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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)

Grant number: 16/22490-8
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): January 01, 2017
Effective date (End): January 24, 2020
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal researcher:Humberto Tonhati
Grantee:Diercles Francisco Cardoso
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Associated scholarship(s):18/11460-6 - Genome-wide scan for loci under recent selection in indicine and taurine beef breeds using a composite measure., BE.EP.PD

Abstract

Positive selection increases the frequency of favorable alleles, causing special genomic patterns in the vicinity of these alleles that are named signatures of selection. Domestication, breed formation and selection schemes causes positive selection and promotes genomic signatures of selections. The identification of signatures of selection is currently a huge interest of population genetics, because it may help deciphering the genetic bases of phenotypic diversity in species/breeds and provide functional information about genomic regions and genes. The current project come up with two parallel studies, both intending to scan for selection signatures, being one of them with beef cattle breeds and a second one with dairy buffaloes. Briefly, the aim of this project are: (1) to study signature of selection in the Nellore breed, with a bigger population than used in previous studies; (2) to compare de linkage disequilibrium patterns between Angus and Nellore breeds; (3) to apply a composite method to detect section signatures in Angus and Nellore breeds; (4) to analyze the genomic individual inbreeding levels in a dairy buffaloes population; and (5) to perfume the first study about signature of selection in buffaloes. In order to achieve that, it will be used around 4000 Nellore animals genotyped with the BovineHD - 700K array (Illumina); 700 Angus animals genotyped with the GGP-HD - 150K array (Neogen) and 384 buffaloes genotyped with the Axion Buffalo - 90K array (Affymetrix). The iHS statistic (integrated Haplotype Score) will be used to scan signature of selection in Nellore (1) and water buffaloes (5). The comparisons of linkage disequilibrium between Angus and Nellore (2) will be done through analyses of linkage disequilibrium decay and linkage phase on the two populations, and with regional comparisons of linkage patterns. The composite method to identification of selection signature applied on Angus and Nellore population (3) will be the DCMS (de-correlated composite of multiple signals), which match within and between populations tests. The genomic inbreeding and scan for regions of low genetic diversity in buffaloes (4) will be done with ROH statistic. (AU)

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
NASCIMENTO, V, A.; CARDOSO, D. F.; SANTOS, D. J. A.; ROMERO, A. R. S.; SCALEZ, D. C. B.; BORQUIS, R. R. A.; NETO, F. R. A.; GONDRO, C.; TONHATI, H. Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo. JOURNAL OF DAIRY SCIENCE, v. 104, n. 2, p. 1917-1927, FEB 2021. Web of Science Citations: 1.
CARDOSO, DIERCLES FRANCISCO; FERNANDES JUNIOR, GERARDO ALVES; BECKER SCALEZ, DAIANE CRISTINA; CARVALHO ALVES, ANDERSON ANTONIO; BRAGA MAGALHAES, ANA FABRICIA; BRESOLIN, TIAGO; VENTURA, RICARDO VIEIRA; LI, CHANGXI; DE SENA OLIVEIRA, MARCIA CRISTINA; PORTO-NETO, LAERCIO RIBEIRO; CARVALHEIRO, ROBERTO; DE OLIVEIRA, HENRIQUE NUNES; TONHATI, HUMBERTO; ALBUQUERQUE, LUCIA GALVAO. Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle. SCIENTIFIC REPORTS, v. 10, n. 1 MAY 29 2020. Web of Science Citations: 2.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.