Elucidating genetic diversity and population structure of Alpine x Beetal goats using pedigree analysis

Abstract

Pedigree analysis is essential for effective management of the breeding program and to keep the inbreeding under acceptable limits. Alpine x Beetal is a crossbred population of goats, bred at National Dairy Research Institute (NDRI) Karnal for last five decades. This germplasm is adapted to the tropical climate and has high milk potential as well as prolificacy. Objective of this study was to elucidate the genetic diversity and population structure in the flock of the Alpine x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 5656 animals from the year 1971–2021. Animals born between 2014 and 2017 were 283, considered as reference cohort. Results revealed that the average generation interval was 3.40 years for the complete pedigree. The average inbreeding coefficient and the average relatedness for the whole population were 4.77% and 7.84%, respectively, and 9.65% and 11.98% respectively, for the reference population. High inbreeding coefficient and average relatedness in the reference cohort demonstrated the impact of closed gene pool and demands immediate intervention for management of genetic diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 for the complete pedigree which illustrates that few ancestors were responsible for genetic diversity in the flock. This resulted in the decline of effective population size (51.39). Effective number of founders (fe), ancestors (fa), and founder genomes equivalents (fg) were 24, 12, and 4.17, respectively. The (fe/fa) ratio in the reference population was 2 indicating the occurrence of the bottleneck effect in the flock. To lessen inbreeding and augment genetic diversity in the flock, the use of sires with lower average relatedness and the use of appropriate mating strategies are recommended.