The breeding of high-quality beef cattle breeds is crucial for the development of animal husbandry, and whole-genome resequencing is widely applicated in the field of molecular breeding. Advantages in growth and reproductive traits exist in Pinan cattle compared with other cattle breeds, but there is limited research on its genomic mechanism. Using whole-genome resequencing, the genetic structure and genomic selection signatures in Pinan cattle were investigated in this study. Phylogenetic, cluster, and admixture analysis results indicated that Pinan cattle have a closer genetic relationship with Kholmogory cattle and China north cattle breeds. Through a selective sweep strategy, 207 and 54 candidate genes related to growth and reproduction and immunity, respectively, were identified in the Pinan cattle population. Given the crucial role of the glutamate–cysteine ligase catalytic (GCLC) gene in muscle antioxidative defense, the high frequency of allele T of the GCLC c.429 C>T locus in the Pinan cattle population might partially contribute to the advantages of Pinan cattle in growth performance. This study laid the foundation for the genetic improvement in Chinese local beef cattle and provide background for the studies on the growth and development of Pinan cattle.

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.