1. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups
- Author
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Jaime Araujo Cobuci, Robson Jose Cesconeto, Stéphane Joost, José Braccini, Samuel Rezende Paiva, Concepta McManus, ROBSON JOSE CESCONETO, UFRGS, STÉPHANE JOOST, ECOLE POLYTECHNIQUE FÉDÉRALE DE LAUSANNE (EPFL), SWITZERLAND, CONCEPTA MARGARET MCMANUS, UNB, SAMUEL REZENDE PAIVA, Cenargen, JAIME ARAUJO COBUCI, UFRGS, and JOSE BRACCINI, UFRGS.
- Subjects
0301 basic medicine ,Conservation genetics ,Germplasm ,molecular markers ,Range (biology) ,Sus scrofa ,Biology ,Population structure ,03 medical and health sciences ,Gene bank ,Animal genetic resources ,Genotype ,Allele ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,Nature and Landscape Conservation ,Original Research ,Genetics ,Ecology ,population structure ,animal genetic resources ,Breed ,030104 developmental biology ,conservation genetics ,Molecular markers - Abstract
Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011–0.134). The frequency of these markers indicated a clear north–south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.
- Published
- 2017