Genome-Wide Association Study Identified a Quantitative Trait Locus and Two Candidate Genes on Sus scrofa Chromosome 2 Affecting Vulvar Traits of Suhuai Pigs

Genetic parameters of vulva traits and impact of vulva scores on gilts culling in Large White pigs

Vulva morphologies represent significant traits in pig production. Recent studies suggest that vulva size can be predictive of the reproductive performance of gilts. This study aimed to analyse the genetic parameters of vulva traits, including vulva length, vulva width, and vulva angle score (VAS), as well as litter traits, including total number born, number born alive, number stillborn, and piglet survival rate, across three Large White pig strains (PIC, Topigs, and Canadian). We estimated the correlations between vulva traits and litter performance, as well as the reasons for culling gilts. In this study, single-trait and multitrait models were employed to estimate the heritability and genetic correlations between vulva and litter traits. The heritabilities of vulva traits ranged from 0.167 to 0.426, whereas the heritability of litter traits ranged from 0.013 to 0.147. The VAS in Topigs Large White pigs exhibited the highest heritability. The genetic correlation coefficients between vulva length and width in PIC and Topigs Large White pigs were significantly positively correlated, ranged from 0.585 to 0.767. No significant correlation was found between vulva and litter traits. Subsequently, we scored the vulva traits according to previously reported studies, linear relationship analysis between vulva score and reasons for culling gilts revealed that gilts with larger vulva widths had a lower risk of culling. The average vulva width score of the gilts that were culled due to prolonged oestrus was significantly lower (2.75) compared to that of gilts with normal oestrus (2.90). In the population of gilts aged 220-230 days, the gilts with higher vulva angle scores had a lower risk of culling due to vulva inflammation with purulent discharge. The results suggest that selecting vulva traits in replacement gilts is an effective strategy to reduce gilt culling rates.

Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs

Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) for LTN on SSC17, two significant SNPs (rs342855242 and rs80813115) for RTN on SSC2 and SSC9, and two significant SNPs (rs327003548 and rs326943811) for TTN on SSC5 and SSC6. Among them, four novel QTL were discovered. The Bayesian fine-mapping method was used to fine map the QTL identified in the GWAS of the imputed data, and the confidence intervals of QTL affecting LTN (SSC17: 45.22-46.20 Mb), RTN (SSC9: 122.18-122.80 Mb) and TTN (SSC5: 14.01-15.91 Mb, SSC6: 120.06-121.25 Mb) were detected. A total of 52 candidate genes were obtained. Furthermore, we identified five candidate genes, WNT10B, AQP5, FMNL3, NUAK1 and CKAP4, for the first time, which involved in breast development and other related functions by gene annotation. Overall, this study provides new molecular markers for the breeding of teat number in pigs.