Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Abstract

Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (F_ST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.

Keywords: Abigar cattle; adaptation; selection signature; thermotolerance; tropical environment.

Figure 1

Genetic diversity and population structure of the five studied breeds (ABI = Abigar, ANK = Ankole, BAR = Barca, HOL = Holstein, NDA = N’Dama). (a) Principal component plots for the first two PCAs, (b) Neighbor–joining tree of the relationships between the five cattle breeds (50 animals), (c) Admixture analysis results for five cattle breeds at K = 2 to 4.

Figure 2

Summary statistics for patterns of genomic variation. (a) Average genome-wide nucleotide diversity (100 kb window with 50 kb step size); (b) The length of the ROHs in the five studied breeds; (c) The distribution of the total number of ROHs in each breed. The median value of this diversity is indicated by a horizontal line within the box, while the box itself represents the first and third quartiles of the distribution. Data points that fall outside the whiskers are considered outliers. (d) The genome-wide linkage disequilibrium (LD) decay for each breed; (e) The observed (O(HET)) and Expected (E(HET)) heterozygosity of each breed.

Figure 3

Analysis of selective sweeps in Abigar cattle (a) Manhattan plots F_ST selection scan; (b) Manhattan plots Pi selection scan; The horizontal dash lines represent the 0.5% outlier regions in both of the selection scan methods; (c) Venn diagrams of genes shared by Pi and F_ST selection scan methods.

Figure 4

Nucleotide diversity and population differentiation (F_ST, Abigar, and Holstein cattle breeds) plot of DNAJC18 gene.