Morphometric and microsatellite-based comparative genetic diversity analysis inBubalus bubalisfrom North India

Abstract

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

“…Highly variable SSR markers extracted in the present study could be utilized to find genetic diversity ( Barker et al, 1997 ; Zhang et al, 2020 ). The SSR markers from different breeds could be used to find polymorphic SSRs ( Moore et al, 1995 ) and their utilization in the study of genetic diversity of respective breeds ( Moioli et al, 2001 ; Merdan et al, 2019 ; Vohra et al, 2021 ; Ünal et al, 2021 ). We also extracted ∼270000 polymorphic SSRs in the Mediterranean buffalo breed with respect to Murrah, Bangladesh, Jaffrabadi, and Egyptian breeds.…”

Revealing the genetic diversity of Sumbawa endemic horse using microsatellite-based DNA fingerprint

“…Microsatellite DNA markers have been widely used to study genetic diversity because they are randomly distributed throughout the genome, codominant, and have high polymorphism (Putman and Carbone 2014). Microsatellite markers have been widely used for genetic diversity analysis in plants (Saptadi et al 2020;Parmar et al 2022), poultry (Luis-Chincoya et al 2021, cattle (Agung et al 2019), buffalo (Vohra et al 2021), and horses (Kim et al 2021). In Indonesia, research on livestock genetic diversity still needs to be done because some of the genetic resources of native Indonesian livestock are threatened with extinction due to a small population and limited distribution (Sutarno et al 2015).…”