Genetic diversity and relationship among Indian goat breeds based on microsatellite markers

In India, goat breeds are mainly defined by their geographical position, morphological characteristics and production performance. However, there is no comprehensive information on genetic structuring of all 20 well defined breeds of the country. Genetic diversity and relationship between all the breeds were investigated based on 25 microsatellite markers. In total, 412 alleles were observed from 1034 DNA samples of these breeds. The most diverse breeds were Kanniadu and Sirohi, and the least diverse breed was Osmanabadi. Gene diversity for each breed ranged from 0.73 in Sirohi to 0.61 in Osmanabadi. The genetic distance tended to be lowest (0.092) between Jamunapari and Marwari and the widest (0.519) between Kanniadu and Zalawadi. The genetic differentiation between different pairs of the breeds was significantly different from zero. The majority of the loci in almost all the breeds were heterozygote deficit. The overall Fis value (0.183) was moderate and significantly different from zero. The F-Stat analysis revealed that 83.5% of the genetic variability in studied breeds was due to differences among individuals within the breed and 16.5% due to unique allelic differences between the breeds. The breeds can be clustered into three major genetic groups according to their physio-geographical origin.