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Background <p>Birth weight is a critical economic trait in livestock production. However, its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays. In this study, we utilized low-coverage whole-genome sequencing (lcWGS) to genotype 3,007 Hu sheep, bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection.</p> Results <p>LcWGS with high imputation accuracy (97.8% allelic concordance) enabled genome-wide association studies (GWAS) identifying two novel quantitative trait loci (QTLs) on chromosomes 6 and 9. The chromosome 9 QTL encompassed a regulatory region functionally linked to <i>PLAG1</i> expression through expression quantitative trait locus (eQTL) mapping. Compared with wild-type homozygotes, heterozygous carriers of the lead SNP (chr9:g.35920172A &gt; G) presented a 9.85% increase in birth weight (3.35&#xa0;kg vs. 3.68&#xa0;kg; Δ = 0.33&#xa0;kg). Notably, the derived allele of this SNP exhibited low frequencies of &lt; 0.1 across most global sheep breeds except Dorper, highlighting its potential for selective breeding applications. Leveraging lcWGS data, haplotype-based fine-mapping prioritized three candidate causal variants. A secondary QTL on chromosome 6 colocalized with the FecB mutation, a well-established locus associated with increased litter size. Intriguingly, individuals carrying one FecB allele showed a 6.18% reduction (0.22 kg) in birth weight, which tentatively indicates potential pleiotropic influences on both growth and reproductive traits.</p> Conclusion <p>This study demonstrates the utility of lcWGS as a cost-effective, high-resolution tool for dissecting complex traits in livestock. Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through cost-effective, genome-wide approaches.</p>

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Fine mapping genetic variants affecting birth weight in sheep: a GWAS of 3007 individuals using low-coverage whole genome sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年8月12日

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  • Ran Li,
  • Yuheng Bai,
  • Maqiang Zhao,
  • Xinyue Zhang,
  • Haiyan Wang,
  • Bo Feng,
  • Shuo Zhang,
  • Huanhuan Zhang,
  • Gang Ren,
  • Xihong Wang,
  • Yu Jiang

摘要

Background

Birth weight is a critical economic trait in livestock production. However, its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays. In this study, we utilized low-coverage whole-genome sequencing (lcWGS) to genotype 3,007 Hu sheep, bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection.

Results

LcWGS with high imputation accuracy (97.8% allelic concordance) enabled genome-wide association studies (GWAS) identifying two novel quantitative trait loci (QTLs) on chromosomes 6 and 9. The chromosome 9 QTL encompassed a regulatory region functionally linked to PLAG1 expression through expression quantitative trait locus (eQTL) mapping. Compared with wild-type homozygotes, heterozygous carriers of the lead SNP (chr9:g.35920172A > G) presented a 9.85% increase in birth weight (3.35 kg vs. 3.68 kg; Δ = 0.33 kg). Notably, the derived allele of this SNP exhibited low frequencies of < 0.1 across most global sheep breeds except Dorper, highlighting its potential for selective breeding applications. Leveraging lcWGS data, haplotype-based fine-mapping prioritized three candidate causal variants. A secondary QTL on chromosome 6 colocalized with the FecB mutation, a well-established locus associated with increased litter size. Intriguingly, individuals carrying one FecB allele showed a 6.18% reduction (0.22 kg) in birth weight, which tentatively indicates potential pleiotropic influences on both growth and reproductive traits.

Conclusion

This study demonstrates the utility of lcWGS as a cost-effective, high-resolution tool for dissecting complex traits in livestock. Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through cost-effective, genome-wide approaches.