Research on Runs of Homozygosity (ROH) in cattle is primarily autosome centric, excluding X chromosomes. This study investigates X chromosome-SNP based inbreeding (FROH) in seven Indian native cattle breeds, categorized as dairy, draft, or dual-purpose. To explore recent and ancient inbreeding or selection events, ROH were divided into two length classes; > 1 Mb (reflecting events from 50 to 12.5 generations ago) and > 8 Mb (events from 12.5 generations ago). The mean number of ROH on the X chromosome per individual varied across breeds, with Tharparkar exhibiting the lowest (8.31 ± 1.57) and Kangayam the highest (12.15 ± 0.61). Ongole possessed the longest ROH segment, measuring 143.82 Mb. In terms of genomic coverage, ROH on the X chromosome spanned the greatest length in Tharparkar (79.38 Mb, 57.10% of the chromosome) and the least in Kangayam (29.05 Mb, 19.50%). The inbreeding coefficient based on ROH segments exceeding 1 Mb (FROH > 1 Mb) was highest in Kangayam (0.16 ± 0.001), while intermediate values were observed in Sahiwal (0.12 ± 0.001), Gir (0.15 ± 0.01), Hariana (0.15 ± 0.001), and Ongole (0.12 ± 0.01). When considering longer ROH segments (> 8 Mb), Tharparkar demonstrated the highest level of inbreeding (0.44 ± 0.13), whereas Kangayam recorded the lowest (0.03 ± 0.02). Comparison with previous autosomal ROH studies of the same breeds revealed different patterns of recent inbreeding (FROH > 8 Mb). Kangayam displayed the highest autosomal inbreeding (0.113 ± 0.059), with Hariana (0.042 ± 0.031) and Sahiwal (0.043 ± 0.048) showing intermediate levels. Contrasting X-chromosomal and autosomal based inbreeding (FROH > 8 Mb) are likely attributable to factors such as varying recombination rates, and sex-specific inheritance patterns. Focusing on FROH > 1 Mb for the X chromosome helps mitigate the influence of random inheritance due to sex-linked transmission. However, due to the X chromosome’s complexity, autosomal-based genomic inbreeding (FROH) estimates may be more reliable. High-frequency ROH islands on the X chromosome contained genes and quantitative trait loci (QTLs) associated with immunity, milk production, and reproduction. Notably, the draft breed Kangayam had a higher prevalence of ROH islands linked to reproduction traits, suggesting greater reproductive efficiency compared to dairy breeds. These findings highlight the potential of these genomic regions for future X chromosome-wide association studies targeting agronomically significant traits in cattle.

Comparative insights into X-chromosome and autosomal autozygosity in zebu cattle

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发表日期：

2025年8月17日

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Kusum Mehla,
Rangasai Chandra Goli,
Dibyasha Kar,
Indrajit Ganguly,
Sanjeev Singh,
Satpal Dixit

摘要

Research on Runs of Homozygosity (ROH) in cattle is primarily autosome centric, excluding X chromosomes. This study investigates X chromosome-SNP based inbreeding (F_ROH) in seven Indian native cattle breeds, categorized as dairy, draft, or dual-purpose. To explore recent and ancient inbreeding or selection events, ROH were divided into two length classes; > 1 Mb (reflecting events from 50 to 12.5 generations ago) and > 8 Mb (events from 12.5 generations ago). The mean number of ROH on the X chromosome per individual varied across breeds, with Tharparkar exhibiting the lowest (8.31 ± 1.57) and Kangayam the highest (12.15 ± 0.61). Ongole possessed the longest ROH segment, measuring 143.82 Mb. In terms of genomic coverage, ROH on the X chromosome spanned the greatest length in Tharparkar (79.38 Mb, 57.10% of the chromosome) and the least in Kangayam (29.05 Mb, 19.50%). The inbreeding coefficient based on ROH segments exceeding 1 Mb (F_ROH > 1 Mb) was highest in Kangayam (0.16 ± 0.001), while intermediate values were observed in Sahiwal (0.12 ± 0.001), Gir (0.15 ± 0.01), Hariana (0.15 ± 0.001), and Ongole (0.12 ± 0.01). When considering longer ROH segments (> 8 Mb), Tharparkar demonstrated the highest level of inbreeding (0.44 ± 0.13), whereas Kangayam recorded the lowest (0.03 ± 0.02). Comparison with previous autosomal ROH studies of the same breeds revealed different patterns of recent inbreeding (F_ROH > 8 Mb). Kangayam displayed the highest autosomal inbreeding (0.113 ± 0.059), with Hariana (0.042 ± 0.031) and Sahiwal (0.043 ± 0.048) showing intermediate levels. Contrasting X-chromosomal and autosomal based inbreeding (F_ROH > 8 Mb) are likely attributable to factors such as varying recombination rates, and sex-specific inheritance patterns. Focusing on F_ROH > 1 Mb for the X chromosome helps mitigate the influence of random inheritance due to sex-linked transmission. However, due to the X chromosome’s complexity, autosomal-based genomic inbreeding (F_ROH) estimates may be more reliable. High-frequency ROH islands on the X chromosome contained genes and quantitative trait loci (QTLs) associated with immunity, milk production, and reproduction. Notably, the draft breed Kangayam had a higher prevalence of ROH islands linked to reproduction traits, suggesting greater reproductive efficiency compared to dairy breeds. These findings highlight the potential of these genomic regions for future X chromosome-wide association studies targeting agronomically significant traits in cattle.