ABSTRACT
BACKGROUND: Swamp-type buffaloes with varying degrees of white spotting are found exclusively in Tana Toraja, South Sulawesi, Indonesia, where spotted buffalo bulls are highly valued in accordance with the Torajan customs. The white spotting depigmentation is caused by the absence of melanocytes. However, the genetic variants that cause this phenotype have not been fully characterized. The objective of this study was to identify the genomic regions and variants responsible for this unique coat-color pattern. RESULTS: Genome-wide association study (GWAS) and selection signature analysis identified MITF as a key gene based on the whole-genome sequencing data of 28 solid and 39 spotted buffaloes, while KIT was also found to be involved in the development of this phenotype by a candidate gene approach. Alternative candidate mutations included, in addition to the previously reported nonsense mutation c.649 C > T (p.Arg217*) and splice donor mutation c.1179 + 2T > A in MITF, a nonsense mutation c.2028T > A (p.Tyr676*) in KIT. All these three mutations were located in the genomic regions that were highly conserved exclusively in Indonesian swamp buffaloes and they accounted largely (95%) for the manifestation of white spotting. Last but not the least, ADAMTS20 and TWIST2 may also contribute to the diversification of this coat-color pattern. CONCLUSIONS: The alternative mutations identified in this study affect, at least partially and independently, the development of melanocytes. The presence and persistence of such mutations may be explained by significant financial and social value of spotted buffaloes used in historical Rambu Solo ceremony in Tana Toraja, Indonesia. Several de novo spontaneous mutations have therefore been favored by traditional breeding for the spotted buffaloes.
Subject(s)
Buffaloes , Genome-Wide Association Study , Microphthalmia-Associated Transcription Factor , Proto-Oncogene Proteins c-kit , Animals , Buffaloes/genetics , Microphthalmia-Associated Transcription Factor/genetics , Proto-Oncogene Proteins c-kit/genetics , Genomics/methods , Mutation , Phenotype , Indonesia , Polymorphism, Single Nucleotide , Pigmentation/genetics , Whole Genome SequencingABSTRACT
Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.
ABSTRACT
The objective of this research was to find the basic data on genetic diversity of mtDNA D-Loop in Aceh cattle and its association with Bhutanese, Chinese, and Indian cattle. There were sixty samples of DNA which had been sequenced; i.e. Banda Aceh (11), Saree (20), and Indrapuri (29). To the best of our knowledge this is the first published data on the complete mitochondrial D-Loop sequence of Aceh cattle. Results show that Aceh cattle have the closest relationship to Bos indicus and have been influenced by Bos taurus. The closest genetic ranges among Aceh cattle, Bhutanese, Chinese, Indian and Zebu were Aceh-Zebu (0.0138), Aceh-Bhutanese (0.0156), Aceh-Chinese (0.0190) and Aceh-Indian (0.0193). D-Loop mtDNA analyses showed that there were 27 haplotypes in which twenty-one samples spread in haplotype 1, two samples were in haplotype 2, and the other four haplotypes had various samples in the range of three to seventeen samples. One sample of Aceh cattle from Saree has a closest maternal genetic with B. taurus. One of the four mutations among the star-shaped clusters on median joining network was a new specific haploid-group in Aceh cattle. From this finding it could be assumed that Aceh cattle form a specific haplotype and it can be conclude that Aceh cattle are animal genetic resources from Aceh in Sumatera Island that have to be preserved.
