Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data

TY - JOUR

T1 - Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data

AU - Zhang, Zhe

AU - Zhang, Qianqian

AU - Xiao, Qian

AU - Sun, Hao

AU - Gao, Hongding

AU - Yang, Yumei

AU - Chen, Jiucheng

AU - Li, Zhengcao

AU - Xue, Ming

AU - Ma, Peipei

AU - Yang, Hongjie

AU - Xu, Ningying

AU - Wang, Qishan

AU - Pan, Yuchun

PY - 2018/12/1

Y1 - 2018/12/1

N2 - 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 SNPs 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 PRM1 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.

AB - 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 SNPs 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 PRM1 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.

KW - Chinese indigenous pigs

KW - imputation

KW - inbreeding

KW - ROH islands

KW - selection sweep

U2 - 10.1111/age.12730

DO - 10.1111/age.12730

M3 - Journal article

C2 - 30324759

AN - SCOPUS:85054908781

SN - 0268-9146

VL - 49

SP - 579

EP - 591

JO - Animal Genetics

JF - Animal Genetics

IS - 6

ER -