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<p>The Karan Fries (KF), a newly developed dairy cattle (Holstein Friesian × Tharparkar), after nine generations of <i>inter se</i> mating (mating among crossbreds) by maintaining a stable, composite breed structure, is expected to preserve some heterosis or hybrid vigour through the retention of heterozygosity and selective pressure for performance traits. Although a decline in productivity is generally seen from F1 to later <i>inter se</i> generations, the rate of loss of heterosis slows down, allowing the population to reach a new equilibrium. This seems to be an interesting proposition. Therefore, to assess the retained heterosis and to evaluate the current status of the KF population, the present study was conducted, which included a sizeable phenotyped and genotyped animals (<i>n</i> = 355). The analysis identified a stabilized genomic architecture with a mean exotic inheritance of 64.34 ± 0.74% (predominantly Holstein Friesian) and an indigenous contribution of 35.66 ± 0.95% (primarily Tharparkar). Genomic indicators of heterosis revealed a mean Genomic Retained Heterosis (RH<sub>g</sub>) of 59% which accounts for 15.82% of the total observed KF average yield (4153.14 ± 167.32&#xa0;kg). Genomic Retained Heterozygosity (RHET<sub>g</sub>) of 0.44%. Notably, a near-perfect correlation (<i>r</i> = 0.98) was observed between these two metrics, indicating that RHET<sub>g</sub> can be used interchangeably with RH<sub>g</sub> to assess heterosis and its effects in instances where parental genotypic records were absent. Linear regression analysis demonstrated that RH<sub>g</sub> was a primary driver of productivity, with Total Milk Yield (TMY) increasing by 1113.81 ± 301.91&#xa0;kg per unit increase in RH<sub>g</sub> (<i>p</i> &lt; 0.001). The impact on TMY was significantly larger than on 305-day milk yield (339.08 ± 282.92&#xa0;kg), suggesting that genomic heterosis specifically enhances lactation persistence and environmental robustness. A joint-model GWAS identified 182 SNPs with significant additive effects and 117 SNPs with significant dominance effects for TMY. Functional annotation revels candidate genes for milk synthesis (<i>SLC25A1</i>, <i>PIP4K2A</i>, <i>LATS2</i>), heat stress resilience (<i>DNAJB5</i>, <i>DNAJC1</i>), and immunological defence (<i>ARHGAP15</i>, <i>LPAR3</i>). Protein network analysis identified the Mitochondrial Ribosomal Protein (MRP) family, specifically hub gene <i>MRPL22</i>, as the central driving gene for both additive and dominance components. These findings confirm that KF cattle effectively leverage retained heterosis to integrate high production potential with robust tropical climatic adaptability.</p>

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Influence of genomic retained heterosis on lactation persistence and tropical resilience: leveraging joint-model GWAS to quantify non-additive variance in India’s Karan Fries population

  • 期刊论文

  • 发表日期：

    2026年7月20日

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  • Ishmeet Kumar,
  • Jayesh Vyas,
  • Asad Khan,
  • Gargi Ramola,
  • I. Ilayaraja,
  • Lal Muansangi,
  • Anil Chitra,
  • Pritam Pal,
  • Ritik Kumar Singh,
  • M. L. Kamboj,
  • T. V. Raja,
  • Anupama Mukherjee,
  • Sabyasachi Mukherjee

摘要

The Karan Fries (KF), a newly developed dairy cattle (Holstein Friesian × Tharparkar), after nine generations of inter se mating (mating among crossbreds) by maintaining a stable, composite breed structure, is expected to preserve some heterosis or hybrid vigour through the retention of heterozygosity and selective pressure for performance traits. Although a decline in productivity is generally seen from F1 to later inter se generations, the rate of loss of heterosis slows down, allowing the population to reach a new equilibrium. This seems to be an interesting proposition. Therefore, to assess the retained heterosis and to evaluate the current status of the KF population, the present study was conducted, which included a sizeable phenotyped and genotyped animals (n = 355). The analysis identified a stabilized genomic architecture with a mean exotic inheritance of 64.34 ± 0.74% (predominantly Holstein Friesian) and an indigenous contribution of 35.66 ± 0.95% (primarily Tharparkar). Genomic indicators of heterosis revealed a mean Genomic Retained Heterosis (RHg) of 59% which accounts for 15.82% of the total observed KF average yield (4153.14 ± 167.32 kg). Genomic Retained Heterozygosity (RHETg) of 0.44%. Notably, a near-perfect correlation (r = 0.98) was observed between these two metrics, indicating that RHETg can be used interchangeably with RHg to assess heterosis and its effects in instances where parental genotypic records were absent. Linear regression analysis demonstrated that RHg was a primary driver of productivity, with Total Milk Yield (TMY) increasing by 1113.81 ± 301.91 kg per unit increase in RHg (p < 0.001). The impact on TMY was significantly larger than on 305-day milk yield (339.08 ± 282.92 kg), suggesting that genomic heterosis specifically enhances lactation persistence and environmental robustness. A joint-model GWAS identified 182 SNPs with significant additive effects and 117 SNPs with significant dominance effects for TMY. Functional annotation revels candidate genes for milk synthesis (SLC25A1, PIP4K2A, LATS2), heat stress resilience (DNAJB5, DNAJC1), and immunological defence (ARHGAP15, LPAR3). Protein network analysis identified the Mitochondrial Ribosomal Protein (MRP) family, specifically hub gene MRPL22, as the central driving gene for both additive and dominance components. These findings confirm that KF cattle effectively leverage retained heterosis to integrate high production potential with robust tropical climatic adaptability.