Water buffalo (Bubalus bubalis) has been associated with human since pre-historic times. It is one of the oldest domesticated livestock species and continues to be used as a source of milk, meat, and as a draft animal. It is an important dairy animal not only on the Indian subcontinent but also in South-East Asian countries. There are 170 million buffaloes in world, out of which 97% are in Asia, 2% in Africa mainly in Egypt, and 0.2% in Europe mainly in Italy (FAO 2004). Water buffalo comprise only 11.1% of the world’s bovid population, still people depends more on water buffalo than any other domesticated species in the world. The population of water buffalo has increased at the rate of about 2% per year world-wide in last 20 years. Water buffalo were domesticated 3000-6000 years ago, due to their economic importance in many highly populated countries. They provide more than 5% of the world’s milk supply, which contains less water and more fat, lactose, protein, and minerals than cow milk. They have leaner meat with less fat and cholesterol than beef. Asia has nearly 97% of buffaloes and is an integral part of agriculture in India, China, Pakistan, Nepal, Bangladesh, Thailand, Myanmar and Malaysia. Buffaloes are in family Bovidae with a diploid count of chromosomes being 48 (swamp) and 50 (riverine). An elucidated genome of the river buffalo will contribute enormously to a better understanding of its genome evolution in Ruminantia, specifically in domestic Bovidae.
Genomic Resources of Water Buffalo
Genome sequencing has significantly advanced in recent years. Information on cattle genomics exists in public domain but scanty information is available for buffalo. India has sequenced buffalo genome in network mode at National Bureau of Animal Genetic Resources, Karnal and Central Institute for Research on Buffaloes, Hissar. The main objective of this is to improve breeding of animal having higher genotypic and phenotypic potentials. The buffalo assembly represents 91 to 95 % coverage with cattle assembly B-tau 4.0 as reference. The BuffSatDB considers all the chromosomes (1-24, X, M,U) sequenced at NBAGR, India for development of microsatellite marker database. Copy of data used in BuffSatDB was obtained from the URL (http://210.212.93.84/bbu_2.0alpha/) and is available on request.
(Tantia et al. 2011).
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Microsatellite markers
Microsatellites, also known as Simple Sequence Repeats (SSRs) or short tandem repeats (STRs), are repeating sequences of specific DNA which contains mono-, di-, tri-, or tetra-, penta- or hexa- tandem repeats such as (A)n, (CA)n, (GA)n, (GTA)n, (ATT)n, (GATA)n, (ATTTT)n, (ACGTCG)n. Genomes are scattered with these repeats. Repeats of longer units form minisatellites or satellite DNA. With the discovery of tandem iterations of simple sequence motifs, the term microsatellites was further coined.
Molecular markers have several advantages over the traditional phenotypic markers that are available in buffalo. They are unaffected by environment, detectable in all stages of development and ubiquitous in number covering the entire genome. Development of molecular markers is important in for construction of linkage map, fingerprinting of strains for breeding, and marker-assisted selection. STRs are being used extensively in studies involving Forensics, Population Genetic structure analysis, establishment of Kinship, Conservation Genetics, Linkage Mapping, Marker Assisted Breeding etc .
Microsatellites can be analysed using different protocols as per the lab’s budget, labour and speed required. In the past years different protocols have been tested and standardised for population studies, polymorphism estimations, genetic mapping etc.
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