Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species

Autor(es)

de Abreu Santos, Daniel Jordan ^{[1, 2]} ; Ferreira de Camargo, Gregorio Miguel ^[2] ; Cardoso, Diercles Francisco ^[2] ; Buzanskas, Marcos Eli ^[3] ; Aspilcueta-Borquis, Rusbel Raul ^[2] ; Hurtado-Lugo, Naudin Alejandro ^[2] ; de Araujo Neto, Francisco Ribeiro ^{[2, 4]} ; de Albuquerque, Lucia Galvao ^[2] ; Ma, Li ^[1] ; Tonhati, Humberto ^[2]

Afiliação do(s) autor(es)

^[1] Univ Estadual Paulista, UNESP, Dept Ciencias Exatas, Sao Paulo - Brazil

^[2] Dept Zootecnia, Jaboticabal, SP - Brazil

^[3] Univ Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 - USA

^[4] Inst Fed Goiano, Campus Rio Verde, Rio Verde, GO - Brazil

• Tipo de documento: Artigo Científico
• Fonte: G3-GENES, GENOMES, GENETICS; v. 10, n. 7, p. 2327-2343, JUL 2020.
• Citações Web of Science: 0

Resumo

The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome ofBos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as {[}(shorter BTA length - SNP position in shorter BTA)] and larger BTA length as {[}shorter BTA length + (larger BTA length - SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes. (AU)

• Processo FAPESP: 10/20887-1 - Aplicação de informações genômicas no melhoramento genético de bubalinos leiteiros
• Beneficiário: Humberto Tonhati
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 17/00462-5 - Homologia genômica entre bovinos e búfalos e comparação de diferentes algoritmos de máquinas de aprendizagem para a imputação de genótipos no genoma bubalino
• Beneficiário: Daniel Jordan de Abreu Santos
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 15/12396-1 - Imputação de genótipos de marcadores no genoma bubalino e seu impacto nas avaliações genômicas da produção de leite e seus constituintes
• Beneficiário: Daniel Jordan de Abreu Santos
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado