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<p>India’s non-descript cattle, comprising 52% of the 193.46&#xa0;million cattle population, are pivotal to the nation’s genetic diversity but contribute only 9.82% to milk production, highlighting a critical need for their genomic characterization so as to utilize this information in conservation and breeding strategies. This study uses the Bovine GGP50K SNP chip to determine the genetic uniqueness, population structure, ancestry proportion, and conservation status of two significant indigenous cattle populations from the Vidarbha region of Maharashtra, Umarda (UM) and Pahadi/Melghati (PAH), which form the foundation of the local subsistence economy. A total of 18 breeds/populations including three taurine breeds were subjected to genomic analysis using Bovine GGP50K SNP chip. Higher heterozygosity (UM: Ho = 0.332, He = 0.417; PAH: Ho = 0.351, He = 0.416) and effective population sizes (UM: Ne = 67; PAH: Ne = 129 at the 13th generation) in these two indigenous cattle populations indicated substantial genetic resilience. Bayesian clustering via ADMIXTURE at K = 10 using 1000 AIMs revealed a distinct UM ancestry component (61.63%), suggestive of historical isolation, while PAH with 39.19% ancestry formed cluster with other indicine breeds, reflecting extensive gene flow. The <i>f₃</i> statistics indicated admixture in PAH from Brown Swiss and Dangi (f₃ = -0.002647, Z = -3.619), attributed to historical crossbreeding, whereas UM exhibited no admixture, indicating its genetic uniqueness. Local ancestry analysis identified <i>Bos taurus</i> introgression on chromosome (Chr) 13 in UM, with the CBLN4 gene associated with udder morphology, which suggested its adaptation for dairy traits. These findings underscore the genetic distinctiveness of UM and shared ancestry of PAH, advocating for their preservation and targeted breeding to enhance productivity in smallholder systems. This genomic insight aligns with global efforts to safeguard livestock biodiversity, offering a foundation for sustainable cattle improvement in India.</p>

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Genome-wide SNP evidence for the genetic uniqueness of indigenous cattle population

  • 期刊论文

  • 发表日期：

    2025年12月22日

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  • Kiyevi G. Chishi,
  • Sanjeev Singh,
  • Rangasai Chandra Goli,
  • K. K. Kanaka,
  • Indrajit Ganguly,
  • S. V. Kuralkar,
  • Sat Pal Dixit

摘要

India’s non-descript cattle, comprising 52% of the 193.46 million cattle population, are pivotal to the nation’s genetic diversity but contribute only 9.82% to milk production, highlighting a critical need for their genomic characterization so as to utilize this information in conservation and breeding strategies. This study uses the Bovine GGP50K SNP chip to determine the genetic uniqueness, population structure, ancestry proportion, and conservation status of two significant indigenous cattle populations from the Vidarbha region of Maharashtra, Umarda (UM) and Pahadi/Melghati (PAH), which form the foundation of the local subsistence economy. A total of 18 breeds/populations including three taurine breeds were subjected to genomic analysis using Bovine GGP50K SNP chip. Higher heterozygosity (UM: Ho = 0.332, He = 0.417; PAH: Ho = 0.351, He = 0.416) and effective population sizes (UM: Ne = 67; PAH: Ne = 129 at the 13th generation) in these two indigenous cattle populations indicated substantial genetic resilience. Bayesian clustering via ADMIXTURE at K = 10 using 1000 AIMs revealed a distinct UM ancestry component (61.63%), suggestive of historical isolation, while PAH with 39.19% ancestry formed cluster with other indicine breeds, reflecting extensive gene flow. The f₃ statistics indicated admixture in PAH from Brown Swiss and Dangi (f₃ = -0.002647, Z = -3.619), attributed to historical crossbreeding, whereas UM exhibited no admixture, indicating its genetic uniqueness. Local ancestry analysis identified Bos taurus introgression on chromosome (Chr) 13 in UM, with the CBLN4 gene associated with udder morphology, which suggested its adaptation for dairy traits. These findings underscore the genetic distinctiveness of UM and shared ancestry of PAH, advocating for their preservation and targeted breeding to enhance productivity in smallholder systems. This genomic insight aligns with global efforts to safeguard livestock biodiversity, offering a foundation for sustainable cattle improvement in India.