Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs

Abstract

The Chinese Erhualian pig has the highest record for litter size in the world. However, the genetic mechanism of its high prolificacy remains poorly understood. In our study, large phenotypic variations in litter size were found among Erhualian sows. Significant differences in total number born (TNB) and corpora lutea numbers were observed between sows with high and low estimated breeding values (EBVs) for TNB. To identify single nucleotide polymorphisms (SNPs) associated with TNB, a selective genomic scan was conducted on 18 sows representing the top 10% and 18 sows representing the bottom 10% of EBVs of 177 sows using Illumina Porcine SNP60 genotype data. Genome-wide fixation coefficient (F ) values were calculated for each SNP between the high- and low-EBV groups. A total of 154 SNPs were significantly differentiated loci between the two groups. Of the top 10 highest F SNPs, rs81399474, rs81400131 and rs81405013 on SSC8 and rs81434499 and rs81434489 on SSC 12 corresponded to previously reported QTL for litter size. The other five SNPs, rs81367039 on SSC2, rs80891106 on SSC7, rs81477883 on SSC12 and rs80938898 and rs80971725 on SSC14, appeared to be novel QTL for TNB. Significant associations between rs81399474 on SSC8 and TNB were confirmed in 313 Erhualian sows. Forty genes were identified around the top 10 highest F SNPs, of which UCHL1, adjacent to rs81399474, and RPS6KB1 and CLTC, adjacent to rs81434499, have been reported to affect the ovulation rate in pig. The findings can advance understanding of the genetic variations in litter size of pigs.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

“…FIGURE 4 | Neighbor-joining tree based on the Reynold's genetic distances for selected 32 pig and wild boar populations. (Silva et al, 2017); number of ribs in pigs, MESP1 on SSC7 (Zhu et al, 2015); meat-to-fat ratio in pigs, DEAF1 on SSC2 (Falker-Gieske et al, 2019); pregnancy rate in pigs, PPID on SSC8 (Gu et al, 2014); steroid receptor activity, CYP-40 on SSC8 (Ratajczak et al, 2015); brain development in horses, DLGAP1 on SSC6 (Schubert et al, 2014); salivary secretion in pigs, KCNMA1 on SSC14 (Li et al, 2013); reproduction in pigs, CWH43 on SSC8 (He et al, 2017); bone weight in cattle, FAM184B on SSC8 (Xia et al, 2017) and cardiovascular disease (Pérez-Montarelo et al, 2014); spermiogenesis in mouse, AMPH on SSC9; boar taint, NWD2 on SSC8 (Drag et al, 2018); melanocyte function in dogs, ARHGAP12 on SSC10 (Kluth and Distl, 2013); female pregnancy in pigs, RAPGEF2 on SSC8 (Pérez-Enciso et al, 2009); growth traits in cattle, KSR2 on SSC14 (Puig-Oliveras et al, 2014); vascular smooth muscle contraction in sheep, SPSB4 on SSC13 (Yang et al, 2016); and back-fat fatty acid composition, APBB1IP on SSC10 (Zappaterra et al, 2018). In addition, we identified several SNPs in the two Croatian breeds that were located in non-coding intergenic regions and that were present in various pig breeds as well as to other domestic animal species, including cattle, sheep and horse.…”

Genome‐wide association study for reproductive traits in a Large White pig population

“…2015) and ovulation rate (He et al . 2017), have been conducted, but knowledge about the complex genetic mechanism for reproductive performance still remains insufficient. Therefore, the aim of this study was to detect novel genetic variants and identify candidate genes for reproductive traits by performing a GWAS in a Large White pig population.…”

Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs

“…EHL pig is the representative of the high fecundity of Chinese local pigs [29], and MS pig is one of the Chinese breeds that were introduced into France in 1979 due to high fertility [30]. We found that the litter size of EHL and MS pigs were significantly higher than that of SH and TPE-L pigs.…”