Identification of a Genome-Wide Significant SNP on Chromosome 5 Associated with Adult Body Weight in Nanyang Cattle via Whole-Genome Resequencing and GWAS

DOI: https://doi.org/10.62517/jbdc.202601301

Author(s)

Pengpeng Zhang1, Mengru Sheng1, Xun Zhou1, Dongtak Jeong2,*

Affiliation(s)

1College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China 2Department of Medicinal & Life Science, College of Science and Convergence Technology, Hanyang University—ERICA, Ansan, Republic of Korea *Corresponding Author

Abstract

Adult body weight is an economically decisive trait in beef cattle production, directly governing carcass yield and the overall profitability of the production chain. Chinese indigenous cattle breeds, although well adapted to local environments, are characterized by relatively small body frames and consequently lower meat yields, which has contributed to a persistent national shortfall in beef supply. Marker-assisted selection offers a route to accelerate the genetic improvement of body weight in these populations, but its application depends on the discovery of reliable, breed-appropriate molecular markers. In this study, we performed whole-genome resequencing on a population of 285 healthy Nanyang cattle, generating approximately 30 Gb for each cattle. Then a genome-wide association study was conducted using a mixed linear model to dissect the genetic basis of adult body weight. After stringent quality control of sequencing reads, alignment to the ARS-UCD1.2 reference assembly, and variant filtering, association analysis identified a single nucleotide polymorphism located on chromosome 5 (Chr5:108852977) that reached the genome-wide significance threshold (P = 4.67 × 10⁻⁸). This locus carries a T/C allelic substitution with an estimated additive effect of 9.23 ± 1.36, with the T allele associated with significantly heavier adult body weight. A 189-bp genomic fragment flanking the variant (with the SNP at position 137) was characterized, a dedicated PCR primer pair was designed, and the genotype was validated by Sanger sequencing. The identified marker provides a novel, breed-specific molecular tool for the early selection of superior heavy-weight Nanyang cattle and offers a simple, rapid, and specific alternative to conventional genotyping approaches such as PCR-RFLP.

Keywords

Nanyang Cattle; Adult Body Weight; Genome-Wide Association Study; Single Nucleotide Polymorphism; Whole-Genome Resequencing

References

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