Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations

Abstract

Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.

Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

“…Several heterozygosity islands harboured genes previously reported in association with immune response, rather than with healthrelated QTL. Duroc and Large White shared the ROHet island on SSC2 (91.8-93.63 Mb), which was reported as ROH island by Schiavo, Bovo, Bertolini, et al (2020) in Calabrese breed and partially overlapped the ROHet island detected in a Duroc sample (Ruan et al, 2022). This island harbours the EDIL3, an immune-related gene that was reported 3 times upregulated in umbilical-herniaaffected Landrace pigs (Souza et al, 2020).…”

“…Finally, Cinta Senese, Casertana, Mora Romagnola, and cosmopolitan breeds outlined ROHet islands on SSC2, SSC6, SSC14, and SSC15 that mapped genes and QTL linked to productive traits (Howard et al, 2015;Kim et al, 2021;Li et al, 2011;Qi et al, 2022;Zappaterra et al, 2021;Zhang et al, 2015). In particular, the heterozygosity-rich segment, observed on SSC6 (54.2-55.9 Mb) in Duroc, Landrace, Large White, and Pietrain, correlates with QTL for average daily gain, daily feed intake, fat androstenone level, mean corpuscular haemoglobin concentration and meat colour, and partially overlapped a ROHet island detected by Ruan et al (2022) in a Duroc sample.…”

“…Among the genes harbouring this region, the IQ motif containing G (IQCG) was identified as a candidate gene for sperm motility in Large White and Landrace pig breeds (Marques et al, 2018). The ROHet island located on SSC14 (46.5-47.9 Mb) in Pietrain and Cinta Senese breeds was reported as a ROH island in Duroc (Schiavo, Bovo, Bertolini, et al, 2020) and partially overlapped the ROHet island detected in a Duroc population by Ruan et al (2022). In particular, this region evidenced 11 markers previously reported in association with umbilical hernia QTL (Grindflek et al, 2018).…”

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

“…In addition, Meyermans et al [33] has shown that MAF and LD pruning severely impact ROH analyses and recommend to avoid MAF and LD pruning prior to ROH analyses based on medium density genotypes. Meanwhile, ROHet has far less characterized than ROH in livestock, especially in pigs [16] , [60] . Biscarini et al [57] presented the results of the first sensitivity analysis for ROHet and varied the number of missing and homozygous SNPs allowed inside ROHet.…”

Insights into the architecture of human-induced polygenic selection in Duroc pigs

“…The variant rs346331089 located in the intron of SPATA6 , which is one of sperm-specific genes. Previous studies suggested the regulation of the expression pattern of SPATA6 linked to spermatogenesis in Hu sheep [ 45 ] and inactivation of SPATA6 leaded to acephalic spermatozoa and male sterility in mice [ 46 ]. These results above manifested high-intensity directional selection on certain economic traits might influenced the number of teats in pigs.…”