Explicating the genetic diversity and population structure of Saanen x Beetal goats using pedigree analysis

Abstract

Pedigree analysis is required to assess the genetic diversity and population structure of a close breeding population in order to effectively manage the breeding program and keep inbreeding under acceptable limits. Saanen x Beetal is a crossbred population of goats, reared at National Dairy Research Institute (NDRI) Karnal for the last five decades. This germplasm has been acclimated to a tropical climate and has a higher milk potential and prolificacy. Objective of this study was to elucidate the genetic diversity, population structure, and inbreeding in the flock of the Saanen x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 2603 animals from the year 1971–2021. Animals born between 2014–2017 were considered as a reference cohort. Results revealed that the average generation interval was 3.44 years for the complete pedigree. The average inbreeding coefficient and the average relatedness were 4.20% and 6.87%, respectively, for the complete pedigree and 10.78% and 10.80%, for the reference population. Higher inbreeding coefficient and average relatedness in the reference cohort demonstrated impact of enclosed gene pool and demands immediate intervention for managing diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 and 3 for the complete pedigree and reference cohort, respectively, which illustrates the fact that very few ancestors were responsible for genetic diversity in the flock, which results in the decline of effective population size. Effective number of founders (fe), ancestors (fa), and founder genome equivalents (fg) were 15, 7, and 3.11, respectively. The (fe/fa) ratio in the reference population was 2.14 indicating the occurrence of the bottleneck effect in the flock. We observed that inbreeding was non-significant for all reproductive traits except for age at first service and age at first kidding. To lessen inbreeding and augment genetic diversity in the flock, the stratified breeding plan needs to be followed, where, mate sele ction would be based on relatedness. Furthermore, introduction of unrelated Saanen and Beetal crosses will help alleviate the inbreeding accumulation.

Assessing genetic parameters for first parity reproductive traits for early selection in Saanen × Beetal goats of India

“…The climate is subtropical. The temperature of this farm ranges from 0 to 45°C and annual rainfall ranges from 760 to 960 mm (Sahoo et al., 2023a; Upadhyay et al., 2024a).…”

“…Green fodder supplementation was also provided to these animals. During winters, animals were provided with Berseem, Lucerne and Mustard, whereas Maize, Napier and Sorghum were given as green fodder in summer and rainy season (Sahoo et al., 2023c).…”

“…Saanen × Beetal (S × B) is a closed nucleus crossbred flock developed during the All India Coordinated Research Project (AICRP) in the early 1970s by importing the exotic breed Saanen to cross with the native breed Beetal to improve its milk‐producing ability. Being reared for more than five decades, this crossbred is exhibiting high milk‐producing ability and prolificacy (Sahoo et al., 2023c). For gaining maximum profit, selecting best performing animals is important.…”

Optimizing selection strategy for enhancing reproduction efficiency in Indian crossbred goats using milk productivity as a selection criterion

“…Chawla et al (1981) analysed the genetic parameters of lactation traits in these crossbreds. The detailed study on reproductive performance of the Alpine × Beetal goats was carried out by Sahoo et al (2023b), however the milk production and reproductive efficiency, its genetic variance and selection strategy for futuristic breeding has not yet been defined.…”

“…The present flock of Alpine × Beetal has an average 4.77% overall inbreeding and effective population size of 51.39 (Sahoo et al., 2023a). The Alpine × Beetal goats at NDRI are prolific with average overall prolificacy of 32% and are adapted to Karnal's tropical climate (Sahoo et al., 2023b). However, the success of crossbreeding programmes in goats is contingent upon various factors, including the selection of breeding individuals.…”