BMC Genomics (Jun 2022)

Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data

  • Shunjin Zhang,
  • Zhi Yao,
  • Xinmiao Li,
  • Zijing Zhang,
  • Xian Liu,
  • Peng Yang,
  • Ningbo Chen,
  • Xiaoting Xia,
  • Shijie Lyu,
  • Qiaoting Shi,
  • Eryao Wang,
  • Baorui Ru,
  • Yu Jiang,
  • Chuzhao Lei,
  • Hong Chen,
  • Yongzhen Huang

DOI
https://doi.org/10.1186/s12864-022-08645-y
Journal volume & issue
Vol. 23, no. 1
pp. 1 – 10

Abstract

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Abstract Background Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide. Results Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). Conclusion In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.

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