Exploration of allelic variants in short tandem repeats (STRs) flanking milk production QTLs and their association with milk production traits in Indian water buffaloes.

Short tandem repeats (STRs) are co-dominant, highly polymorphic marker loci, distributed throughout the genome and useful for identification and mapping of QTLs associated with variation in traits of economic significance. Allelic variants were identified in STRs located in close vicinity of cattle QTLs for milk production,, viz. BMS713, BM6404, BM4513, BM121, BM6105, TGLA245, BL1100, BMS1948, BMS711, BM1443, BM1706, BM6438, BM143, BM415, ETH131, ETH 2, and BM1329 in 109 water buffaloes of Murrah breed. All loci except TGLA245 exhibited polymorphism of varying degree. The observed number of alleles, effective number of alleles, PIC value, observed heterozygosity, and expected heterozygosity across all STR loci averaged 4.12 ± 0.22, 3.20 ± 0.22, 0.60 ± 0.04, 0.34 ± 0.05, and 0.66 ± 0.03, respectively. Goodness of fit (chi-square) and likelihood ratio (G square) test demonstrated that the population exhibited a deviation from HWE for all the loci. FIS was positive and ranged from 0.22 to 1.00. Least square analysis of variance exhibited significant effects of BM4513, ETH131, BM713, and BM6105 on first lactational total lactation milk yield, 305-day milk yield, lactation length, and dry period respectively. None of the STRs could exhibit significant effect on peak yield.