Jyoti Joshi

Identification of SNPs and their validation in camel (Camelus bactrianus and Camelus dromedarius)

The dromedary (Camelus dromedarius) and the bactrian camel (Camelus bactrianus) are among the last species that have been domesticated around 3000-6000 years ago. To understand relationship between genetic and phenotypic variations in camel, single nucleotide polymorphism (SNP) markers covering the coding part of genome were developed. These gene-associated SNPs can themselves be causative SNPs for traits. The main objective of this work was to identify SNPs from coding regions using high-throughput next generation sequencing. The data was generated on two tissues as 75bp paired end reads by using Illumina platform. These reads were generated were mapped on cattle genes (Ensemble gene version 69.0). The mapping was carried out separately for each tissue and camel species. The mapped reads were analysed for SNP identification based on coverage depth. The 374 SNPs were validated using a set of 672 camels using golden gate assay of Illumina. The SNPs identified in this report provides a much needed resource for genetic studies in camel and shall contribute to the development of a high density SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for genome association studies and whole genome-based selection in camel.

Genetic Variation and Phylogenetic Relationships of Indian Buffaloes of Uttar Pradesh

India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes.

Assessment of Genetic Variability and Structuring of Riverine Buffalo Population (Bubalus bubalis) of Indo-Gangetic Basin

The buffalo population of Uttar Pradesh (UP) constitutes 26.1% of the total buffalo population of India, yet this population has not been classified into distinct breeds or subpopulations due to lack of systematic study. Genetic variation at 30 microsatellite loci was examined and statistical analysis was carried out to reveal genetic diversity, demographic parameters of these buffaloes and to investigate the existence of population substructures underlying geographical distribution. The mean number of alleles per locus was 13.26 and mean effective number of alleles was 3.74, whereas mean observed and expected heterozygosities were found to be 0.57 and 0.67 in UP buffaloes. Principal component analysis (PCA) based on allele frequency data revealed subclustering of UP buffalo population. Bayesian analysis result also revealed clear membership of individuals into five clusters indicating a genetic subdivision within the UP buffalo population. The buffaloes of Western and Central regions of UP were subtly separated while buffaloes of Tarai area and Bhadawari buffaloes revealed distinctive population structure. The buffaloes of Mau, Ballia and Ghazipur districts of Eastern region also had a distinctive genetic structure. The analysis of data on buffaloes of Indo-Gangetic plains revealed that population was in mutation drift equilibrium. The observed mean M ratio in the population was above the critical significance value (Mc) suggesting that it has not suffered any severe reduction in effective population size. The statistical tests revealed a historical constancy of size of buffalo in this geographical area. The high level of genetic variability indicates UP buffalo population is a vast reservoir of genetic diversity and this shall help in taking informed conservation decisions and sustainable utilization.