Scholarlink

<p>Understanding population structure, effective population size (Ne), and inbreeding is fundamental for conservation and genetic improvement of livestock. In domestic water buffalo, a key contributor to Indian agriculture, genomic insights remain limited compared to those of cattle. In this study, we utilised double digest restriction-site associated DNA sequencing (ddRAD-seq) to investigate linkage disequilibrium (LD), Ne, haplotype structure, and Runs of Homozygosity (ROH) based inbreeding in five Indian indigenous buffalo breeds namely, Bhadawari (BHA), Mehsana (MEH), Murrah (MUR), Pandharpuri (PAN), and Surti (SUR). After stringent quality control, 232,463 high-confidence SNPs were retained for subsequent analyses. LD decay patterns revealed slower breakdown in MEH, consistent with stronger selection and reduced gene flow, while MUR exhibited the most rapid decay, reflecting a large breeding base and wider dissemination. Ne estimates further supported these trends, with MUR showing the largest effective size (155-3597 across 13-999 generations) and MEH the smallest (45-1771), indicating greater vulnerability to drift. Haplotype block analysis highlighted extensive recombination and diversity in MUR, contrasted by fewer but larger haplotypes in MEH. ROH profiles identified elevated genomic autozygosity in MEH (<i>F</i><sub><i>ROH</i></sub> = 0.091621) compared to moderate-to-low levels in MUR (<i>F</i><sub><i>ROH</i></sub> = 0.027198) and SUR (<i>F</i><sub><i>ROH</i></sub> = 0.050559), underscoring breed-specific demographic histories. Collectively, these results demonstrate pronounced differences in genomic diversity, inbreeding, and historical demography among Indian buffalo breeds. Our findings emphasize the importance of genomic monitoring for balancing selection with long-term genetic health, and provide a critical foundation for designing sustainable breeding and conservation strategies in Indian buffalo.</p>

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Genomic diversity patterns based on effective population size, haplotype blocks and runs of homozygosity in Indian water buffalo breeds

  • 期刊论文

  • 发表日期：

    2026年3月26日

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  • Rangasai Chandra Goli,
  • Kiyevi G. Chishi,
  • Oguru Sai Sruthi,
  • Chandana Sree Chinnareddyvari,
  • Nidhi Sukhija,
  • K. K. Kanaka

摘要

Understanding population structure, effective population size (Ne), and inbreeding is fundamental for conservation and genetic improvement of livestock. In domestic water buffalo, a key contributor to Indian agriculture, genomic insights remain limited compared to those of cattle. In this study, we utilised double digest restriction-site associated DNA sequencing (ddRAD-seq) to investigate linkage disequilibrium (LD), Ne, haplotype structure, and Runs of Homozygosity (ROH) based inbreeding in five Indian indigenous buffalo breeds namely, Bhadawari (BHA), Mehsana (MEH), Murrah (MUR), Pandharpuri (PAN), and Surti (SUR). After stringent quality control, 232,463 high-confidence SNPs were retained for subsequent analyses. LD decay patterns revealed slower breakdown in MEH, consistent with stronger selection and reduced gene flow, while MUR exhibited the most rapid decay, reflecting a large breeding base and wider dissemination. Ne estimates further supported these trends, with MUR showing the largest effective size (155-3597 across 13-999 generations) and MEH the smallest (45-1771), indicating greater vulnerability to drift. Haplotype block analysis highlighted extensive recombination and diversity in MUR, contrasted by fewer but larger haplotypes in MEH. ROH profiles identified elevated genomic autozygosity in MEH (FROH = 0.091621) compared to moderate-to-low levels in MUR (FROH = 0.027198) and SUR (FROH = 0.050559), underscoring breed-specific demographic histories. Collectively, these results demonstrate pronounced differences in genomic diversity, inbreeding, and historical demography among Indian buffalo breeds. Our findings emphasize the importance of genomic monitoring for balancing selection with long-term genetic health, and provide a critical foundation for designing sustainable breeding and conservation strategies in Indian buffalo.