Coat Color Variation at the Beginning of Horse Domestication

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.

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

Advances in Bioinformatics ◽

10.1155/2016/1286510 ◽

2016 ◽

Vol 2016 ◽

pp. 1-27 ◽

Cited By ~ 3

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.

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

Physiological Reports ◽

10.14814/phy2.13700 ◽

2018 ◽

Vol 6 (10) ◽

pp. e13700 ◽

Cited By ~ 10

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

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Evidence of Coat Color Variation Sheds New Light on Ancient Canids

PLoS ONE ◽

10.1371/journal.pone.0075110 ◽

2013 ◽

Vol 8 (10) ◽

pp. e75110 ◽

Cited By ~ 20

Author(s):

Morgane Ollivier ◽

Anne Tresset ◽

Christophe Hitte ◽

Coraline Petit ◽

Sandrine Hughes ◽

...

Keyword(s):

Coat Color ◽

Color Variation

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A Blond Coat Color Variation in Meadow Vole (Microtus pennsylvanicus)

Journal of Heredity ◽

10.1093/jhered/93.3.209 ◽

2002 ◽

Vol 93 (3) ◽

pp. 209-210 ◽

Cited By ~ 2

Author(s):

J. T. Curtis

Keyword(s):

Coat Color ◽

Microtus Pennsylvanicus ◽

Color Variation ◽

Meadow Vole

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

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2017000800007 ◽

2017 ◽

Vol 52 (8) ◽

pp. 615-622 ◽

Cited By ~ 4

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.

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

10.32469/10355/69867 ◽

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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