Abstract

Simple SummaryRuns of homozygosity (ROH) are the DNA segments that harbor uninterrupted stretches of homozygous genotype segments in the genome that are present in an individual due to the transmission of identical haplotypes from parents to their offspring. ROHs are widely used as predictors of whole-genome inbreeding levels in animals and identify highly selected genomic regions. In this study, we investigated the ROH distributions on the whole genome in three pig populations (Landrace, Songliao black and Yorkshire pigs). Moreover, inbreeding coefficients based on ROH were calculated and genes were annotated in the genomic regions with a high frequency of ROH. Results showed that Songliao black pigs had higher inbreeding in recent generations and ten genes related to economically important traits were located within ROH regions. Our findings provide a reference for developing breeding programs to maintain diversity and fitness in these breeds.Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.

Highlights

  • Runs of homozygosity (ROH) were first introduced by J Gibson et al [1], who defined the ROH as contiguous homozygous genotype segments in the genome that are present in an individual due to the transmission of identical haplotypes from parents to their offspring

  • 37,540, 36,476 and 36,180 SNPs and 83, 86 and 477 individuals were retained from the Landrace, Songliao and Yorkshire pigs, respectively

  • We identified a total of 10 genes reported to be associated with pig economic traits based on genomic regions with a high frequency of ROH

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Summary

Introduction

Runs of homozygosity (ROH) were first introduced by J Gibson et al [1], who defined the ROH as contiguous homozygous genotype segments in the genome that are present in an individual due to the transmission of identical haplotypes from parents to their offspring. Inbreeding is the mating of relatives, which can increase homozygosity in a population, and with an increase in the inbreeding level, the probability of homozygosity of harmful recessive genes increases, which can lead to decreases in the fecundity, viability and phenotype of offspring, which is referred to as inbreeding depression [6]. There are several factors influencing the generation of ROH, such as inbreeding, natural and artificial selection, genetic drift and population bottlenecks [7,8]; inbreeding is considered the most important factor [9,10,11]. ROH distribution pattern in the animal genome; the number, length, distribution and frequency of ROH in animal genomes provide rich genetic background information, such as animal population histories and inbreeding levels [12,13,14].

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