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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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]
Total Authors: 10
Affiliation:
[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
Total Affiliations: 4
Document type: Journal article
Source: G3-GENES, GENOMES, GENETICS; v. 10, n. 7, p. 2327-2343, JUL 2020.
Web of Science Citations: 0
Abstract

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)

FAPESP's process: 10/20887-1 - Application of genomic information for the genetic improvement of dairy buffalo
Grantee:Humberto Tonhati
Support Opportunities: Regular Research Grants
FAPESP's process: 17/00462-5 - Genomic homology between cattle and buffaloes and comparison of different machine learning methods for genotype imputation in buffalo genome
Grantee:Daniel Jordan de Abreu Santos
Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
FAPESP's process: 15/12396-1 - IMPUTATION OF MARKER GENOTYPES IN BUFFALO GENOME AND ITS IMPACT ON GENOMIC EVALUATION OF MILK YIELD AND CONTENT
Grantee:Daniel Jordan de Abreu Santos
Support Opportunities: Scholarships in Brazil - Post-Doctoral