Author:
Zhang Shunjin,Yao Zhi,Li Xinmiao,Zhang Zijing,Liu Xian,Yang Peng,Chen Ningbo,Xia Xiaoting,Lyu Shijie,Shi Qiaoting,Wang Eryao,Ru Baorui,Jiang Yu,Lei Chuzhao,Chen Hong,Huang Yongzhen
Abstract
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.
Funder
China Agriculture Research System of MOF and MARA
Henan Beef Cattle Industrial Technology System
Science-Technology Foundation for innovation and creativity of Henan Academy of Agricultural Sciences
Publisher
Springer Science and Business Media LLC
Reference88 articles.
1. Decker JE, McKay SD, Rolf MM, Kim J, Molina Alcalá A, Sonstegard TS, Hanotte O, Götherström A, Seabury CM, Praharani L. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 2014;10(3):e1004254.
2. Chen N, Cai Y, Chen Q, Li R, Wang K, Huang Y, Hu S, Huang S, Zhang H, Zheng Z. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun. 2018;9(1):1–13.
3. Bai Y, Sartor M, Cavalcoli J. Current status and future perspectives for sequencing livestock genomes. J Anim Sci Biotechnol. 2012;3(1):1–6.
4. Georges M, Charlier C, Hayes B. Harnessing genomic information for livestock improvement. Nat Rev Genet. 2019;20(3):135–56.
5. Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front Genet. 2015;6:167.