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

item Blackburn, Harvey
item Krehbiel, Bethany
item ERICSSON, SCOTT - Sul Ross State University
item Wilson, Carrie - Welsh
item CAETANO, ALEX - Embrapa
item PAIVA, SAMUEL - Embrapa

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2017
Publication Date: 5/1/2017
Citation: Blackburn, H.D., Krehbiel, B.C., Ericsson, S.A., Wilson, C.S., Caetano, A., Paiva, S.R. 2017. A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford). PLoS One. 12(5): e0176474.

Interpretive Summary: The ability for beef cattle to adapt to environmental stresses, such as heat, could become more important as climates change. This experiment evaluated the genetic diversity of 225 nationally sampled Hereford cattle from different ecoregions using molecular markers. The U. S. was partitioned into five ecoregions for this study: warm arid (WA), warm humid (WH), transition zone (TZ), cool arid (CA) and cool humid (CH). Molecular markers included those associated with production traits and an animal's ability to respond to environmental stresses (i.e., hot temperatures). The results showed how genetic frequencies changed among the ecoregions; suggesting that cattle may have responded to natural selection pressures caused by the environment they were raised. Importantly the results suggest that sufficient genetic variability within the Hereford breed exists and can be used to adapt the breed to varying climate change conditions.

Technical 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 partitioned into five subpopulations born in different 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). Coefficients of genetic relationship were computed and used to delete animals from the analysis which had large genetic ties across ecoregions. This reduced the data set from 577 animals to 225 animals for the study that were genotyped with 50K SNP BeadChip or 770K SNP bovine BeadChip. SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 SNPs thought to be associated with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis allele frequencies for a subset of the 66 SNPs (n = 15) not in HWE or under selection among the five ecoregions were compared. The three analyses (using 14,312, 66 and 15 SNPs) 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 among 15 SNPs not in HWE showed ecoregion differences, in particular the divergence between WA and WH. Summation of these results suggest the presence of genetic variability that can be used to acclimatize a temperately derived breed to various ecoregions and as climate change becomes an important factor in cattle production.