Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil
| Autor: | Daniele Ribeiro de Lima Reis Faza, Marco Antonio Machado, Ricardo Zanella, Luiz Otávio Campos da Silva, M. S. M. Albuquerque, Andréa Alves do Egito, Pamela Itajara Otto, Fabyano Fonseca e Silva, João Cláudio do Carmo Panetto, L.L. Verardo, Luciana Correia de Almeida Regitano, Marcos Vinícius Gualberto Barbosa da Silva |
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| Přispěvatelé: | PAMELA ITAJARA OTTO, Universidade Federal de Santa Maria, LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE, LUIZ OTAVIO CAMPOS DA SILVA, CNPGC, ANDREA ALVES DO EGITO, CNPGC, MARIA DO SOCORRO MAUÉS ALBUQUERQUE, RICARDO ZANELLA, Universidade de Passo Fundo, MARCOS VINICIUS GUALBERTO B SILVA, CNPGL., LUCAS LIMA VERARDO, Universidade Federal dos Vales do Jequitinhonha e Mucuri, FABYANO FONSECA E SILVA, Universidade Federal de Viçosa, MARCO ANTONIO MACHADO, CNPGL, JOAO CLAUDIO DO CARMO PANETTO, CNPGL, DANIELE RIBEIRO DE LIMA REIS FAZA, CNPGL |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Linkage disequilibrium Rusticidade Genética Animal Population Runs of Homozygosity Biology QH426-470 Homozygosity Fertilidade Animal 03 medical and health sciences Effective population size Milk production Genetics milk production education Genoma Genetics (clinical) Original Research Genetic association fertility Bovino Animal fertility education.field_of_study runs of homozygosity homozygosity islands behavior 0402 animal and dairy science 04 agricultural and veterinary sciences rusticity 040201 dairy & animal science Breed Comportamento Animal Produção Leiteira 030104 developmental biology Evolutionary biology Population size Molecular Medicine Rusticity Gado Purebred Inbreeding Animal behavior effective population size linkage disequilibrium |
| Zdroj: | Frontiers in Genetics, Vol 12 (2021) Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice) Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA Frontiers in Genetics |
| ISSN: | 1664-8021 |
| DOI: | 10.3389/fgene.2021.702822/full |
| Popis: | Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle. |
| Databáze: | OpenAIRE |
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