A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

Abstract

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.

Genome-wide associations and detection of potential candidate genes for direct genetic and maternal genetic effects influencing dairy cattle body weight at different ages

“…The four significant SNPs, i.e. ARS - BFGL - NGS - 39379 for BW0 and BW1314, ARS - BFGL - NGS - 5139 for BW0, ARS - BFGL - NGS - 107035 for BW0, and ARS - BFGL - NGS - 109317 for BW0, had a significant impact on BW [49], live weight [50], carcass retail beef yield [43], and hot carcass weight [51] in beef and crossbred beef cattle.…”

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

“…Ideally, we could exploit within breed variation to produce pure Bos taurus individuals suited to the full range of environments in the US without sacrificing performance for growth, maternal, or carcass traits. Previous work has identified the presence of extensive GxE in beef cattle populations [78][79][80] , but limited work exploring the genomic basis of local adaptation has occurred 81 .…”

Recent land use and management changes decouple the adaptation of livestock diversity to the environment

“…Regarding contemporary distributions, stronger positive coefficients are found for the environmental factors, except for precipitation seasonality, in bovine and ovine, but not in caprine species distribution ( Fig. 2 [20][21][22][23][24][25][26][27][28][29][30][31][32][33][34] ). On the contrary, the associations of the distributions of porcine and equine breed richness with environmental factors remain invariant regardless whether past or present distributions are considered.…”

“…For example, although breeds being highly locally adapted is claimed as a chief reason for their worth, especially in the context of climate change 19 , there are still gaps in our knowledge about the mechanisms involved in breeds adaptations 3 , 20 . However some efforts have been done in that direction in recent decades 21 – 23 . Besides, even when in situ is supposedly the preferred conservation option 24 , most research focuses on breed genetics and animal production.…”