Dataset Information

MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens).

ABSTRACT: Small numbers of domestic yak (Bos grunniens) were imported to North America in the late 19th century indirectly from the Qinghai-Tibetan Plateau. Coat color of yak is of interest for fiber production, aesthetics, and as a potential indicator of recent hybridization with cattle. North American yak are classified into 3 major coat color patterns depending upon the presence and extent of white markings. They are further classified by nose pigmentation (black or gray). The aim of this study was to identify loci involved in white patterning and nose pigmentation of North American yak. Genotyping by mass spectrometry of markers identified through Sanger and whole-genome sequencing revealed a 388 kb haplotype of KIT associated in a semi-dominant manner with white coloration in this population of yak. This KIT haplotype is similar to both a haplotype found in white-faced Chinese yak and to haplotypes found in cattle but is divergent from other Bos species such as bison, gaur, and banteng. Melanocortin 1 receptor (MC1R) was implicated as a dominant determinant of black nose color with a single haplotype containing 2 missense mutations perfectly associated with the phenotype. The MC1R haplotype associated with black nose pigment is also similar to cattle haplotypes. No cattle studied, however, shared either of the 2 haplotypes associated with color in yak, suggesting these alleles were introgressed into yak before they were imported to North America. These results provide molecular insight into the history of North American yak and information from which breeders can determine possible color outcomes of matings.

SUBMITTER: Petersen JL

PROVIDER: S-EPMC7530542 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens).

Petersen Jessica L JL Kalbfleisch Theodore S TS Parris Morgan M Tietze Shauna M SM Cruickshank Jenifer J

The Journal of heredity 20200401 2

Small numbers of domestic yak (Bos grunniens) were imported to North America in the late 19th century indirectly from the Qinghai-Tibetan Plateau. Coat color of yak is of interest for fiber production, aesthetics, and as a potential indicator of recent hybridization with cattle. North American yak are classified into 3 major coat color patterns depending upon the presence and extent of white markings. They are further classified by nose pigmentation (black or gray). The aim of this study was to ...[more]

PMID: 31714577

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Project description:Background: Genetic testing for pedigree accuracy is critical for managing genetic diversity in North American (NA) yak ( Bos grunniens), a population expanded mostly from imported zoological park specimens. DNA testing also enhances species conservation by identifying recent B. taurus F1 hybrid ancestors (within three generations). Biallelic single nucleotide polymorphisms (SNPs) can accomplish either task, but increases the marker count and costs necessary to achieve both. Our aim was to identify novel, multifunctional, triallelic yak SNPs (tySNPs), with each having two alleles for yak parentage testing, and a third allele for identifying recent cattle introgression. Methods: Genome sequences were aligned to the cattle UMD3.1 assembly and SNPs were screened for 1) heterozygosity in a NA and a Chinese yak, 2) a third allele at high frequency in cattle, and 3) flanking sequences conserved in both species. Subsequently, tySNPs were filtered for unique alignment to the haplotype-resolved F1 yak assembly. Allele frequencies were estimated in a subset of 87 tySNPs by genotyping 170 NA yak. Results: We identified 610 autosomal tySNPs, distributed in 441 clusters with 5 Mb average genome spacing. The average NA yak minor allele frequency was high (0.296), while average introgressed cattle alleles were low (0.004). In simulations with tySNPs, 28 were sufficient for globally-unique animal identification (P I=5.81x10 -12), 87 were able to exclude 19 random bulls from parentage at the 99% level without using the dam's genotype (P E=5.3x10 -4), and 87 were able to detect F1 hybridization events after three generations of yak backcrosses (1/16th B. taurus germplasm). Conclusions: Identifying animals, determining parentage and detecting recent hybridization events was efficient with as few as 87 tySNPs. A similar triallelic approach could be used with other bottlenecked Bos species that hybridize with cattle, such as NA plains bison ( B. bison).

Project description:Background and aimMitochondrial genome has aseries of characteristics such as simple structure, no recombination, maternalinheritance, stable structure, fast evolution rate, and high copy number. Moreover, it is easy to be sequenced,contains high-resolution phylogenetic information, and exists in a wide rangeof taxa. Therefore, it is widely used in the study of biological phylogeny. Atpresent, phylogenetic studies focus mainly on D-loop region, cytochrome b gene,and protein-coding sequence. Phylogenetic studies using the mitochondrialcomplete sequence are rarely reported in yak. Therefore, the present studyaimed to construct phylogenetic tree using yak mitochondrial complete sequenceand compare the subsequent results with previous findings obtained usingpartial sequences.ResultsComplete mitochondrial sequences of five yakpopulations from Qinghai and Xinjiang were obtained. The mitotype diversity ofthe five populations was Xueduo yak (0.992 ± 0.015), Pamir yak (0.990 ± 0.014),Yushu yak (0.963 ± 0.033), Qilian yak (0.948 ± 0.036), and Huanhu yak (0.905 ±0.048), which showed a higher mitotype diversity compared with other breeds fromthe previous reports, including Jiulong yak, Maiwa yak, Zhongdian yak, andTianzhu yak. A total of 78 mitotypes were obtained from 111 individuals. Amongthese, Yushu yak, Huanhu yak, Xueduo yak, and Qilian yak all shared mitotypes,but the Pamir yak did not share mitotypes with these four populations.Phylogenetic analysis showed that yak populations were separable into threedistinct branches. The analysis identified a new phylogenetic branch containingboth wild and domestic yaks. The 155 mitotypes found in 206 individuals weredivided into 3 haplogroups by mitotype clustering. Thehaplogroup was not associated with the geographical distribution of yaks. Theyaks in the same population or the same ecological environment were distributedin different haplogroups. Among the threehaplogroups, haplogroup A and haplogroup B showed a star-shaped distribution ofmitotypes. The central mitotypes were widely distributed and had a highfrequency.ConclusionsThegenetic diversity of yaks in Qinghai was high. Both domestic and wild yaks clusteredinto three branches.

Project description:BACKGROUND:The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population of yak termed as the Jinchuan yak has been identified with over half its members own a thoracolumbar vertebral formula of T15L5 instead of the natural T14L5 arrangement. The novel T15L5 positioning is a preferred genetic trait leading to enhanced meat and milk production. Selective breeding of this trait would have great agricultural value and exploration of the molecular mechanisms underlying this trait would both accelerate this process and provide us insight into the development and regulation of somitogenesis. RESULTS:Here we investigated the genetic background of the Jinchuan yak through resequencing fifteen individuals, comprising five T15L5 individuals and ten T14L5 individuals with an average sequencing depth of >?10X, whose thoracolumbar vertebral formulae were confirmed by anatomical observation. Principal component analysis, linkage disequilibrium analysis, phylogenetic analysis, and selective sweep analysis were carried out to explore Jinchuan yak's genetic background. Three hundred and thirty candidate markers were identified as associated with the additional thoracic vertebrae and target sequencing was used to validate seven carefully selected markers in an additional 51 Jinchuan yaks. The accuracies of predicting 15 thoracic vertebrae and 20 thoracolumbar vertebrae with these 7 markers were 100.00 and 33.33% despite they both could only represent 20% of all possible genetic diversity. Two genes, PPP2R2B and TBLR1, were found to harbour the most candidate markers associated with the trait and likely contribute to the unique somitic number and identity according to their reported roles in the mechanism of somitogenesis. CONCLUSIONS:Our findings provide a clear depiction of the Jinchuan yak's genetic background and a solid foundation for marker-assistant selection. Further exploitation of this unique population and trait could be promoted with the aid of our genomic resource.

Dataset Information

MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens).

Publications

MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens).

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