Genetic diversity and population structure of Jamunapari goat in India using pedigree analysis

Pedigree records of 6821 Jamunapari goats of India were collected from 1980 to 2011 and used to evaluate the population structure and genetic diversity in this flock. Animals born between 2009 and 2011 represented the current reference population. The average pedigree completeness index (PCI) and numbers of equivalent complete generations (EqG) were estimated for the entire (PCI = 0.18, EqG = 2.24) and reference (PCI = 0.31, EqG = 3.45) populations. The average generation interval was 3.33 years. The average inbreeding coefficient and the average relatedness were 0.46 and 1.06%, respectively, for the entire population and 0.77 and 3.87% for the reference population. The rate of inbreeding was 0.06% per generation. The effective population size (N_e), estimated from increases in inbreeding coefficients between the first and third equivalent complete generations, was 52.65, but periodic introductions of unrelated breeding males resulted in average inbreeding levels in the reference population that were lower than those predicted from the estimate of N_e. Effective numbers of founders (f_e), ancestors (f_a), founder genomes equivalents (f_g), and non-founder genomes (f_ng) were 51, 39, 25.8, and 48.2, respectively. The f_e/f_a ratio in the reference population was 1.31 and indicated that occasional bottlenecks had occurred in the population. The 14 most influential ancestors contributed 50% of the genetic variability in the reference population, with a maximum individual contribution of 9.25%. Approximately 1.9% of the initial heterozygosity had been lost from the population, indicating that substantial genetic diversity still exists in this flock.