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

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, F_ST, 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.

Keywords: DCMS; Genetic diversity; Pinan cattle; Population Structure; WGS.

Fig. 1

Population structure of Pinan cattle and its relationship with several breeds in the world. (A) ADMIXTURE was used with K = 2 and K = 4 for model-based clustering among different cattle. Color them by geographical area and label them with the breed. Neighbor-joining trees (B) and principal component analysis (C) separated the cattle breeds (199 animals in total) into seven categories

Fig. 2

A The nucleotide diversity of 12 different cattle breeds. The black line in the boxplot is the median line and the outside points are outliers. B Genome-wide average LD decay is estimated from each breed. Different colored lines represent different breeds. The legend in the middle is shared by both figures

Fig. 3

Manhattan plot of the selective signals detected by the DCMS method in the Pinan cattle. The dashed lines indicade the significant threshold level at a FDR of 5% (q-value < 0.05)