Genome-Wide Association Study of Body Weight Trait in Yaks

Wang, Jiabo; Li, Xiaowei; Wei, Peng; Zhong, Jincheng; Jiang, Mingfeng

doi:10.3390/ani12141855

Cited by 5 publications

(1 citation statement)

References 34 publications

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“…A total of 47.15 million markers, including SNPs, Indels and other variants, were detected using the BWA-SAMtools-GATK pipeline [Wang J, et al 2022] program with default parameters. 3,584,464 SNPs remained after filtering by GATK and PLINK software, distributed on average on 29 autosomes and 1 X chromosome.…”

Section: Resultsmentioning

confidence: 99%

pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model

Liu

Chai

Wei

et al. 2022

Preprint

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Yak is a unique large animal species living in the Qinghai-Tibet Plateau and the surrounding Hengduan Mountains, and has evolved several regional variety resources due to the special geographical and ecological environment in which it lives. Therefore, it is of great importance to investigate the genetic composition of body size traits among breeds in multiple regions for yak breeding and production. A genome-wide association analysis was performed on 94 yak individuals (a total of 31 variety resources) for five body size traits (body height, body weight, body length, chest circumference, and circumference of cannon bone). The individuals were clustered following known population habitat. The kinship of grouping individuals was used in the CMLM. This provided compressed mixed linear model was named pCMLM method.Total of 3,584,464 high-quality SNP markers were obtained on 30 chromosomes. Principal component analysis using the whole SNPs do not accurately classify all populations into multiple subpopulations, a result that is not the same as the population habitat. Six SNP loci were identified in the pCMLM-based GWAS with statistically significant correlation with body height, and four candidate genes (FXYD6, SOHLH2, ADGRB2, and OSBPL6), which in the vicinity of the variant loci, were screened and annotated. Two of these genes, ADGRB2 and OSBPL6, are involved in biological regulatory processes such as body height regulation, adipocyte proliferation and differentiation.Based on the previous population information, the pCMLM can provide more sufficient associated results when the conventional CMLM can not catch optimum clustering groups. The fundamental information for quantitative trait gene localization or candidate gene cloning in the mechanism of yak body size trait formation.

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Section: Resultsmentioning

confidence: 99%

pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model

Liu

Chai

Wei

et al. 2022

Preprint

Self Cite

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Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

Lan,

Fu,

et al. 2024

J Animal Sci Biotechnol

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Background The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes. Results We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a ‘two-haplotype genomic hybridization model’ for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations. Conclusions The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.

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Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information

Liu

Wang

Qin

et al. 2023

Animals

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Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including FXYD6, SOHLH2, ADGRB2, and OSBPL6, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.

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Genome-Wide Association Study of Body Weight Trait in Yaks

Cited by 5 publications

References 34 publications

pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model

pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information

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