Effect of single-nucleotide polymorphisms on specific reproduction parameters in Hungarian Large White sows

Abstract

The aim of this study was to reveal the effect of single-nucleotide polymorphisms (SNPs) on the total number of piglets born (TNB), the litter weight born alive (LWA), the number of piglets born dead (NBD), the average litter weight on the 21st day (M21D) and the interval between litters (IBL). Genotypes were determined on a high-density Illumina Porcine SNP 60K BeadChip. Data screening and data identification were performed by a multi-locus mixed-model. Statistical analyses were carried out to find associations between individual genotypes of 290 Hungarian Large White sows and the investigated reproduction parameters. According to the analysis outcome, three SNPs were identified to be associated with TNB. These loci are located on chromosomes 1, 6 and 13 (−log10P = 6.0, 7.86 and 6.22, the frequencies of their minor alleles, MAF, were 0.298, 0.299 and 0.364, respectively). Two loci showed considerable association (−log10P = 10.35 and 10.46) with LWA on chromosomes 5 and X, the MAF were 0.425 and 0.446, respectively. Seven loci were found to be associated with NBD. These loci are located on chromosomes 5, 6, 13, 14, 15, 16 and 18 (−log10P = 10.95, 5.43, 8.29, 6.72, 6.81, 5.90, and 5.15, respectively). One locus showed association (−log10P = 5.62) with M21D on chromosome 1 (the MAF was 0.461). Another locus was found to be associated with IBL on chromosome 8 (−log10P = 7.56; the MAF was 0.438). The above-mentioned loci provide a straightforward possibility to assist selection by molecular tools and, consequently, to improve the competitiveness of the Hungarian Large White (HLW) breed.

Meta-Analysis of SNPs Determining Litter Traits in Pigs

“…First, dataset A ( Tables S1–S5 ; Supplementary_Tables ) refers to the data generated from significant SNPs reported in GWASs performed for five traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birth weight (LWT), and corpus luteum number (CLN). Second, dataset B refers to data created from full GWAS results for TNB generated in five studies [ 10 , 22 , 23 , 24 , 25 ] ( Table 1 ).…”

“…Dataset B was created by merging complete results of GWAS for TNB from five publications: Uimari et al [ 22 ], Sell-Kubiak et al [ 23 ], Ma et al [ 25 ], Balogh et al [ 24 ], and Zhang et al [ 10 ]. The dataset created after merging the results from the five GWASs consisted of 63,531 SNPs available for further analysis.…”

Meta-analysis of SNPs determining litter traits in pigs

“…First, dataset A (Tables S1-S5; Supplementary_Tables) refers to the data generated from signi cant SNPs reported in GWAS performed for ve traits: total number born (TNB) number born alive (NBA), stillborn (SB), litter birthweight (LWT), and corpus luteum number (CLN). Second, dataset B refers to data created from full GWAS results for TNB generated in ve studies: [10,[22][23][24][25] (Table 1).…”

“…As a result of MA performed on dataset B two SNPs were found to be signi cantly associated with TNB. First, rs80945731, located on SSC14:62633073, was available in four out of ve evaluated populations [10,22,24,25]. Based on Ensembl Sscrofa11.1, this SNP is located in the intron region of the FAM13C gene.…”

“…Dataset B was created by merging complete results of GWAS for TNB from ve publications: Uimari et al [22], Sell-Kubiak et al [23], Ma et al [25], Balogh et al [24], and Zhang et al [10]. The dataset created after merging the results from ve GWAS, consisted of 63,531 SNPs available for further analysis.…”