We performed Bayesian clustering analysis using STRUCTURE software with genotype data on 33,063 commercial single nucleotide polymorphism (SNP) markers in 4,348 Japanese Black fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. When the number of the assumed clusters in STRUCTURE was 2, the steers from Hyogo prefecture were clearly separated from the others. This indicates the usefulness of the STRUCTURE analysis with commercial SNP markers for the clarifications of the difference of the genetic constitutions of each prefecture. Next, genomic predictions for carcass traits were conducted using a statistical model including the proportions of the clusters as partial linear regressions. Genomic breeding values predicted by the model without the STRUCTURE covariates were likely to be divided into the part of explaining the STRUCTURE analysis and the remaining part. This result shows the possibility that the accuracy of genomic prediction depends on the degree of information of the genomic population structure.

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The six Bubalus species include the two species of anoa, the tamaraw, the Asian wild water buffaloes, and the domesticated riverine and swamp buffaloes. However, the phylogenetic relationships and taxonomic positions of the Bubalus species have few published data and are still unresolved. Thus, this paper aimed to elucidate the relationship among these species of the genus Bubalus using the variation of the control region of mtDNA D-loop. This study generated D-loop sequences from 17 riverine buffaloes from India and Brazil that Philippine government imported. The analysis also included 836 D-loop sequences of Bubalus species from the Asia region that were retrieved from NCBI Genbank. Results revealed the highest genetic distance between tamaraw and lowland anoa, while the lowest was between the tamaraw and swamp buffalo, which confirmed their taxonomic assignment to belong to the same genus but different species. Moreover, a total of 853 sequences of 368 nucleotide sites from Bubalus species included 61 haplotypes with 214 nucleotide sites. The branch supported two major groups, the first group from the sub-species of anoa and the second group from tamaraw and domesticated water buffaloes. The genetic distance, phylogenetic, and Median-Joining structure analyses highlighted that domesticated riverine and swamp buffaloes have distinct maternal ancestry and showed the tamaraw's close affinity to the swamp lineage B. In addition, these results showed the shared common ancestry between the tamaraw and swamp buffaloes, suggesting that the evolution of tamaraw occurred prior to the domestication of swamp buffaloes.

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