# Identification of Genomic Variants and Candidate Genes for Reproductive Traits and Growth Traits in Pishan Red Sheep Using Whole-Genome Resequencing

## TL;DR

This study identifies genetic variants and genes in Pishan red sheep that are linked to high reproduction and growth traits, offering insights for better breeding practices.

## Contribution

The study discovers 90 key genes and 59 genetic markers related to growth and reproduction in Pishan red sheep using whole-genome resequencing.

## Key findings

- Over 53 million high-quality SNPs were identified in Pishan red sheep.
- Genes like BMPRIB and HPGDS were found to influence litter size through specific biological pathways.
- A genome-wide association study identified 59 SNPs linked to growth and reproductive traits.

## Abstract

Sheep breeding plays a key role in agriculture, but efficiently improving traits like reproduction and growth remains a challenge. Pishan red sheep, a unique breed known for year-round fertility, high birth rates, and strong genetic traits, offer valuable insights into these traits. This study explored the genetic basis of their superior qualities by analyzing their entire DNA. Researchers identified over 53,968,686 high-quality SNPs and discovered 90 key genes linked to growth, reproduction, and disease resistance. Notably, genes such as BMPRIB and HPGDS were found to influence litter size through specific biological pathways. Additionally, 59 genetic markers tied to growth (e.g., body size) and reproduction (e.g., fertility) were pinpointed. These findings help to explain why Pishan red sheep excel in these traits and provide practical tools for farmers and breeders to select animals with desirable characteristics more accurately. By applying this knowledge, breeding programs can develop healthier, more productive sheep, boosting agricultural efficiency and supporting sustainable farming practices.

Sheep have evolved remarkable phenotypic diversity through artificial and natural selection, with reproductive traits being pivotal for breeding economics. As a unique genetic resource, Pishan red sheep exhibit exceptional advantages, including perennial estrus, high fecundity, and stable hereditary characteristics, establishing them as an optimal model for investigating reproductive genetics. In this study, we performed whole-genome resequencing of Pishan red sheep, generating 9084.81 Gb of raw data and identifying 53,968,686 high-quality single-nucleotide polymorphisms (SNPs). Through selective sweep analysis, 92 genomic regions under selection were detected, containing 90 positional candidate genes significantly associated with growth, reproduction, and immune functions. Notably, we revealed BMPRIB, UNC5C, PDLIM5, GRID2, and HPGDS as core positional candidate genes influencing litter size, operating through the TGF-beta and Thyroid hormone signaling pathways. A genome-wide association study (GWAS) further identified 59 trait-related SNPs, including 39 loci linked to growth traits (affecting positional candidate genes such as PROM1, TAPT1, LDB2, and KIF16B) and 20 loci of positional candidate genes associated with reproductive traits (involving ASPA, RAP1GAP2, PHIP, and WDR82).These findings not only elucidate the molecular basis of superior reproductive performance in Pishan red sheep, but also provide functional markers for precision breeding.