绵羊全基因组ROH检测及候选基因鉴定

doi:10.11843/j.issn.0366-6964.2019.08.004

Abstract

Abstract: The aim of this study was to evaluate inbreeding among different sheep populations and detect genes related to economic traits of sheep based on the information of runs of homozygosity (ROH). Based on Illumina Ovine SNP50 BeadChip, we performed genome-wide ROH scan for 440 individuals from 10 sheep populations. The number, length and frequency of ROH were counted in each population and the genomic inbreeding coefficient(F_ROH) was calculated based on ROH. The genomic regions with high frequency in ROH were annotated. A total of 25 920 ROH fragments were identified in the 10 sheep populations. The number, length, frequency and distribution of ROH varied among these sheep populations. The average number of ROH per population ranged from 10.17 (Sunite) to 95.99 (Dorper), the average length of ROH per population ranged from 2.04 Mb (Tibetan sheep from Sichuan) to 4.71 Mb (Lop), and the average genomic inbreeding coefficients (F_ROH) ranged from 0.010 (Sunite) to 0.172 (Dorper) in sheep populations. The average F_ROH in commercial sheep breeds from abroad (Dorper and German Mutton Merino sheep) were higher than that in the indigenous sheep populations in China. Among Chinese indigenous sheep populations, Tibetan sheep from Tibet (0.085) had the highest average genomic inbreeding coefficient. Moreover, twenty-six genes related to economic traits of sheep located in the genomic regions with high frequency in ROH were identified. Among these genes, NCAPG, LCORL, PRKAA2, FAIM2 and HYDIN were associated with growth and development traits, LEPR, WNT10B and NCKAP5L were related to fat metabolism, and CDIPT, CAPN3 and FGF9 involved in meat quality and carcass traits. The inbreeding coefficients calculated based on ROH would provide reference for breeding and preservation of the 10 sheep populations and the candidate genes identified could be used for marker-assisted selection in sheep breeding.

CLC Number:

S826.2

LIU Jiaxin, WEI Xia, DENG Tianyu, XIE Rui, HAN Jianlin, DU Lixin, ZHAO Fuping, WANG Lixian. Genome-wide Scan for Run of Homozygosity and Identification of Corresponding Candidate Genes in Sheep Populations[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(8): 1554-1566.

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Genome-wide Scan for Run of Homozygosity and Identification of Corresponding Candidate Genes in Sheep Populations

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