Ambika Baldev Gaikwad

Analysis of genetic diversity of Indian mango cultivars using RAPD markers

Summary Random amplified polymorphic DNA analysis was carried out in 29 Indian mango cultivars comprising popular landraces and some advanced cultivars. PCR amplification with 24 primers generated 314 bands, 91.4% of which were polymorphic. Jaccard’s similarity between pairs of cultivars ranged between 0.318 and 0.75 with a mean of 0.565. A UPGMA dendrogram showed the majority of the cultivars from northern and eastern regions of India clustering together and separate from southern and western cultivars. Analysis of molecular variance revealed that 94.7% of the genetic diversity in mango existed within regions. However, differences among regions were significant; northern and eastern regions formed one zone and western and southern regions formed another zone of mango diversity in India.

DNA fingerprinting of Indian cashew (Anacardium occidentale L.) varieties using RAPD and ISSR techniques

Indian cashew breeding programme has produced 24 selections and 11 hybrids with increased yield and excellent nut characters. Molecular profiles of these varieties were developed using a combination of five RAPD and four ISSR primers pre-selected for maximum discrimination and repeatability. A total of 94 markers were generated which discriminated all the varieties with a probability of identical match by chance of2.8 × 10-11. There was no correlation between the relationships based on molecular data and the pedigree of the varieties. Narrow range of average similarity values among major cashew breeding centres with only 3.6% of molecular variance partitioned between them was attributed to the exchange of genetic material in developing varieties. Difference in the average similarity coefficients between selections and hybrids was low indicating the need and scope for identification of more parental lines in enhancing the effectiveness of hybridisation programme.

Molecular Characterization of Brinjal (Solanum melongena L) Cultivars using RAPD and ISSR Markers

Molecular characterization of 19 advanced cultivars and landraces of brinjal was carried out using RAPD and ISSR markers. Twenty-nine RAPD primers generated a total of 240 amplified fragments, while 23 anchored and non-anchored ISSR primers produced 299 fragments. Of these, 66 (27.5%) RAPD and 56 (18.73%) ISSR fragments were polymorphic. All the cultivars could be distinguished based on RAPD and/or ISSR profiles. A set of two RAPD primers, OPW 11 and OPX 07, was adequate to distinguish all the 19 cultivars. On the other hand, a minimum of ten ISSR primers were required to achieve the same result. Eleven cultivars could be identified by the unique presence or absence of one to four markers. The correlation between primer Rp and the number of cultivars distinguished by RAPD was r = 0.873, while that for ISSR it was r = 0.327. The correlation between PIC of primer and the number of cultivars distinguished was r = 0.324 for RAPD, while for ISSR primers it was r = − 0.066. The probability of chance identity between two cultivars for RAPD and ISSR markers was calculated as 8.94×10−4 and 2.25×10−2, respectively. The average Jaccard’s similarity coefficient between cultivars based on combined RAPD and ISSR data was estimated to be 0.919. The UPGMA analysis grouped the cultivars into three main clusters with significant bootstrap support. While the cultivars bred at Indian Agricultural Research Institute, New Delhi formed one sub-cluster; others did not show a prominent region-based clustering.

Genetic analysis and historical perspective of cashew (Anacardium occidentale L.) introduction into India.

Cashew (Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plants commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct these events by investigating the level of genetic variation and genetic structure of cashew populations collected from different geographical regions of India. A total of 91 individuals from four populations were analysed using AFLP markers and morphometric data. AFLP analysis based on 354 polymorphic loci revealed Indian cashew to have low but relatively substantial genetic diversity for an introduced species (H(E) = 0.262 and I(S) = 0.404). Twenty-seven qualitative and quantitative traits also revealed the existence of considerable morphometric variation (24% around the mean values). Bayesian cluster analysis based on AFLP data did not indicate the existence of definite population differentiation. Morphometric analysis allocated 12% variation among all four populations, whereas AFLP variation observed in cashew individuals was entirely within populations. The results, supporting the possibility of cashew having been introduced into India repeatedly over a period of time but at a single location (west coast), are discussed and their implications for germplasm management are described.

DNA Fingerprinting of Some Mango (Mangifera indica L) Cultivars Using Anchored-ISSR Markers

Twelve Indian mango cultivars were fingerprinted using anchored-ISSR primers. Out of total 161 bands amplified, 113 (70.2%) were polymorphic, the polymorphism ranging from 50% to 94.1% depending upon the primer. One primer [5′ HVH(CA)7T 3′] with highest genotype index could uniquely identify each of the cultivars studied. Fingerprints based on polymorphic markers amplified by the 10 primers had a 6.75 x 10-12 probability of identical match by chance, indicating a high degree of uniqueness in the anchored-ISSR based fingerprinting. UPGMA dendrogram based on Jaccard’s similarity showed Himayath as the most diverse of the 12 cultivars and the rest of the cultivars clustered into two groups at 0.69 similarity coefficient.

Analysis of spatial distribution of genetic diversity and validation of Indian foxtail millet core collection

Foxtail millet [Setaria italica (L.) P. Beauv.] is an important small millet, grown as a short duration, drought tolerant crop across the world. This crop can be grown on wide ranges of soil conditions and has an immense potential for food and fodder in rainfed and arid regions of the India. In the present study, 31 primer pairs (27 SSR and 4 EST-SSR) were used to analyse the genetic diversity in 223 core collection accessions. Analysis resulted in detection of a total of 136 alleles with an average of 4.38 alleles per locus. Among these 136 alleles, 22 were rare, 70 were common and 44 were frequent. The PIC value ranged from 0.01 to 0.86 with an average of 0.31. The average number of observed alleles ranged from 2.0 (northern hills of India accessions) to 4.06 (exotic) with an average of 2.72. The mean Shannon’s Information Index ranged from 0.44 (northern hills of India) to 0.69 (exotic) with an average of 0.52. Pair-wise Fst values indicated little to moderate genetic differentiation among the group of accessions. UPGMA clustering grouped the accessions into two major groups while analysis for population substructure indicated presence of four subpopulations. However there was no statistically well supported grouping of the accessions based on eco-geographic specificities. The core collection designated here represented substantial genetic diversity at molecular level, hence may be a good source of diversity for use in foxtail improvement programs in the region.

Molecular Genetic Diversity Analysis of Commercial Mango (Mangifera indica L.) Cultivars Employed as Parents in Hybrid Development in India

Mango hybridization programmes use commercial cultivars as parents. Twenty three such popular cultivars of mango belonging to different regions of India were analyzed by employing multi-locus marker techniques to measure the genetic diversity existing among them. Twelve unanchored ISSR primers (114 markers) and 15 AFLP primer-pair combinations (1,073 markers) revealed average gene diversity over loci to be 0.231 and 0.257 respectively. Mango cultivars from southern India were found to be significantly different (p<0.001). In order to decipher how these markers are inherited, three popular hybrids ‘Amrapali’, ‘Mallika’ and ‘Ratna’ were compared with their parents for band sharing information. Number of ISSR markers shared between pairs of parents and their hybrid was nearly 20% more than that of AFLP markers, endorsing the conserved nature of ISSR profiles. Our observations on (i) genetic relatedness among popular cultivars and (ii) band sharing pattern among parents and hybrids have implications on mango germplasm collection and breeding activities.

Identification of genes associated with stress tolerance in moth bean [Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop

Moth bean is the most drought and heat tolerant cultigens among Asian Vigna. We performed comparative transcriptome analysis of moth bean cultivar “Marumoth” under control and stress condition. De novo transcriptome assembly was carried out by using Velvet followed by Oases softwares. Differential expression analyses, SSR identification and validation and mapping of pathways and transcription factors were conducted. A total of 179,979 and 201,888 reads were generated on Roche 454 platform and 48,617,205 and 45,449,053 reads were generated on ABI Solid platform for the control and stressed samples. Combined assembly from Roche and ABI Solid platforms generated 16,090 and 15,096 transcripts for control and stressed samples. We found 1287 SSRs and 5606 transcripts involved in 179 pathways. The 55 transcription factor families represented 19.42% of total mothbean transcripts. In expression profiling, ten transcripts were found to be up-regulated and 41 down-regulated while 490 showed no major change under moisture stress condition. Stress inducible genes like Catalase, Cyt P450 monooxygenase, heat shock proteins (HSP 90 and HSP 70), oxidoreductase, protein kinases, dehydration responsive protein (DRP), universal stress protein and ferridoxin NADH oxidoreductase genes were up-regulated in stressed sample. Genes which might be involved in moisture stress tolerance in moth bean were identified and these might be useful for stress tolerance breeding in moth bean and other related crops.

Detection and characterization of polymorphic simple sequence repeats markers for the analysis of genetic diversity in Indian mungbean [Vigna radiata (L.) Wilczek]

Mungbean is a widely cultivated grain legume in Asia, Africa and South America. In this study, 52 varieties of mungbean were profiled with 39 polymorphic SSR primers after screening a total 315 SSR primers. A total of 96 alleles were scored from the 39 primers with an average of 2.46 alleles per locus indicating the low diversity among varieties. The Neis genetic diversity index and the Shannon information index of SSR primers varied from 0 to 0.649 and 0 to 1.169, respectively. The results showed that the potential transferability of adzuki bean primers (83.3%) was greater than the cowpea primers (25%). The varieties profiled were grouped into four major clusters. But the clustering pattern did not reflect on their geographical origin. Further, the AMOVA indicated presence of moderate genetic differentiation among groups compared to higher differentiation among varieties within populations. The SSR markers identified here will add valuable genomic resources for germplasm characterization, cultivar identification and assessment of genetic diversity of mungbean varieties.