Pedigree-based analysis of population structure and genetic diversity in high-milch Vrindavani crossbred cattle of India

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Abstract
The present study aimed to elucidate the population structure and genetic diversity along with the estimation of genealogical parameters in Vrindavani cattle using pedigree data. The study was based on pedigree data on 12,718 animals, spread across multiple generations during a 52-year period (between 1971 and 2023). The pedigree data was used to estimate different population genealogical parameters including the generation interval; pedigree completeness; rate and level of inbreeding; effective population size; and parameters characterizing the probabilities of gene origin. The ENDOG program was used for estimation of different parameters while using population after 2010 as reference cohort. The results revealed the maximum number of generations (MG) to be 13, while the numbers of completed (CG) and equivalent generations (EqG) were 3.23 and 1.95, respectively. The mean generation interval for the population was 6.9 years. The average inbreeding coefficient of animals in the whole and reference population was 1.11 and 3.44%, respectively; with 0.68% rate of inbreeding per generation. The average additive relationship among all the animals and those in the reference population was 1.16 and 5.49%, respectively. The average effective population sizes for the maximum, equivalent, and complete generations were 115.56, 56.42, and 46.02, respectively. The effective population size on the basis of regression and log-regression on birth date was 77.40 and 71.24, respectively. The probabilities of gene origin were estimated by the effective number of founders (fe) and ancestors (fa), which was 115 and 78, respectively. The fe/fa ratio in the reference population was 1.20, indicating that occasional bottlenecks may have occurred in the population. The analysis revealed a loss of 5.3% of total heterozygosity as compared to base population, though significant variability exists in the latest generations. The results revealed that considerable genetic variability exists within the population that may be exploited through appropriate breed improvement programs targeting various economic traits.

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