Whole-genome resequencing of major populations revealed domestication-related genes in yaks

Peng, Wei; Fu, Changqi; Shu, Shi; Wang, Guowen; Wang, Hui; Yue, Binglin; Zhang, Ming; Liu, Xinrui; Liu, Yaxin; Zhang, Jun; Zhong, Jincheng; Wang, Jiabo

doi:10.1186/s12864-024-09993-7

Cited by 3 publications

(1 citation statement)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…GRID2 (glutamate ionotropic receptor delta-type subunit 2) is linked to the central suspensory ligament in Chinese Holstein cows [61]. It is strongly related to dry matter intake, average daily gain, birth weight and milk fat yield in cattle [62]. However, earlier research indicated that GRID2 plays a role in the sexual maturity of Simmental cattle, the temperament trait of sheep and the litter size of goat [63][64][65].…”

Section: Functional Enrichment Analysismentioning

confidence: 99%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

View full text Add to dashboard Cite

Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

show abstract

Section: Functional Enrichment Analysismentioning

confidence: 99%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

View full text Add to dashboard Cite

show abstract

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

Chen,

Luo,

Jia

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

Background Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ($$\:{F}_{HOM}$$, $$\:{F}_{L\&H}$$, $$\:{F}_{VR1}$$, $$\:{F}_{VR2}$$, and $$\:{F}_{YAN}$$), as well as two segment-based estimators of runs of homozygosity (ROH, $$\:{F}_{ROH}$$) and homozygous-by-descent (HBD, $$\:{F}_{HBD}$$). Functional implications were analyzed for the positional candidate genes located within the related genomic regions. Results A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ($$\:{F}_{HOM}$$), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of $$\:{F}_{ROH}$$ and $$\:{F}_{HBD}$$, however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals. Conclusions We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.

show abstract

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Li,

Liu,

Ahmed

et al. 2024

Front. Genet.

View full text Add to dashboard Cite

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands.Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors.Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors.Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

show abstract

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

Cited by 3 publications

References 38 publications

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Contact Info

Product

Resources

About