scholarly journals A potential regulatory region near the EDN3 gene may control both harness racing performance and coat color variation in horses

2018 ◽  
Vol 6 (10) ◽  
pp. e13700 ◽  
Author(s):  
Kim Jäderkvist Fegraeus ◽  
Brandon D. Velie ◽  
Jeanette Axelsson ◽  
Rachel Ang ◽  
Natasha A. Hamilton ◽  
...  
Keyword(s):  
Coat Color ◽  
Regulatory Region ◽  
Color Variation ◽  
Racing Performance ◽  
Harness Racing

scholarly journals A novel enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice

2021 ◽  
Author(s):  
T Brock Wooldridge ◽  
Andreas F Kautt ◽  
Jean-Marc Lassance ◽  
Sade S McFadden ◽  
Vera S Domingues ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Coat Color ◽  
Atlantic Coast ◽  
Parallel Evolution ◽  
Regulatory Region ◽  
Color Variation ◽  
Coding Region ◽  
Peromyscus Polionotus ◽  
Southeastern Us ◽  
Gene Assay

Identifying the genetic basis of repeatedly evolved traits provides a way to reconstruct their evolutionary history and ultimately investigate the predictability of evolution. Here, we focus on the oldfield mouse (Peromyscus polionotus), which occurs in the southeastern United States, where it exhibits considerable coat-color variation. Dorsal coats range from dark brown in mice inhabiting mainland habitat to near white on the white-sand beaches of the southeastern US, where light pelage has evolved independently on Florida's Gulf and Atlantic coasts as an adaptation to visually hunting predators. To facilitate genomic analyses in this species, we first generated a high-quality, chromosome-level genome assembly of P. polionotus subgriseus. Next, in a uniquely variable mainland population that occurs near beach habitat (P. p. albifrons), we scored 23 pigment traits and performed targeted resequencing in 168 mice. We find that variation in pigmentation is strongly associated with a ~2 kb region approximately 5 kb upstream of the Agouti-signaling protein (ASIP) coding region. Using a reporter-gene assay, we demonstrate that this regulatory region contains an enhancer that drives expression in the dermis of mouse embryos during the establishment of pigment prepatterns. Moreover, extended tracts of homozygosity in this region of Agouti indicate that the light allele has experienced recent and strong positive selection. Notably, this same light allele appears fixed in both Gulf and Atlantic coast beach mice, despite these populations being separated by >1,000km. Given the evolutionary history of this species, our results suggest that this newly identified Agouti enhancer allele has been maintained in mainland populations as standing genetic variation and from there has spread to, and been selected in, two independent beach mouse lineages, thereby facilitating their rapid and parallel evolution.

scholarly journals Introgression drives repeated evolution of winter coat color polymorphism in hares

2019 ◽  
Vol 116 (48) ◽  
pp. 24150-24156 ◽  
Author(s):  
Iwona Giska ◽  
Liliana Farelo ◽  
João Pimenta ◽  
Fernando A. Seixas ◽  
Mafalda S. Ferreira ◽  
...  
Keyword(s):  
Coat Color ◽  
Color Change ◽  
Regulatory Region ◽  
Bird Species ◽  
Color Polymorphism ◽  
Genomic Region ◽  
Population History ◽  
Color Variation ◽  
Source Population ◽  
Whole Genome

Changing from summer-brown to winter-white pelage or plumage is a crucial adaptation to seasonal snow in more than 20 mammal and bird species. Many of these species maintain nonwhite winter morphs, locally adapted to less snowy conditions, which may have evolved independently. Mountain hares (Lepus timidus) from Fennoscandia were introduced into the Faroe Islands in 1855. While they were initially winter-white, within ∼65 y all Faroese hares became winter-gray, a morph that occurs in the source population at low frequency. The documented population history makes this a valuable model for understanding the genetic basis and evolution of the seasonal trait polymorphism. Through whole-genome scans of differentiation and single-nucleotide polymorphism (SNP) genotyping, we associated winter coat color polymorphism to the genomic region of the pigmentation gene Agouti, previously linked to introgression-driven winter coat color variation in the snowshoe hare (Lepus americanus). Lower Agouti expression in the skin of winter-gray individuals during the autumn molt suggests that regulatory changes may underlie the color polymorphism. Variation in the associated genomic region shows signatures of a selective sweep in the Faroese population, suggesting that positive selection drove the fixation of the variant after the introduction. Whole-genome analyses of several hare species revealed that the winter-gray variant originated through introgression from a noncolor changing species, in keeping with the history of ancient hybridization between the species. Our findings show the recurrent role of introgression in generating winter coat color variation by repeatedly recruiting the regulatory region of Agouti to modulate seasonal coat color change.

scholarly journals Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 305-311
Author(s):  
G Pielberg ◽  
C Olsson ◽  
A-C Syvänen ◽  
L Andersson
Keyword(s):  
Coat Color ◽  
Allelic Diversity ◽  
Growth Factor Receptor ◽  
Small Sample ◽  
Color Variation ◽  
Large White ◽  
High Genetic Diversity ◽  
High Allelic Diversity ◽  
Stem Cell Growth Factor ◽  
New Alleles

Abstract Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits.

36 The DMRT3 “Gait keeper” mutation affects harness racing performance and riding traits in Finnhorses

2015 ◽  
Vol 35 (5) ◽  
pp. 399 ◽  
Author(s):  
K. Jäderkvist ◽  
L. Johansson ◽  
A. Mykkänen ◽  
M. Mäenpää ◽  
L.S. Andersson ◽  
...  
Keyword(s):  
Racing Performance ◽  
Harness Racing

scholarly journals In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

2016 ◽  
Vol 2016 ◽  
pp. 1-27 ◽  
Author(s):  
Kristopher J. L. Irizarry ◽  
Randall L. Bryden
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Coat Color ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Color Variation ◽  
Factor Binding ◽  
Conserved Sequence ◽  
Evolutionarily Conserved

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

scholarly journals Evidence of Coat Color Variation Sheds New Light on Ancient Canids

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e75110 ◽  
Author(s):  
Morgane Ollivier ◽  
Anne Tresset ◽  
Christophe Hitte ◽  
Coraline Petit ◽  
Sandrine Hughes ◽  
...  
Keyword(s):  
Coat Color ◽  
Color Variation

scholarly journals Coat Color Variation at the Beginning of Horse Domestication

Science ◽  
2009 ◽  
Vol 324 (5926) ◽  
pp. 485-485 ◽  
Author(s):  
A. Ludwig ◽  
M. Pruvost ◽  
M. Reissmann ◽  
N. Benecke ◽  
G. A. Brockmann ◽  
...  
Keyword(s):  
Coat Color ◽  
Color Variation ◽  
Horse Domestication

scholarly journals Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus

2017 ◽  
Vol 52 (8) ◽  
pp. 615-622 ◽  
Author(s):  
Lilian Cristina Gomes Cavalcanti ◽  
José Carlos Ferrugem Moraes ◽  
Danielle Assis de Faria ◽  
Concepta Margaret McManus ◽  
Alcebiades Renato Nepomuceno ◽  
...  
Keyword(s):  
Coat Color ◽  
Color Variation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Low Frequencies ◽  
Melanocortin 1 Receptor ◽  
Tyrosinase Related Protein

Abstract: The objective of this work was to identify single nucleotide polymorphisms (SNPs) in resequencing data from MC1R, ASIP, and TYRP1 genes derived from Crioula sheep (Ovis aris) with different coat colors. Polymorphisms in the ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor), and TRYP1 (tyrosinase-related protein 1) genes were analyzed in 115 sheep from Embrapa’s conservation nucleus of crioula sheep, in Brazil. A total of 7,914 bp were sequenced per animal, and 14 SNPs were identified. Two additional assays were performed to detect duplications and deletions in the ASIP gene. Ninety-five percent of the coat color variation was explained by epistatic interactions observed between specific alleles in the MC1R and ASIP genes. Evidence suggests an important role of TYRP1 variants for wool color, despite their low frequencies. The marker panel was efficient enough in predicting coat color in the studied animals and, therefore, can be used to implement a marker-assisted selection program in the conservation nucleus of sheep of the crioula breed.

scholarly journals Detecting subtle variation in two cryptic primate families (tarsiidae and lorisidae) through morphology and genetics

2018 ◽  
Author(s):  
◽  
Rachel Anne Munds
Keyword(s):  
Candidate Gene ◽  
Cryptic Species ◽  
Evolutionary History ◽  
Coat Color ◽  
Color Variation ◽  
Cranial Variation ◽  
The Family ◽  
History Of ◽  
Slow Moving ◽  
African Genus

Cryptic species look morphologically similar but in fact are several different species lumped together. This is problematic as it hinders conservation efforts and makes it challenging to infer the evolutionary history of an organism. This dissertation research aims to improve our understanding of the evolution and variation of cryptic, nocturnal primates. Over 60% of primates are threatened with extinction, and many nocturnal species are poorly understood. Research aimed at elucidating species will help conserve them. To do so, I examined the multivariate craniodental allometry of the three genera of tarsiers. Tarsiers are small-bodied, nocturnal primates that have evolved to extreme-carnivorous niche. In order to see better at night their eyes have increased dramatically in size. Such evolution has led to minimal cranial variation among the three groups, despite millions of years of separation. Yet, two distinct groups were found through allometric analyses. Genetics is another tool that can discern the evolution and variation of cryptic species. The slow moving lorises of Asia and Africa appear morphologically similar, making it a challenge to determine their evolutionary history or variation. By using a multi-gene approach, I was able to determine the family is monophyletic with four distinct genera. Furthermore, analyses of a candidate gene that impacts coat color variation, found that the darker colored African genus has more mutations along its branch that result in amino acid changes than the vibrantly colored lorises in Asia. Such a result suggests that a transition to or a maintenance of a darker phenotype is conserved or that other genes besides this one candidate gene influence coat variation. Overall, I was able to find that through a variety of methods, it is possible to detect variation and the evolutionary history of cryptic species.

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