Colours of domestication Cieslak, Michael; Reissmann, Monika; Hofreiter, Michael ...
Biological reviews of the Cambridge Philosophical Society,
11/2011, Letnik:
86, Številka:
4
Journal Article
Recenzirano
During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In ...contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat‐colour‐associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat‐colour variants. Recent studies demonstrate that this selection for coat‐colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat‐colour‐associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat‐colour‐associated genes act.
Yellow seed is a desirable trait with great potential for improving seed quality in Brassica crops. Unfortunately, no natural or induced yellow seed germplasms have been found in Brassica napus, an ...important oil crop, which likely reflects its genome complexity and the difficulty of the simultaneous random mutagenesis of multiple gene copies with functional redundancy. Here, we demonstrate the first application of CRISPR/Cas9 for creating yellow‐seeded mutants in rapeseed. The targeted mutations of the BnTT8 gene were stably transmitted to successive generations, and a range of homozygous mutants with loss‐of‐function alleles of the target genes were obtained for phenotyping. The yellow‐seeded phenotype could be recovered only in targeted mutants of both BnTT8 functional copies, indicating that the redundant roles of BnA09.TT8 and BnC09.TT8b are vital for seed colour. The BnTT8 double mutants produced seeds with elevated seed oil and protein content and altered fatty acid (FA) composition without any serious defects in the yield‐related traits, making it a valuable resource for rapeseed breeding programmes. Chemical staining and histological analysis showed that the targeted mutations of BnTT8 completely blocked the proanthocyanidin (PA)‐specific deposition in the seed coat. Further, transcriptomic profiling revealed that the targeted mutations of BnTT8 resulted in the broad suppression of phenylpropanoid/flavonoid biosynthesis genes, which indicated a much more complex molecular mechanism underlying seed colour formation in rapeseed than in Arabidopsis and other Brassica species. In addition, gene expression analysis revealed the possible mechanism through which BnTT8 altered the oil content and fatty acid composition in seeds.
ABSTRACT
Animals that occupy temperate and polar regions have specialized traits that help them survive in harsh, highly seasonal environments. One particularly important adaptation is seasonal coat ...colour (SCC) moulting. Over 20 species of birds and mammals distributed across the northern hemisphere undergo complete, biannual colour change from brown in the summer to completely white in the winter. But as climate change decreases duration of snow cover, seasonally winter white species (including the snowshoe hare Lepus americanus, Arctic fox Vulpes lagopus and willow ptarmigan Lagopus lagopus) become highly contrasted against dark snowless backgrounds. The negative consequences of camouflage mismatch and adaptive potential is of high interest for conservation. Here we provide the first comprehensive review across birds and mammals of the adaptive value and mechanisms underpinning SCC moulting. We found that across species, the main function of SCC moults is seasonal camouflage against snow, and photoperiod is the main driver of the moult phenology. Next, although many underlying mechanisms remain unclear, mammalian species share similarities in some aspects of hair growth, neuroendocrine control, and the effects of intrinsic and extrinsic factors on moult phenology. The underlying basis of SCC moults in birds is less understood and differs from mammals in several aspects. Lastly, our synthesis suggests that due to limited plasticity in SCC moulting, evolutionary adaptation will be necessary to mediate future camouflage mismatch and a detailed understanding of the SCC moulting will be needed to manage populations effectively under climate change.
•We have identified genes by GWAS which are involved in well-established MAPK and PI3K-AKT signalling pathways, affecting biochemical process of coat colour production.•Due to introduction of exotic ...blood to continue the process of development of Vrindavani cattle, a very low FST value was observed suggesting outbreeding of the population.•This work provides a preliminary information to carry forward researches on genomic basis of coat colour patterns in crossbred cattle
Coat colour and various patterns are the hallmarked qualitative traits studied in cattle as well as other livestock; however, variation in this trait is resultant of interactions and epistasis of a set of genes rather than being a product of a single gene. In this study, GWAS has been conducted from 50K SNP genotype data, with a stratified approach on Vrindavani cattle (n=48). The study was conducted in two sets of an experiment wherein set I treats all the solid colours (n=18) as controls and rest spotted or patchy types as cases (n=30), and set II treats brown and brown with white spots as controls (n=15), and rest as cases (n=33). After quality check (MAF>0.01, genotyping rate>90%, and H-W equilibrium at p≤ 0.001) of genotype data, 37247 SNPs were further used for accomplishing Genome-Wide Association Study (GWAS) with coat colour. The distinct phenotypes were classified into four different sub-groups that are solid black, black with white patches, solid brown, and brown with white patches along with greyish white. The allele frequency difference was checked in all sub-groups. The GWAS was conducted in PLINK v1.7 and for graphical representation R was used. Two SNPs in set I and 20 in set II were found to be significantly associated with coat colour in Vrindavani cattle. A ±500 Kb genome scan around the significant SNPs revealed gene BDNF for SNP DIAS-217 in set I and FGF18 for SNP ARS-BFGL-NGS-105192, and CACNA2D1, and HGF for SNP BTB-01885061 in set II, are present around these SNPs. In KEGG-based pathway enrichment analysis, all the above-mentioned genes were found to be involved in well-established MAPK and PI3K-AKT signalling pathways, affecting the biochemical process of coat colour production. Genome-wide FST values were low to moderate across the genome, however few associated SNPs had moderate to high FST values indicating their power in differentiating the subgroups according to coat colour phenotype. This study provides a preliminary report of markers and genes involved in coat colour expression and revealed that the reported genes around the associated SNPs are involved in brown with white spotting phenotype. However, further researches in this field are essential for a more conclusive result.
Nguni cattle are a Sanga type breed with mixed
B. taurus
and
B. indicus
ancestry and proven resistance to ticks, diseases and other harsh conditions of the African geographical landscape. The ...multi-coloured Nguni coats have found a niche market in the leather industry leading to breeding objectives towards the promotion of such diversity. However, there is limited studies on the genomic architecture underlying the coat colour and patterns hampering any potential breeding and improvement of such trait. This study investigated the genetics of base coat colour, colour-sidedness and the white forehead stripe in Nguni cattle using coat colour phenotyped Nguni cattle and Illumina Bovine HD (770K) genotypes. Base coat colour phenotypes were categorised into eumelanin (
n
= 45) and pheomelanin (
n
= 19). Animals were categorised into either colour-sided (
n
= 46) or non-colour-sided (
n
= 94) and similarly into presence (
n
= 15) or absence (
n
= 67) of white forehead stripe. Genome-wide association tests were conducted using 622,103 quality controlled SNPs and the Efficient Mixed Model Association eXpedited method (EMMAX) implemented in Golden Helix SNP Variation Suite. The genome-wide association studies for base coat colour (eumelanin vs. pheomelanin) resulted into four indicative SNPs on BTA18 and a well-known gene, MC1R, was observed within 1 MB from the indicative SNPs (p < 0.00001) and found to play a role in the melanogenesis (core pathway for melanin production) and the MAPK signalling pathway. GWAS for colour-sidedness resulted in four indicative SNPs, none of which were in close proximity to the KIT candidate gene known for colour-sidedness. GWAS for the white forehead stripe resulted in 17 indicative SNPs on BTA6. Four genes MAPK10, EFNA5, PPP2R3C and PAK1 were found to be associated with the white forehead stripe and were part of the MAPK, adrenergic and Wnt signalling pathways that are synergistically associated with the synthesis of melanin. Overall, our results prove prior knowledge of the role of MC1R in base coat colours in cattle and suggested a different genetic mechanism for forehead stripe phenotypes in Nguni cattle.
•This review summarizes all developments on the genetics and genomics of pigmentation variability in Sus scrofa.•Coat colour variability in the domestic pig is rooted on the domestication processes ...of this species.•Coat colour and eye colour in pigs are affected by several major genes.•Complex allele series are present at the MC1R and KIT genes.•Applications of coat colour gene markers are relevant for breed integrity and authenticity of branded breed pork products.
Among the phenotypic hallmarks of the domestication process of the pig, that independently started in China and East Anatolia and continued in Europe and throughout China, coat colour was one of the earliest targets that was used to differentiate human managed animal cohorts from wild-related populations. In the modern pig breeding and conservation programs for local genetic resources, coat colour has important economic relevance. This review on the genetics and genomics of pigmentation variability in Sus scrofa summarizes all recent developments, concepts and applications derived by the genomic characterization of loci affecting coat colour and eye colour in the pig. It includes a general overview of the biology of pigmentation in mammals, a brief description of the types of coat colours and eye colour patterns in the pig, an overview of the coat colour loci described by classical genetic studies in this species, a detailed description of the genomic regions, genes and their mutations affecting pigmentation in Sus scrofa (including a revisited analysis of the variability in the MC1R and KIT genes and in several other genes: ASIP, TYRP1, EDNRB, KITLG, OCA2 and SLC45A2) and the application of the related available genomic information in selection and breeding plans and for the authenticity of pork products.
•Agromorphological trait variability between and within landraces.•This is the first report of the trichome and stoma types in Bambara groundnut.•There are differences in trichome type and density ...between grouped landraces.•Leaf anatomy can be used in the selection of landraces with favourable traits.
In many parts of Sub-Saharan Africa, female subsistence farmers rely on the production of underutilized crops such as Bambara groundnut (Vigna subterranea (L.) Verdc) for both sustenance and generating income. Bambara groundnut is, however, grown at a low rate especially in South Africa. Although it has the potential to yield high amounts of seed and can grow under adverse weather conditions, amongst offering other benefits, it remains underutilized and under-researched. To date there are no improved varieties. Farmers therefore rely on indigenous knowledge systems to select varieties based on their preferences, thereby unconsciously contributing to genetic erosion of the crop. Improved varieties are important for adaptability under environmental stochasticity. This study was conducted to determine whether seed coat colour can be used as a basis for selecting Bambara groundnut landraces with favourable agronomic traits for breeding programs and development of genetically enhanced varieties. A completely randomized design with ten replications was used to assess whether landraces classified based on seed coat colour are both morphologically and genetically similar. Significant differences (P<0.05) in the yield parameters, number of pods per plant, and growth habit were observed. This suggests that some genotypes yield more seed than others. Anatomical assessment of the leaf revealed that there are genotypes with high trichome density and two types of trichomes on the same plant. These characteristics make those plants more resilient to disease pressure than others. There is, however, little evidence that these findings are related to the seed coat colour. Attributing one character i.e. seed coat colour to genetic diversity is therefore reductive and should not be undertaken.
•Sensory organs and nerves are particularly affected because of the shared origin of melanocytes and neurocytes.•Disorders related to specific coat colour phenotypes also occur in the skin ...(melanoma), reproductive tract and immune system.•The behaviour and fitness of an individual can be related to its coat colour phenotype.•Domestic species and laboratory pets have a huge range of coat colour variation and related disorders.•Pleiotropic effects of coat-colour associated mutations are rare in wild species based on the purifying natural selection.
The characterisation of the pleiotropic effects of coat colour-associated mutations in mammals illustrates that sensory organs and nerves are particularly affected by disorders because of the shared origin of melanocytes and neurocytes in the neural crest; e.g. the eye-colour is a valuable indicator of disorders in pigment production and eye dysfunctions. Disorders related to coat colour-associated alleles also occur in the skin (melanoma), reproductive tract and immune system. Additionally, the coat colour phenotype of an individual influences its general behaviour and fitness. Mutations in the same genes often produce similar coat colours and pleiotropic effects in different species (e.g., KIT reproductive disorders, lethality, EDNRB megacolon and LYST CHS). Whereas similar disorders and similar-looking coat colour phenotypes sometimes have a different genetic background (e.g., deafness EDN3/EDNRB, MITF, PAX and SNAI2 and visual diseases OCA2, RAB38, SLC24A5, SLC45A2, TRPM1 and TYR). The human predilection for fancy phenotypes that ignore disorders and genetic defects is a major driving force for the increase of pleiotropic effects in domestic species and laboratory subjects since domestication has commenced approximately 18,000 years ago.
•Genetic analyses were performed in order to identify the Extensión locus genotypes•Nine strategies for removal of animals carrying undesirable alleles were evaluated•Results are very promising for ...management of Berrenda en Negro conservation program•The most suitable strategy was to prioritise the elimination of EDe animals•Coat markers might be used to differentiateproducts from others breeds ones
‘Berrenda en Negro’ (BN) is an endangered Spanish cattle breed with substantial ecological and cultural value and meat quality. Phenotypically, it is differentiated by its black-sided coat pattern. The goal of this study were to analyse the presence of unwanted alleles at the MC1R locus (E+ and e) and propose appropriate selective strategies for their eradication from the population. Both goals were based on the identification of genotypes of the MC1R locus using genetic markers and DNA microsatellites, to identify changes in the genetic variability of the resulting populations after applying selective strategies to decrease the frequency of red and wild-type alleles. Introgression and crossbreeding of BN with other Iberian cattle breeds in the past has left undesirable E+ and e alleles, with frequencies of 7 and 12%, respectively. The extent to which the genetic variability of the BN population could be affected by selection strategies was quantified in terms of the number of affected animals and farms, effective population size (Ne) of the remaining genetic variability, and loss of gene diversity and allelic richness. The neutral genetic diversity found in BN suggested that selection strategies for the MC1R gene are possible. These strategies should be implemented progressively, in combination with extensive mating control. The best strategy to eliminate unwanted MC1R alleles in the short term would be to remove all cattle with the EDe genotype in the first phase, followed by a second phase, in which the EDE+ genotype would be eradicate after the recovery of the population to its effective size. The results of this study will assist the BN Breeders Association to managing the conservation program for the breed.
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