Whole genome sequencing of zebu and Brazilian locally adapted taurine breeds for identifying selection signatures

Abstract

It is noteworthy that great efforts have been made to improve our knowledge of locally adapted breeds worldwide, and with a better understanding of the genetic difference between breed types, locally adapted breeds can be an important source of genetic information leading to the discovery and validation of genomic regions and DNA variants controlling important traits. The objective of this study is to describe the main effects of selection and adaptation in zebu and Brazilian locally adapted cattle breeds through the use of signatures of selection using Next Generation Sequencing data. Sequence data from Sindi (n=11), Caracú Caldeano (n=10), and Crioulo Lageano (n=10) breeds were available from Embrapa Dairy Cattle - Juiz de Fora. Quality control of FASTQ-files will be done using FASTQC 0.11.5. Reads will be mapped to the reference genome UMD3.1 using the BWA 7.15 software and converted into binary format using SAMtools 1.6. Sequenced animals will be used as a reference for imputation of whole sequence data from high density SNP marker panel. Data from Sindi (n=60), Caracú Caldeano (n=60), and Crioulo Lageano (n=30) breeds genotyped with the Illumina BovineHD BeadChip available from Embrapa Dairy Cattle - Juiz de Fora will be used for validation. Selection signatures will be identified by the novel statistic named De-correlated composite of multiple signals, which combines the outcomes of several complementary tests. Different elementary selection signatures statistics will be computed for each SNP position or window. A selection signature region will be assumed if at least one SNP within a 500 kb window around the selected locus exceeded the empirical significance threshold of 5% false positive rate. The Map Viewer of the bovine genome UMD3.1.1 will be used for identification of genes within significant regions. DAVID v6.8 tool will be used to identify Gene Ontology (GO) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways using the list of genes located in putatively regions and the Bos taurus annotation file as background. The results obtained in this study will allow a better characterization of zebu and Brazilian locally adapted breeds, allow using them more deeply as a genetic reservoir in germplasm bank and as a reservoir of livestock genetic diversity resource upon climate change and adaptation. (AU)