Global Whole-Genome Resequencing of Beef Cattle Reveals Characteristic Traits Related Genes in Pinan Cattle

TL;DR

This study uses whole-genome resequencing to uncover genetic factors behind the superior traits of Pinan cattle, such as rapid growth and early sexual maturity.

Contribution

The study identifies 98 candidate genes and 13 high-confidence missense mutations linked to key traits in Pinan cattle through selective sweep analysis.

Findings

Selective sweep analysis identified 98 candidate genes related to growth, reproduction, and immunity in Pinan cattle.

Thirteen high-confidence missense mutations were found to potentially underlie key economic traits in the population.

The T alleles at NDN c.581T > A and PARVA c.893T > A loci may explain the sexual precocity and rapid growth of Pinan cattle.

Abstract

Whole-genome resequencing has been increasingly applied to beef cattle genetic breeding. As a superior indigenous breed in Henan Province, Pinan cattle exhibit rapid growth, early sexual maturity, and high dressing percentage, making them an important component of Chinese local beef cattle genetic resources. However, their genomic variation remains poorly characterized. Here, we performed whole-genome resequencing on Pinan cattle to assess genetic diversity and conducted selective sweep analysis to identify candidate genes and loci linked to key economic traits. This study provides insights into the molecular basis of Pinan cattle’s superior traits and supports marker-assisted breeding for growth and reproductive performance.

Beef cattle breed improvement holds strategic significance in the livestock industry. Pinan cattle, developed through years of selective breeding in Xinye County, Henan Province, exhibit superior traits including thin skin, fine bone structure, rapid growth, high dressing percentage, excellent meat yield, and superior feed efficiency. However, research on the genetic characteristics of Pinan cattle remains in its infancy. In this study, we investigated population genetic diversity and positive selection signals in Pinang cattle based on whole-genome resequencing data. Using a selective sweep approach, we identified 98 candidate genes associated with growth, reproduction, and immunity, along with 13 high-confidence missense mutations, which may underlie key traits in this population. Based on the critical roles of the NDN and PARVA genes in reproduction and muscle development, the predominant T allele at the NDN c.581T > A and PARVA c.893T > A loci in the Pinan cattle population may partially explain their advantages in sexual precocity and rapid growth compared to other breeds or populations. This study provides an important theoretical basis for the genetic improvement of native beef cattle and lays a scientific foundation for further investigation into the growth and development mechanisms of Pinan cattle.

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