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Chinese Livestock and Poultry Breeding ›› 2026, Vol. 22 ›› Issue (6): 72-80.doi: 10.19543/j.cnki.1673-4556.20260602.007cstr: 32418.14.j.cnki.1673-4556.20260602.007

• Germplasm Utilization • Previous Articles     Next Articles

Population genetic structure analysis and molecular mating of Jinnan cattle based on genome-wide SNP loci

Duanyang Ren(), Wenxia Li, Xinpei Wang, Xi Wang()   

  1. Institute of Ecological Agriculture and Animal Husbandry, Shanxi Agricultural University, Shuozhou, 036002, Shanxi
  • Received:2026-02-26 Online:2026-06-26 Published:2026-07-06
  • Contact: Xi Wang E-mail:ren457842071@163.com;wxphilip@aliyun.com

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Abstract:

Objective This study aims to analyze the genetic diversity and population genetic structure of the conservation population of Jinnan cattle, evaluate genomic relationships among individuals, and conduct molecular mating, thereby better protecting and utilizing the genetic resources of Jinnan cattle. Method A total of 161 Jinnan cattle (46 bulls and 115 cows) were genotyped using the bovine 20 K single nucleotide polymorphism (SNP) chip. After quality control, the genotypic data were used to analyze genetic diversity, population genetic structure, and calculate genomic relationships. Genetic contributions of bulls were optimized to minimize inbreeding coefficients in the next generation while maintaining population genetic diversity. Result The results showed that after quality control, 17070 SNP loci were retained. The average observed heterozygosity of the individuals was 0.387, the average expected heterozygosity was 0.386, and the mean SNP polymorphism information content was 0.305. A total of 1,907 runs of homozygosity (ROH) were detected, with an average length of 7.754 Mb and an average of 12.973 ROH segments per individual. The average inbreeding coefficient based on ROH was 0.060. According to the family evolutionary tree, this Jinnan cattle population can be clearly divided into more than 8 families. The genetic diversity of this population is 0.888. Based on the relationship matrix constructed by whole-genome SNP loci, the genetic relationship between individuals ranges from -0.107 to 0.521.When SNPs were divided into haplotype blocks to build the relationship matrix, pairwise relationships ranged from 0 to 0.269 with a mean of 0.112. By optimizing bull genetic contributions to minimize next-generation inbreeding, the top 10 bulls accounted for 57.639% of the total genetic contribution. Conclusion In summary, the conservation population of Jinnan cattle has abundant genetic diversity and low inbreeding level. The kinship estimated based on haplotypes can provide a theoretical basis for scientific mating and conservation utilization of Jinnan cattle.

Key words: Jinnan cattle, Whole genome SNP chip, Genetic diversity, Population genetic structure, Molecular mating

CLC Number: 

  • S823

Fig. 1

Distribution of SNPs on each chromosome after quality control"

Fig. 2

Analysis of population genetic diversity"

Fig. 3

Analysis of locus heterozygosity and individual heterozygosity"

Fig. 4

Principal component analysis of the Jinnan cattle population"

Fig. 5

Heatmap of IBS genetic distance for Jinnan cattle population"

Fig. 6

Family tree of Jinnan cattle population"

Fig. 7

Heatmap of the whole-genome SNP-based relationship matrix of Jinnan cattle"

Fig. 8

Molecular mating analysis of Jinnan cattle based on haplotypes"

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