Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Abstract

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

Investigating the Short-Term Effects of Cold Stress on Metabolite Responses and Metabolic Pathways in Inner-Mongolia Sanhe Cattle

“…Inner-Mongolia Sanhe is a dual-purpose cattle breed in China that has been an important genetic resource for studying the effects of cold stress response on blood biochemical parameters [ 31 ], gene expression profile in the peripheral blood [ 9 ], characterization of genetic variation related to cold tolerance [ 14 ], and signatures of selection related to thermal tolerance [ 32 ]. However, serum metabolome and metabolic regulation in response to severe cold exposure had not been studied in this population.…”

Breeding Strategies for Weather Resilience in Small Ruminants in Atlantic and Mediterranean Climates

“…In addition to other phenotypes that provide a comprehensive approach to select for resilience to thermal stress, other approaches have been also used to understand the biological mechanisms underpinning climatic adaptation and to identify potential genes of interest. A recent study from Freitas et al (2021) identified signatures of selection for thermal stress in cattle, using climatic divergent breeds and providing several potential candidate genes related to heat stress. Similarly, metabolomics can also provide potential biomarkers of resilience to particular conditions such as heat stress (Tian et al, 2016;Contreras-Jodar et al, 2019).…”

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

“…Pairwise comparison of genetic differentiation of sheep breeds adapted to different environments identified selection signatures in the genes MITF, FGF5, MTOR, TRHDE and TUBB3 that have been associated with high-altitude adaptation [156]. An F ST statistic approach applied to cattle breeds reared in different environments identified several genes under positive selection for thermal tolerance [157]. HapFLK detected the Nebulin Related Anchoring Protein gene (NRAP) to be under selection for adaptation to cold environments [158], ACSS2, ALDOC, EPAS1, EGLN1 and NUCB2 to be under selection for high-altitude adaptation in cattle [159], and DNAJC28, GNRH1 and MREG to be associated with heat stress adaptation in sheep [160].…”

“…Cross-population EHH-based tests have been used to detect hot climate adaptation in cattle [166][167][168] and sheep [169][170][171], and hypoxia adaptation in new world camelids [172]. Detecting runs of homozygosity (ROHs) to find regions containing genes associated with adaptation has been demonstrated in several domestic species [157,162,163,173,174]. Selection on a locus, whether artificial for production or natural for adaptation, is associated with the reduction of genetic diversity in the region, creating a "selection signature".…”