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Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data
Author(s) -
Zhang Zhe,
Zhang Qianqian,
Xiao Qian,
Sun Hao,
Gao Hongding,
Yang Yumei,
Chen Jiucheng,
Li Zhengcao,
Xue Ming,
Ma Peipei,
Yang Hongjie,
Xu Ningying,
Wang Qishan,
Pan Yuchun
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12730
Subject(s) - runs of homozygosity , biology , inbreeding , genetics , genotype , population , imputation (statistics) , single nucleotide polymorphism , missing data , gene , statistics , demography , mathematics , sociology
Summary Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity ( ROH ) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced‐representation sequencing method. After imputation and quality control, 60 850 high‐confidence SNP s were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH ‐related variables were compared between imputed and non‐missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction‐related gene PRM 1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.