoxI1e. [ 3 ] [ 11 ]


Inhibition of FoxI1e mRNA maturation by a splice-blocking morpholino shows malformations in the development of epidermis and pervious system and down-regulates of ectoderm specific genes, whereas FoxI1e over-expression inhibits the formation of mesoderm and endoderm. Vegetal structures form late blastula masses that normally would give rise to endoderm and mesoderm, when injected with FoxI1e mRNA, they are able to express ectodermal specific markers (pan-ectodermal E-cadherin, epithelial cytokeratin, neural crest marker Slug and neural marker Sox-2) while endodermal markers (endodermin, Xsox17a) decreased in expression. [ 3 ] [ 4 ]


The  p53  protein binds to the promoters of early mesodermal genes. [ 14 ]  p53 is maternally deposited transcript that forms a transcriptional factor complex with Smad2 and drives the expression of genes involved in mesoderm induction and activation of TGFβ target genes. [ 15 ]  The  zinc (Zn)-finger  nuclear protein XFDL159, expressed in the animal cap, acts as an ectoderm factor their specifies the ectoderm by inhibiting p53 from activating genes for mesoderm differentiation. [ 5 ]


Construction of a cDNA library from animal caps at a stage of 11.5, cloned into expression vector and generated mRNA.  The synthetic RNA was then injected into embryos and the animal caps of these collected embryos were obtained and submitted to  activin  treatment. Xbra was recovered by selecting the clone that represses the mesodermal marker Xbra. [ 5 ]


Since XFDL156 is a factor that interacts with p53, the localization of this protein is in the nucleus (Sasai et al., 2008). The mRNA of XFDL156 is maternally deposited and then expressed zygotically. The gene expression timeline shows a higher level of expression at early gastrula and a half decrease in expression at mid-gastrula and by the stage 20 the expression fades. [ 5 ]


XFDR zinc finger binds to the regulatory region of p53 located at the C-terminal domain and its expression is not affected by the presence of activin, FoxI1e or XLPOU91 transcription factors.


Loss-of-function by morpholino, causes incorrect mesodermal differentiation in the ectoedermal regions; this is caused by the desuppression of mesodermal markers (Xbra, VegT and Mix.2). Gain-of-functions causes decrease in expression of mesodermal markers. [ 5 ]


The human and mouse homologs of XFDR156 are able to complement XFDR function of interacting with p53 and inhibiting it to act as a transcription factor. [ 5 ]


Elective genetic and genomic testing  are DNA tests performed for an individual who does not have an  indication  for testing. An elective  genetic test  analyzes selected sites in the  human genome  while an elective genomic test analyzes the entire  human genome .  Some elective genetic and genomic tests require a physician to order the test to ensure that individuals understand the risks and benefits of testing as well as the results. Other DNA-based tests, such as a  genealogical DNA test  do not require a physician's order.  Elective testing is generally not paid for by health insurance companies.  With the advent of  personalized medicine , [ 1 ]  also called  precision medicine , an increasing number of individuals are undertaking elective genetic and genomic testing.


Genetic testing [ 2 ]  for a variety of disorders has seen many advances starting with  cytogenetics  to evaluate human  chromosomes  for  aneuploidy  and other  chromosome abnormalities . [ 3 ]  The development of  molecular cytogenetics  involving techniques such as  fluorescence in situ hybridization  (FISH) followed, [ 4 ]  permitting the detection of more subtle changes in the  karyotype . [ 5 ] [ 6 ]  Techniques to determine the precise sequence of  nucleotides  in  DNA  by  DNA sequencing , notably  Sanger sequencing  was developed in the 1970s. [ 7 ]  In the 1980s the  DNA microarray  appeared, permitting laboratories to find  copy number variants  associated with disease [ 8 ]  that are below the level of detection of  cytogenetics  but too large to be detected by  DNA sequencing .  In recent years the development of  high-throughput  or next-generation sequencing has dramatically lowered the cost of  DNA sequencing  permitting laboratories to evaluate all 20,000 genes of the  human genome  at once through  exome sequencing  and  whole genome sequencing . [ 9 ]  A catalogue of the many uses of these techniques can be found in the section:  genetic testing .  Most elective genetic and genomic testing employs either a  DNA microarray  or next-generation sequencing.


Historically, all  laboratory tests  were initiated and ordered by a physician or mandated by a state.  Increasingly, patients and families have become more involved in their own health care.  One outcome has been the growing availability of elective genetic and genomic testing that are initiated by a patient but still ordered by a physician. [ 10 ]   Additionally, elective genetic and genomic testing that does not require a physician's order called, direct-to-consumer genetic testing has recently entered the testing landscape. [ 11 ]


Genetic testing  identifies changes in chromosomes, genes, or proteins; some are associated with human disease. There are many different clinical and non-clinical situations in which genetic testing is used. [ 12 ]


Diagnostic testing is used to identify or rule out a specific genetic or chromosomal condition when a particular disorder is suspected based on signs and symptoms present in the patient. [ 13 ]  Catalogues of more than 50,000 tests available worldwide can be found at GeneTests [ 14 ]  and Genetic Testing Registry. [ 15 ]


Predictive and pre-symptomatic testing is carried out in individuals who do not have evidence of the disease under investigation.  This testing includes  Mendelian  conditions and polygenic diseases. [ 16 ]


Carrier testing  is used to identify people who carry one copy of a gene change (also referred to as a variant or mutation) that, when present in two copies, causes a genetic disorder. Carrier testing is typically offered to individuals who are considering pregnancy or are already pregnant, have a family history of a specific genetic disorder and to people in ethnic backgrounds that have an increased risk of specific genetic conditions. [ 17 ]


Pre-implantation genetic diagnosis  (PGD) [ 18 ]  is used in conjunction with  in-vitro fertilization .  In-vitro fertilization  is the process of combining an egg ( oocyte ) and sperm outside of the body with intent of fertilization. [ 19 ]   PGD  is the testing of individual oocytes or embryos for a known genetic condition prior to transferring the embryo to the uterus. Used together, IVF and PGD allow for selection of embryos or oocytes presumably unaffected with the condition.  PGD  can be utilized by individuals or couples who are affected by a condition of genetic origin, or if both individuals are found to be carriers of a recessive genetic condition.


Prenatal testing  is diagnostic testing of a fetus before birth to detect abnormalities in the chromosomes or genes. Samples for this testing are obtained through invasive procedures such as  amniocentesis  or  chorionic villus sampling . [ 20 ]  Prenatal testing is different from  prenatal screening . [ 21 ]


Newborn screening  screens infants a few days after birth to evaluate for evidence of treatable diseases. Most  newborn screening  uses tandem mass spectroscopy [ 22 ]  to detect biochemical abnormalities that suggest specific disorders. DNA-based newborn testing complements existing newborn screening methods and may replace it. [ 23 ]


Pharmacogenomic  tests (also called  pharmacogenetics ) provide information that can help predict how an individual will respond to a medication. [ 24 ]  Changes in certain genes affect drug  pharmacodynamics  (effects on drug receptors) and  pharmacokinetics  (drug uptake, distribution, and metabolism). Identifying these changes makes it possible to identify patients who are at increased risk for adverse effects from drugs or who are likely to be non-responders. Pharmacogenomic testing allows healthcare providers to tailor therapies by adjusting the dose or drug for an individual patient. [ 25 ] [ 26 ]


Identity testing is used to establish whether individuals are related to one another.  It is commonly used to establish  paternity  but can be used to establish relatedness in  adoption and immigration cases.  It is also used in  forensics . [ 27 ]


Ancestry testing (also referred to as  genetic genealogy ) allows individuals to establish their country of origin and ethnic background and identify distant relatives and ancestors. [ 28 ]


Some  phenotypic traits  in humans have a well established genetic basis, while others involve  many genes  or are a  complex mix of genes and environment . [ 29 ]


There are many different types of  genetic testing  that exist. Each is designed to look at different types of genetic changes that can occur. At present, no single genetic test can detect all types of genetic changes.


DNA sequencing  is a method of testing that looks for single letter changes ( single-nucleotide polymorphisms ) in the genetic code. It can also determine when a small number of letters are missing (deletions) or extra (duplications). Sequencing may be performed on a single gene, a group of genes (panel testing), most of the coding region or exons (whole exome sequencing), or most of the genome (whole genome sequencing). With time, this technology is expected to be able to detect any abnormality of the human genome. [ 30 ]


Genotyping  is testing that looks at specific variants in a particular area of the genetic code. This technology is limited only to those specific variants that the test is designed to detect.  SNP genotyping  is a specific form of genotyping. [ 31 ]


Deletion/duplication testing is a type of testing designed to detect larger areas of the genetic code that are missing or extra. [ 32 ]  This technology does not detect single letter variants or very small deletions or duplications. [ 33 ]


Panel testing refers to testing for a specific subset of genes most often related to a particular condition. This usually involves sequencing and may also include deletion/duplication analysis. This is often referred to as multigene panel testing because testing simultaneously examines a number of different genes. For example, an individual may have panel testing for a group of genes known to be associated with a particular type of cancer such hereditary colon cancer or hereditary breast and ovarian cancer. [ 34 ]


Array or  DNA microarrays  look at copy number changes (missing or extra genetic material). [ 8 ]  This testing looks across a large portion of the genome for larger deletions or duplications (also referred to as copy number variation). This technology can not detect single letter changes or very small deletions or duplications.


Chromosome analysis, also known as  karyotyping  refers to testing that assesses whether the expected number of chromosomes are present, whether there is any rearrangement of the chromosomes, and also whether there are any large deletions or duplications. This technology can not detect single letter changes  ( single nucleotide variants ) or small deletions or duplications. [ 35 ]


Non-invasive prenatal screening  screens for specific chromosomal abnormalities such as Down Syndrome in a fetus using  cell-free DNA . [ 36 ]  This screening can also provide information about fetal sex and rhesus (Rh) blood type. A blood sample is drawn from the pregnant mother.  This sample contains DNA from the mother and fetus.  The amount of fetal DNA is assessed to determine if there is extra fetal genetic material present that may indicate an increased risk that the fetus has Down Syndrome or other selected conditions. As this is a screening test, other diagnostic tests such as  amniocentesis  or  chorionic villus sampling  are needed to confirm a diagnosis.


Newborn screening  is a type of testing that assesses risk for certain genetic, endocrine,  metabolic disorders , hearing loss and critical congenital heart defects. Each state determines the exact list of conditions that are screened. [ 37 ]  Early detection, diagnosis, and intervention can prevent death or disability and enable children to reach their full potential. The testing is performed from a few drops of blood collected in the newborn period, often by a heel stick. [ 38 ]  The exact method of testing may vary but often uses levels of specific analytes present in the blood of the baby. Because this is a screening test, additional testing is often necessary to confirm a diagnosis.


People choose to have genetic testing for many reasons. [ 39 ] [ 40 ]  Testing may be beneficial whether the test identifies a gene change or not. A negative result can eliminate the need for unnecessary checkups and screening tests in some cases. A positive result can direct a person toward available screening, management or treatment options. [ 41 ]


, [ 42 ] [ 43 ] [ 44 ]


, [ 42 ] [ 43 ] [ 44 ] [ 45 ]


A patient's  family history  also known as  genealogy , can provide important insight into medical conditions within the family. [ 46 ]  Given that many conditions have a genetic component, gathering an accurate family history can provide important information about an individual's personal risk for many diseases. Healthcare providers can use family history information to assess a patient's risk for disease, recommend testing or screening, suggest diet or other lifestyle habits that may help reduce risk, as well as assess risk of passing conditions on to children. When obtaining a family history, it is helpful to gather health information for the following family members: grandparents, parents, siblings, aunts, uncles and first cousins, and children. In the genetic counseling community this is often referred to as a three generation family history. [ 47 ] [ 48 ] [ 49 ]


Important information to gather about the individuals in the family include:


Some families decide to work together to develop a family history, however, some family members may feel uncomfortable disclosing personal medical information. A number of tools are available to gather family history information. Patients should ask their healthcare provider if their institution has a specific form they prefer to have filled out. The U.S. Surgeon General has created a computerized tool called My Family Health Portrait to help patients  create a family medical history .


Prior to undergoing elective genetic testing, there are many factors that an individual should consider including the scope of testing and potential results in terms of changes to medical management, risk to family members, and impact on legal and financial matters. [ 50 ]


Many patients are concerned about the possibility of  genetic discrimination , the idea that certain individuals or entities would use a patient's genetic information against him or her in order to make employment, insurance policies, or other activities and services difficult or impossible to obtain.  In 2008, a new federal law known as the  Genetic Information Nondiscrimination Act (GINA)  went into effect to help prevent such discrimination.  GINA prohibits the use of genetic information to discriminate in health insurance and employment. GINA does not prevent all types of discrimination, however. For companies with fewer than 15 employees, these employment protections do not apply. GINA's protections do not apply to the US military or to federal government employees. Additionally, life, disability, and long-term care insurance policies are not included among GINA's protections. These may still continue to use genetic information to determine one's eligibility for coverage and/or policy premiums. Because of these important exceptions, an individual considering elective genetic testing should discuss the possibility of genetic discrimination with his or her physician or genetic counselor. [ 53 ]  Some individuals choose to have certain insurance policies in place before undergoing whole genome sequencing so as to prevent future discrimination.


When undergoing elective genetic testing, patients may expect to receive a variety of different results.  In addition to results that may explain a particular symptom or answer a specific question the patient may have had, the scope of elective testing may reveal additional information.  These “secondary findings” may include information about increased risk for both treatable and untreatable genetic diseases, carrier status for recessive conditions, and pharmacogenetic information. Most laboratories permit patients and families to decide what types of secondary findings (if any), they would like to receive. [ 54 ]  It is critical that patients understand the scope of potential results from elective testing and have the opportunity to opt in or out of various results. [ 55 ]


When considering elective genetic testing, it is important to take into account the type and goals of testing.  Providers and patients should be familiar with differing testing methodologies the potential results from each test.  For many individuals, factors such as test cost, scope, and deliverables, in combination with their specific clinical questions, play into the decision to undergo elective testing.
It is also important to recognize that potential results from elective genetic testing are constrained by the current limits of medical knowledge concerning the association between genetics and human disease.  As knowledge of rare genetic factors that confer high risk, as well as common factors that confer lower risks, increases, we will have the ability to learn more about an individual's current and future health. [ 42 ] [ 43 ] [ 44 ] [ 45 ]


Due to their advanced training, genetic counselors have a unique set of skills. Their clinical and psychosocial skills are used to help patients understand their genetic risks, determine which tests are most appropriate for their needs, and explain what the possible test results could mean for both the patient and the family. [ 56 ]  Clinical geneticists often work in tandem with a genetic counselor and play an important role in providing genetic testing, interpreting test results, and explaining the results. [ 57 ]  Given the ever-increasing number of elective genetic and genomic tests offered and the wide variety of issues raised by these tests (see pros & cons above), discussion with a  clinical geneticist  or  genetic counselor  may be helpful. [ 56 ]  Directories of genetics professionals can be found through the  American College of Medical Genetics and Genomics  and the  National Society of Genetic Counselors .


Elective genetic and genomic testing will continue to evolve as the cost of genetic testing technology falls and patients become increasingly involved in their own health care. The rapid drop in cost of whole  exome sequencing  and  whole genome sequencing  in the last five years has resulted in the initiation of several large scale sequencing studies that are systematically evaluating the benefits and limitations of elective genetic and genomic testing. [ 58 ] [ 59 ] [ 60 ]  Many of these studies have specifically focused on healthy individuals pursuing elective WES or WGS.


Other driving forces in the adoption of this type of testing include continued social empowerment of patients regarding their own health care and increasing private and government funded sequencing projects focused on better understanding the biological, environment, and behavioral factors that drive common disease with the hope of developing more effective ways to treat and manage disease. The Million Veteran Program is one example of a government funded project aimed at collecting data from veterans using questionnaires, health record information, and blood samples for testing, including genetic testing. [ 61 ]  Aimed at recruiting 1 million or more Americans to participate in the research cohort, The  Precision Medicine Initiative  will have a large impact on public awareness of  precision medicine  and the importance of using genetic information to treat and manage disease as well as optimize health. [ 62 ]
While elective testing is typically not paid for by health insurance companies, this may change as clinical utility continues to be demonstrated.


Future applications for elective genetic and genomic testing may include:


In  psychology , a trait (or  phenotype ) is called  emergenic  if it is the result of a specific combination of several interacting  genes  (rather than of a simple sum of several independent genes). Emergenic traits will not run in families, but  identical twins  will share them. Traits such as "leadership", "genius" or certain mental illnesses may be emergenic.
Although one may expect epigenetics to play a significant role in the phenotypic manifestation of twins reared apart, the concordance displayed between them can be attributed to emergenesis. [ 1 ]


Emopamil binding protein  is a  protein  that in humans is encoded by the  EBP   gene , located on the  X chromosome . [ 5 ]  The protein is shown to have a high-affinity reception for anti-ischemic drugs, such as  Emopamil , resulting in its discovery and given name. EBP has a mass of 27.3 kDa and resembles the  σ 2 -receptor  that resides in the endoplasmic reticulum of various tissues as an  integral membrane protein . [ 6 ]


Mutations in  EBP  cause  Conradi–Hünermann syndrome  and impairs  cholesterol biosynthesis . [ 7 ]  Unborn males affected with EBP mutations are not expected to be liveborn, (with up to only 5% male births). Individuals, mostly female, that are liveborn with EBP mutations experience  stunted growth , limb reduction and back problems. Later in life, the individual may develop  cataracts  along with coarse hair and hair loss. [ 8 ]


The inhibition of EBP promotes  oligodendrocyte  formation, which may help  remyelination  and thus limit  multiple sclerosis  development.  [ 9 ]


Isolation, replication and characterization of the EBP and EBP-like protein have been performed in  yeast / E. Coli  strains (which lack the EBP protein in nature) to study the high-affinity drug binding effects. [ 6 ]


Endemixit  is a project that studies the effects of reduced population size in five Italian  endemic species  at  risk of extinction . The final objective is to estimate the risk of extinction from genomic data and contribute to the preservation of these species. [ 1 ]  The project was funded by the MUR (Italian Ministry for Research) and coordinated by the Department of Life Sciences and Biotechnology of the  University of Ferrara  with the involvement of five other Italian universities:  Ancona ,  Florence ,  Padua ,  Rome Tor Vergata  and  Trieste . [ 2 ] [ 3 ]


The species considered are all classified in danger or in critical danger of extinction in the  IUCN Red List :


Endemixit is a genomic project applied to the  conservation  of  biodiversity . [ 9 ] [ 10 ]  Five  reference genomes  will be produced (one for each endemic species/subspecies), and 20 to 30 individuals per species will be re-sequenced ( whole genomes  at intermediate coverage). Population genomics analyses will be used to reconstruct past  demographic processes  and to estimate the  genetic load  possibly accumulated due to  genetic drift . The results will be theoretically important to understand the genetic load dynamic. [ 11 ]  Practically, they will provide guidelines and priorities for the conservation of these endemics. [ 12 ]


Endemixit is a partner of the European Reference Genome Atlas ( ERGA ), a pan-European consortium that aims to produce reference genomes of high quality for all European biodiversity to contribute to the protection of the same. [ 13 ]  Endemixit is also affiliated to the Earth Biogenome Project ( EBP ), an international project that aims to sequence the complete  genome  of all  eukaryotic  living beings in 10 years. [ 14 ]


Endoreduplication  (also referred to as  endoreplication  or  endocycling ) is replication of the nuclear  genome  in the absence of  mitosis , which leads to elevated nuclear  gene  content and  polyploidy . Endoreduplication can be understood simply as a variant form of the mitotic  cell cycle  (G1-S-G2-M) in which  mitosis  is circumvented entirely, due to modulation of  cyclin-dependent kinase  (CDK) activity. [ 1 ] [ 2 ] [ 3 ] [ 4 ]  Examples of endoreduplication characterised in  arthropod ,  mammalian , and  plant   species  suggest that it is a universal developmental mechanism responsible for the differentiation and  morphogenesis  of cell types that fulfill an array of  biological  functions. [ 1 ] [ 2 ]  While endoreduplication is often limited to specific cell types in animals, it is considerably more widespread in plants, such that  polyploidy  can be detected in the majority of plant tissues. [ 5 ]  Polyploidy and aneuploidy are common phenomena in cancer cells. [ 6 ]  Given that oncogenesis and endoreduplication likely involve subversion of common cell cycle regulatory mechanisms, a thorough understanding of endoreduplication may provide important insights for cancer biology.


Endoreduplicating cell types that have been studied extensively in  model organisms


Endoreduplication, endomitosis and polytenization are three different processes resulting in polyploidization of a cell in a regulated manner. In endoreduplication cells skip  M phase  completely by exiting the mitotic cell cycle in the G 2  phase after completing the S phase several times, resulting in a mononucleated  polyploid  cell. The cell ends up with twice as many copies of each chromosome per repeat of the S phase. [ 17 ]  Endomitosis is a type of cell cycle variation where mitosis is initiated, but stopped during anaphase and thus cytokinesis is not completed. The cell ends up with multiple nuclei in contrast to a cell undergoing endoreduplication. [ 17 ] [ 18 ]  Therefore depending on how far the cell progresses through mitosis, this will give rise to a mononucleated or  binucleated  polyploid cell. Polytenization arises with under- or overamplification of some genomic regions, creating  polytene chromosomes . [ 3 ] [ 4 ]


Based on the wide array of cell types in which endoreduplication occurs, a variety of hypotheses have been generated to explain the functional importance of this phenomenon. [ 1 ] [ 2 ]  Unfortunately, experimental evidence to support these conclusions is somewhat limited.


In developing plant tissues the transition from mitosis to endoreduplication often coincides with cell differentiation and  morphogenesis . [ 19 ]  However it remains to be determined whether endoreduplication and  polyploidy  contribute to cell differentiation or vice versa. Targeted inhibition of endoreduplication in  trichome  progenitors results in the production of multicellular trichomes that exhibit relatively normal morphology, but ultimately dedifferentiate and undergo absorption into the  leaf epidermis . [ 20 ]  This result suggests that endoreduplication and polyploidy may be required for the maintenance of cell identity.


Cell  ploidy  often correlates with cell size, [ 13 ] [ 15 ]  and in some instances, disruption of endoreduplication results in diminished cell and tissue size  [ 21 ]  suggesting that endoreduplication may serve as a mechanism for tissue growth. Relative to mitosis, endoreduplication does not require  cytoskeletal  rearrangement or the production of new  cell membrane  and it often occurs in cells that have already differentiated. As such it may represent an energetically efficient alternative to  cell proliferation  among differentiated cell types that can no longer afford to undergo mitosis. [ 22 ]  While evidence establishing a connection between ploidy and tissue size is prevalent in the literature, contrary examples also exist. [ 19 ]


Endoreduplication is commonly observed in  cells  responsible for the nourishment and protection of  oocytes  and  embryos . It has been suggested that increased gene copy number might allow for the mass production of proteins required to meet the metabolic demands of  embryogenesis  and early development. [ 1 ]  Consistent with this notion, mutation of the  Myc   oncogene  in  Drosophila   follicle cells  results in reduced endoreduplication and abortive  oogenesis . [ 23 ]  However, reduction of endoreduplication in maize  endosperm  has limited effect on the accumulation of  starch  and storage  proteins , suggesting that the nutritional requirements of the developing embryo may involve the  nucleotides  that comprise the  polyploid  genome rather than the proteins it encodes. [ 24 ]


Another hypothesis is that endoreduplication buffers against  DNA damage  and  mutation  because it provides extra copies of important  genes . [ 1 ]  However, this notion is purely speculative and there is limited evidence to the contrary. For example, analysis of polyploid  yeast  strains suggests that they are more sensitive to  radiation  than  diploid  strains. [ 25 ]


Research in plants suggests that endoreduplication may also play a role in modulating stress responses. By manipulating expression of  E2fe  (a repressor of endocycling in plants), researchers were able to demonstrate that increased cell ploidy lessens the negative impact of drought stress on leaf size. [ 26 ]  Given that the sessile lifestyle of plants necessitates a capacity to adapt to environmental conditions, it is appealing to speculate that widespread polyploidization contributes to their developmental plasticity


The best-studied example of a mitosis-to-endoreduplication transition occurs in  Drosophila  follicle cells and is activated by  Notch signaling . [ 27 ]  Entry into endoreduplication involves modulation of  mitotic  and  S-phase   cyclin-dependent kinase  (CDK) activity. [ 28 ]  Inhibition of  M-phase  CDK activity is accomplished via transcriptional activation of  Cdh / fzr  and repression of the G2-M regulator string/ cdc25 . [ 28 ] [ 29 ]  Cdh/fzr is responsible for activation of the  anaphase-promoting complex  (APC) and subsequent  proteolysis  of the  mitotic   cyclins . String/cdc25 is a  phosphatase  that stimulates mitotic cyclin-CDK complex activity. Upregulation of S-phase CDK activity is accomplished via  transcriptional  repression of the inhibitory  kinase  dacapo. Together, these changes allow for the circumvention of mitotic entry, progression through  G1 , and entry into  S-phase . The induction of  endomitosis  in mammalian  megakaryocytes  involves activation of the  c-mpl  receptor by the  thrombopoietin  (TPO)  cytokine  and is mediated by  ERK1/2  signaling. [ 30 ]  As with Drosophila follicle cells, endoreduplication in megakaryocytes results from activation of  S-phase  cyclin-CDK complexes and inhibition of mitotic cyclin-CDK activity. [ 31 ] [ 32 ]