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Genome-wide scan for loci under recent selection in indicine and taurine beef breeds using a composite measure

Grant number: 18/11460-6
Support type:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): September 01, 2018
Effective date (End): August 31, 2019
Field of knowledge:Agronomical Sciences - Animal Husbandry
Principal Investigator:Humberto Tonhati
Grantee:Diercles Francisco Cardoso
Supervisor abroad: Antonio Reverter-Gomez
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Local de pesquisa : Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia  
Associated to the scholarship:16/22490-8 - Mapping signatures of selection in the genome of main domestic species of the Bovini tribe used as food sources in the livestock, cattle (Bos taurus) and water buffaloes (Bubalus bubalis), BP.PD

Abstract

Approaches combining different univariate statistics into a unique composite metric are suggested improving the power to discern true selection signatures in population genomic data. Here we proposed the genome-wide scan for selection signatures in Nelore and Angus breeds, applying the 'de-correlated composite of multiple signals' method (DCMS), which gather a total of eight distinct statistics into a single composite metric, weighed by the correlation between the pairs of them. The distinct methods compounding DCMS includes: five within-population approaches (Tajima's D, Fu and Li's D*, Fu and Li's F*, Composite Likelihood Ratio - "CLR" and the integrated Haplotype Score - "iHS") and three cross-population approaches (Wright's fixation index - "FST", Cross-Population Composite Likelihood Ratio - "XPCLR" and the Cross-Population Extended Haplotype Homozygosity - "XPEHH"). The population researched in the current study will be composed of around 700 animals from each breed, with genotypic information to around 150K SNPs. After identification of putative selection signatures in each breed they will be narrowly analyzed as to overlapping with known QTL and functionality of genes mapped in there.