Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

Autor(es)

Peripolli, Elisa ^[1] ; Reimer, Christian ^{[2, 3]} ; Ha, Ngoc-Thuy ; Geibel, Johannes ^{[4, 5]} ; Machado, Marco Antonio ^{[6, 7]} ; do Carmo Panetto, Joao Claudio ^[6] ; do Egito, Andrea Alves ^[8] ; Baldi, Fernando ^[1] ; Simianer, Henner ^{[4, 5]} ; Gualberto Barbosa da Silva, Marcos Vinicius ^{[6, 7]}

Afiliação do(s) autor(es)

^[1] Sao Paulo State Univ Unesp, Sch Agr & Vet Sci, BR-14884900 Jaboticabal - Brazil

^[2] Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Albrecht Thaer Weg 3, D-37075 Gottingen - Germany

^[3] Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen - Germany

^[4] Ngoc-Thuy Ha, Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Albrecht Thaer Weg 3, D-37075 Gottingen - Germany

^[5] Ngoc-Thuy Ha, Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen - Germany

^[6] Embrapa Dairy Cattle, BR-36038330 Juiz De Fora - Brazil

^[7] Natl Council Sci & Technol Dev CNPq, BR-71605001 Lago Sul - Brazil

^[8] Embrapa Beef Cattle, BR-79106550 Campo Grande, MS - Brazil

• Tipo de documento: Artigo Científico
• Fonte: BMC Genomics; v. 21, n. 1 SEP 11 2020.
• Citações Web of Science: 1

Resumo

BackgroundThe cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.ResultsA total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds.ConclusionThe current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions. (AU)

• Processo FAPESP: 17/27148-9 - Sequenciamento amplo do genoma de raças zebuínas e brasileiras localmente adaptadas para a identificação de assinaturas de seleção
• Beneficiário: Elisa Peripolli
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Doutorado