基于SNP芯片数据分析不同奶牛场基因组近交系数及筛选功能性基因

doi:10.11843/j.issn.0366-6964.2023.07.017

Abstract

Abstract: This study aimed to estimate whole-genome inbreeding levels of Chinese Holstein cattle from different herds in Henan province by using the runs of homozygosity (ROH), and identify ROH enriched regions and screen candidate genes associated with the traits of economic interest. A total of 900 Chinese Holstein cattle form 7 dairy herds in Henan province were used to detect genome-wide ROH by the GGP Bovine 150K Beadchip. The number, length and frequency of ROH in Holstein population was counted. The genome inbreeding coefficient(F_ROH) was calculated according to ROH, and the high frequency ROH regions were annotated. ROH was identified in all animals, 55 908 ROH were identified, with a mean length of 4.23 Mb. The estimated inbreeding coefficients of ROH in 7 herds ranged from 0.082 (H7) to 0.123 (H2), with an average F_ROH of 0.106 in all animals.Moreover, 79 genes related to the economic traits of dairy cows in the genomic region with high frequency ROH were identified. Among these genes, AKAP3, C5H12orf4, and FGF6 were related to the body size and height of cattle, CAPN3 was associated with carcass and reproductive traits, CHST14 was directly related to pregnancy maintenance and fetal growth, the traits of milk protein composition were affected by IL5RA, and FGF10 was involved in regulating fetal folliculogenesis. Notably, a high-frequency ROH region was detected on chromosome 14(22.78-23.38 Mb), where more than 80% of individuals carried ROH fragments. The genes TGS1, LYN and CHCHD7 related to growth and feed conversion were identified in this region. Evaluation of dairy cattle inbreeding based on ROH information could be a useful tool for selection and mating strategies. The candidate genes identified could be used for marker-assisted selection in dairy cattle breeding.

Key words: runs of homozygosity (ROH), genomic inbreeding coefficient, candidate gene, Chinese Holstein cattle

CLC Number:

S823.91

WANG Zhenyu, ZHANG Saibo, LIU Wenhui, LIANG Dong, REN Xiaoli, YAN Lei, YAN Yuefei, GAO Tengyun, ZHANG Zhen, HUANG Hetian. Genomic Inbreeding Coefficient Analysis and Functional Gene Screening in Different Dairy Farms Based on SNP Chip Data[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2848-2857.

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Genomic Inbreeding Coefficient Analysis and Functional Gene Screening in Different Dairy Farms Based on SNP Chip Data

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