Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Abstract

Dengchuan cattle are the only dairy yellow cattle and endangered cattle among Yunnan native cattle breeds. However, its genetic background remains unclear. Here, we performed whole-genome sequencing of ten Dengchuan cattle. Integrating our data with the publicly available data, Dengchuan cattle were observed to be highly interbred than other cattle in the dataset. Furthermore, the positive selective signals were mainly manifested in candidate genes and pathways related to milk production, disease resistance, growth and development, and heat tolerance. Notably, five genes (KRT39, PGR, KRT40, ESR2, and PRKACB) were significantly enriched in the estrogen signaling pathway. Moreover, the missense mutation in the PGR gene (c.190T > C, p.Ser64Pro) showed a homozygous mutation pattern with higher frequency (83.3%) in Dengchuan cattle. In addition, a large number of strong candidate regions matched genes and QTLs related to milk yield and composition. Our research provides a theoretical basis for analyzing the genetic mechanism underlying Dengchuan cattle with excellent lactation and adaptability, crude feed tolerance, good immune performance, and small body size and also laid a foundation for genetic breeding research of Dengchuan cattle in the future.

Keywords: Chinese cattle; genetic diversity; lactation function; population structure; selection signatures; whole-genome resequencing.

FIGURE 1

Population genetic analysis of Dengchuan cattle. (A) Geographic map indicating the origins of Dengchuan cattle and other cattle analyzed in this study. (B) Principal component analysis of cattle with PC1 against PC2. (C) Neighbor-joining tree of the 78 domesticated cattle. (D) Admixture plot (K = 2, 4) for the 78 cattle individuals. Each individual is shown as a vertical bar divided into K colors.

FIGURE 2

Genetic diversity among 78 samples from nine populations. (A) Estimation of the total number of ROH for each group. The three categories of ROH length: 0.5–1 Mb, 1–2 Mb, and 2–4 Mb, reflecting ancient, historical, and recent inbreeding, respectively. (B) Inbreeding coefficient for each individual. (C) Density plots and Box plots of the nucleotide diversity for each group. (D) Genome-wide average LD decay estimated from each group.

FIGURE 3

Analysis of the signatures of positive selection in the genome of Dengchuan cattle. (A) Manhattan plot of selective sweeps in Dengchuan cattle. (B) Venn diagram showing the gene overlaps among θπ, CLR, Fst, and XP-CLR. (C) Nucleotide diversity and Tajima’s D plots at the ITSN2 gene region. (D) Fst and Tajima’s D plots at the PGR gene region. (E) Regional highlight of the missense mutation of genes enriched in the estrogen signaling pathway. PGR gene showed a high-frequency homozygous mutation site (c.190T > C) in Dengchuan cattle.