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<p>The selection of individuals depends on their predicted breeding values and mating of related individuals that might enhance the proportion of identical alleles by descent. In the present study selection has been practiced continuously in a single herd with limited migration of individuals, thus, understanding the impact of inbreeding is vital for increasing performance in Sahiwal dairy cattle well adapted to tropical condition, however, its quantification and assessment using genomic&#xa0;tools remain unexplored. In this context, we estimated and compared traditional pedigree-based (F<sub>PED</sub>) and multiple genomic-based (F<sub>GRM</sub>, F<sub>UNI</sub>, F<sub>HOM</sub>, F<sub>ROH</sub>) inbreeding coefficients, assessed their correlation and examined their effect on milk composition traits (fat yield, solids-not-fat yield, protein yield and lactose yield). The analysis was conducted on 863 cows with 90 animals genotyped using Illumina Bovine SNP777K chip having pedigree records of 4242 individuals (1955–2024) maintained at ICAR-NDRI, Karnal, India. Mean inbreeding coefficients ranged from 0.008 to 0.41 across different methodologies and an increase of 1% in inbreeding was associated with yield reductions of 1.42–1.98&#xa0;kg, 2.84–3.93&#xa0;kg, 0.27–0.87&#xa0;kg and 0.22–0.43&#xa0;kg in fat yield, solids-not-fat yield, protein yield and lactose yield, respectively. Notably, recent inbreeding showed pronounced adverse effects on milk quality traits than ancient inbreeding, highlighting its importance and contemporary mating practices in breeding programs. High correlations of pedigree inbreeding coefficient with genomic inbreeding estimators reinforce utility of both approaches for inbreeding assessment in Sahiwal population. Our findings underscore the need to integrate pedigree-based and genomic-based measures in breeding strategies emphasising minimal recent inbreeding to limit inbreeding depression and improve sustainability of Sahiwal cattle production system. This study showed that strategic breeding management with controlled mating plans, use of unrelated sires and optimal sire rotation is the need of hour for keeping Sahiwal genetic integrity, adaptability and resilience under tropical dairy systems.</p>

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Longitudinal genomic and pedigree inbreeding metrics reveal inbreeding depression in milk quality traits of Sahiwal cattle maintained in organised herd

  • 期刊论文

  • 发表日期：

    2025年10月31日

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  • Jayesh Vyas,
  • Ishmeet Kumar,
  • Anil Chitra,
  • Gargi Ramola,
  • Sabyasachi Mukherjee,
  • Indrajit Ganguly,
  • Arun Kumar Mishra,
  • Pawan Singh,
  • Udita Chaudhary,
  • Anupama Mukherjee

摘要

The selection of individuals depends on their predicted breeding values and mating of related individuals that might enhance the proportion of identical alleles by descent. In the present study selection has been practiced continuously in a single herd with limited migration of individuals, thus, understanding the impact of inbreeding is vital for increasing performance in Sahiwal dairy cattle well adapted to tropical condition, however, its quantification and assessment using genomic tools remain unexplored. In this context, we estimated and compared traditional pedigree-based (FPED) and multiple genomic-based (FGRM, FUNI, FHOM, FROH) inbreeding coefficients, assessed their correlation and examined their effect on milk composition traits (fat yield, solids-not-fat yield, protein yield and lactose yield). The analysis was conducted on 863 cows with 90 animals genotyped using Illumina Bovine SNP777K chip having pedigree records of 4242 individuals (1955–2024) maintained at ICAR-NDRI, Karnal, India. Mean inbreeding coefficients ranged from 0.008 to 0.41 across different methodologies and an increase of 1% in inbreeding was associated with yield reductions of 1.42–1.98 kg, 2.84–3.93 kg, 0.27–0.87 kg and 0.22–0.43 kg in fat yield, solids-not-fat yield, protein yield and lactose yield, respectively. Notably, recent inbreeding showed pronounced adverse effects on milk quality traits than ancient inbreeding, highlighting its importance and contemporary mating practices in breeding programs. High correlations of pedigree inbreeding coefficient with genomic inbreeding estimators reinforce utility of both approaches for inbreeding assessment in Sahiwal population. Our findings underscore the need to integrate pedigree-based and genomic-based measures in breeding strategies emphasising minimal recent inbreeding to limit inbreeding depression and improve sustainability of Sahiwal cattle production system. This study showed that strategic breeding management with controlled mating plans, use of unrelated sires and optimal sire rotation is the need of hour for keeping Sahiwal genetic integrity, adaptability and resilience under tropical dairy systems.