Genome-Wide Association Studies on the Autosomes and Chromosome X Uncover Genetic Basis of Reproductive Traits in Yorkshire Pigs

TL;DR

This study explores how genes on both autosomes and the X chromosome influence reproductive traits in Yorkshire pigs, revealing new genetic markers that could improve breeding efficiency.

Contribution

The study highlights the previously overlooked role of the X chromosome in reproductive traits and identifies new genetic markers for breeding improvement.

Findings

Genome-wide association studies identified 23 significant SNPs and candidate genes linked to reproductive traits in Yorkshire pigs.

The X chromosome contributed up to 50.9% heritability in some parities, emphasizing its importance in reproductive genetics.

Incorporating X-linked genetic information could enhance genomic selection strategies for improving pig reproduction.

Abstract

Understanding the genetic basis influencing reproductive performance in pigs is essential for improving breeding efficiency and productivity. In this study, we examined the genetic basis of key reproductive traits in Yorkshire pigs by analyzing genetic information from both autosomes and the X chromosome. We identified genetic regions and candidate genes associated with total litter weight of piglets born alive (TLWT_BA), total number born (TNB), total litter weight at 21 days (TLWT_D21), and number of weaned pigs (NWEAN). Importantly, the inclusion of the X chromosome revealed additional genetic effects that are often overlooked in studies focusing solely on autosomes. These findings provide new insights into the genetic determinants of reproduction in pigs and offer useful genetic markers that may support the development of more effective breeding strategies to enhance reproductive efficiency in Yorkshire populations.

Reproductive efficiency is a fundamental determinant of productivity in pig breeding programs. However, the role of the X chromosome in shaping the genetic basis of reproductive traits remains underexplored. To address this problem, Genome-Wide Association Studies were conducted to explore the genetic basis of reproductive traits in Yorkshire pigs. We collected data from 2659 Yorkshire sows, focusing on four reproductive traits across the first three parties. Statistical analyses included principal component analysis, estimation of genetic parameters, and mixed linear model association to identify SNPs and candidate genes. Heritability estimates (h2) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). Genome-wide association analysis identified 23 significant SNPs and candidate genes, including several putatively significant X-linked genes; however, only a single X-linked locus was significantly associated with one trait. These findings demonstrate that, for 9 of the 12 parities, the proportion of total heritability attributable to X-linked variation was 0–2.7%. For the remaining three parities, the corresponding proportions were 8.4%, 21.5%, and 50.9%, while autosomes accounted for most of the genetic variation. In all but one trait, heritability estimated from X-linked GRMs was not significantly different from zero, highlighting the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs.

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