Departamento de Zootecnia, Jaboticabal-SP,
Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, Maryland, and.
G3 (Bethesda). 2020 Jul 7;10(7):2327-2343. doi: 10.1534/g3.120.401090.
The aim of this study was to analyze the genomic homology between cattle () and buffaloes () 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 of ) 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.
本研究旨在分析牛（）和水牛（）的基因组同源性，并通过连锁不平衡分析水牛 SNP 标记与牛基因组组装参考序列，提出水牛基因组重排方案，并与水牛基因组组装序列进行比较。使用牛 SNP （单核苷酸多态性）标记进行了层次聚类、非层次聚类和混合聚类分析。因此，利用特定水牛 SNP 标记面板的连锁不平衡信息推断染色体重排。还分析了亚中着丝粒染色体的单倍型多样性和基因分型准确性。物种间的基因组同源性使我们能够利用牛基因组组装来重排亚中着丝粒染色体，从而重建水牛基因组参考序列。亚中着丝粒染色体的着丝粒区域具有高度连锁不平衡和低单倍型多样性，这使得我们可以对染色体进化进行假设。这表明水牛的亚中着丝粒染色体是由祖先的近端着丝粒染色体融合形成的。融合的时间顺序也被推测出来。此外，水牛和牛重排组装之间的线性回归和基因分型准确性表明，染色体的重排是充分的。当使用牛参考基因组组装时，通过 SNP BTA（牛染色体）计算可以对水牛的亚中着丝粒染色体进行重排：较短的 BTA（水牛染色体的短臂）被表示为[(较短 BTA 长度 - SNP 在较短 BTA 中的位置)]，而较大的 BTA 长度则表示为[较短 BTA 长度 + (较大 BTA 长度 - SNP 在较大 BTA 中的位置)]。最后，所提出的基于连锁不平衡的方法可以应用于阐明其他物种的其他染色体重排事件，从而更好地理解它们的基因组之间的进化关系。
