Diversity assessment of a lesser known buffalo population from Central India and its comparative evaluation reveals presence of sufficient genetic variation and absence of selection

Planned breeding and conservation strategies for a lesser-known population require an assessment of complete genetic diversity and population structure analysis in addition to its morphometric characteristics. In the present study, a comparative analysis of the genetic structure of a rare buffalo population, namely Chhattisgarhi, was extensively studied using a panel of FAO-recommended microsatellite markers along with well-established breeds namely Murrah, Nili-Ravi, Gojri, Kalahandi, and Nagpuri. Mode shift analysis indicated the absence of genetic bottleneck in the recent past. Assessment of genetic diversity indices across all loci indicated the presence of sufficient genetic variation within and between populations. Analysis of molecular variance between the six different buffalo populations attributed 19.05% of the variations to between-population differentiation. Cluster analyses using DAPC and Bayesian approach along with the phylogenetic tree based on UPGMA grouped six populations into three groups. The Chhattisgarhi population was revealed to be genetically closer to Nagpuri and Kalahandi populations. The study reveals the presence of sufficient genetic diversity within the Chhattisgarhi population and indicates the absence of a systematic selection program. We suggest improvement and conservation programs should be planned for this breed in the near future through short-term selection.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

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.

Elucidating the genetic diversity using SSR based markers in Gojri buffalo

A population based study was conducted in a large sample of Gojri buffalo, a less known dairy buffalo from Northern India, to assess its genetic variations using 25 heterologous simple sequence repeats (SSR) marker loci. Primers for markers used in the study were labelled either with VIC, NED, PET or FAM dye. Genotyping of each sample was performed by sequencing the PCR amplicons and thereby, estimating diversity indices based on frequency of different allele sizes. Gojri buffalo had an average of 8.2 alleles per locus with 3.65 mean effective number of locus. The polymorphic information content (PIC) values for studied SSR markers ranged from 0.11–0.81, indicating that all the markers, except ILSTS 19, were informative and suitable for the diversity analysis in the buffalo population. The average observed heterozygosity (Ho) and unbiased expected heterozygosity (uHe) estimate were 0.67 and 0.70, respectively in the population with majority of the markers showing Hardy Weinberg equilibrium. A higher expected heterozygosity in Gojri population indicates presence of sufficient genetic diversity, and a higher overall mean of Shannon’s information index (1.5) support these findings. Moreover, both genetic Bottleneck and Mode Shift analysis indicated absence of genetic bottleneck in the recent past among the studied Gojri population. Population inbreeding estimates (FIS=0.029) indicated an average deficiency of 2.9% and suggests no probable inbreeding in the population. It can be concluded that there is presence of sufficient genetic variations in Gojri population and this information can augment in designing its breeding and conservation programme.