Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.

Zhong Xu,Xiangzhe Zhang,Qiumeng Li,Yang Yue,Qingbo Zhao,Qishan Wang,Yuchun Pan,Hao Sun,Babatunde Shittu Olasege,Zhe Zhang,Peipei Ma

doi:10.3389/fgene.2019.00274

Zhong Xu, Xiangzhe Zhang + Show 9 more

Open Access

https://doi.org/10.3389/fgene.2019.00274

Copy DOI

Abstract

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1–5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

Highlights

Autozygosity refers to homozygosity in which the two alleles are identical by descent (IBD)
We investigated the occurrence and distribution of Runs of homozygosity (ROH) in a sample of 202 Jinhua pigs, in order to characterize genome-wide autozygosity levels and to detect potential ROH islands that may provide insights into past events of selection in this population
To compare the selection signatures obtained from ROH, the integrated haplotype score test was performed within Jinhua pigs

Summary

INTRODUCTION

Autozygosity refers to homozygosity in which the two alleles are identical by descent (IBD) It can result from several different phenomena, such as genetic drift, consanguineous matings, population bottleneck, as well as natural and artificial selection (Curik et al, 2014). Inbreeding may increase the frequency of autozygosity for deleterious alleles with the consequent reduction in individual performance (Ouborg et al, 2010) For these reasons, there is a growing interest in characterizing and understanding inbreeding and autozygosity in Jinhua pigs. We investigated the occurrence and distribution of ROH in a sample of 202 Jinhua pigs, in order to characterize genome-wide autozygosity levels and to detect potential ROH islands that may provide insights into past events of selection in this population. We used genotyping by genome reducing and sequencing (GGRS) (Chen et al, 2013), which was successfully applied to evaluate genetic diversity in Chinese indigenous pig breeds in the Taihu region (Wang et al, 2015)

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION