P. K. Agrawal

In-silico mining, type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS-LRR regions of finger millet with rice.

In recent years, the increased availability of the DNA sequences has given the possibility to develop and explore the expressed sequence tags (ESTs) derived SSR markers. In the present study, a total of 1956 ESTs of finger millet were used to find the microsatellite type, distribution, frequency and developed a total of 545 primer pairs from the ESTs of finger millet. Thirty-two EST sequences had more than two microsatellites and 1357 sequences did not have any SSR repeats. The most frequent type of repeats was trimeric motif, however the second place was occupied by dimeric motif followed by tetra-, hexa- and penta repeat motifs. The most common dimer repeat motif was GA and in case of trimeric SSRs, it was CGG. The EST sequences of NBS-LRR region of finger millet and rice showed higher synteny and were found on nearly same positions on the rice chromosome map. A total of eight, out of 15 EST based SSR primers were polymorphic among the selected resistant and susceptible finger millet genotypes. The primer FMBLEST5 could able to differentiate them into resistant and susceptible genotypes. The alleles specific to the resistant and susceptible genotypes were sequenced using the ABI 3130XL genetic analyzer and found similarity to NBS–LRR regions of rice and finger millet and contained the characteristic kinase-2 and kinase 3a motifs of plant R-genes belonged to NBS–LRR region. The In-silico and comparative analysis showed that the genes responsible for blast resistance can be identified, mapped and further introgressed through molecular breeding approaches for enhancing the blast resistance in finger millet.

Molecular and Biochemical Characterization of Short Duration Quality Protein Maize

Fifty microsatellite or simple sequence repeat (SSR) markers, spread across the maize genome were used for analyzing a set of 19 elite Quality Protein Maize (QPM) lines, including seventeen lines developed in India and two at CIMMYT, Mexico. Polymorphic profiles for 47 SSR loci have aided in differentiating the QPM inbred lines. The polymorphism information content (PIC) values among the inbreds ranged from 0.06 (umc2229) to 0.70 (umc1071) with an average of 0.45 per primer-pair. The genetic relationships as indicated by the cluster analysis of SSR data were largely in congruence with the known pedigree of the QPM lines. The study resulted in identification of two SSR markers, umc1071 and umc1063 with higher PIC values of 0.70 and 0.64, respectively. The tryptophan content among the genotypes was found to vary considerably. Two genotypes viz., VOL 2 and VOL 8 were found to differ significantly for tryptophan content (0.51% and 0.94%, respectively). Both these QPM genotypes being derived from the same non-QPM parent CM 145, makes them ideal for mapping of modifiers for tryptophan content.

Assessment of Genetic Diversity among the Elite Maize (Zea mays L) Genotypes Adapted to North-Western Himalayan Region of India using Microsatellite Markers

Maize is an important crop in the North-Western Himalayan states of India for food, feed and nutritional security of human population. Hybrid maize constitutes the major part of the maize area. Twenty four maize lines including the indigenous and exotic inbreds were amplified using 68 SSR primers, spread over the whole genome. The number of alleles across the primers ranged from two to eleven. The genotypes were grouped into different clusters using NTSYSpc2.11 programme. The clusters were well correlated with agronomic traits and resistance against turcicum blight. The PIC value was found to be highest for the primer bnlg1267 (0.84) while the lowest value was for the primer dupssr14 (0.09) with the mean value of 0.60. From this study we concluded that inbred V 359 is expected to give better combinations with CM 128, CM 129, V 340, V 357 and CM 212 for the development of hybrids suitable for the sub-tropical hill regions of India and elsewhere.

Identification of microsatellite markers for finger millet genomics application through cross transferability of rice genomic SSR markers

In the present investigation, 345 rice genomic SSR markers were used for finding the cross transferability in twelve finger millet accessions. Out of which, 202 SSRs (58.6%) showed transferability among the finger millet genotypes and only 26 (13%) were found to be polymorphic. Thirteen markers were polymorphic between two finger millet genotypes, VR708 and GPU48, whereas five markers were between GE86 and PRM801. These markers can be effectively used in mapping populations for construction of linkage maps. Few putative orthologous regions for grain yield and its components like 1000 grain weight, leaf characteristics and root traits between rice and finger millet were detected. Among the biotic stresses, blast and brown plant hopper (BPH) resistance loci were found to be highly conserved. The PIC values of all the polymorphic loci varied from 0.15 to 0.55. Power Marker grouped the finger millet genotypes into two major clusters based on the races. The average gene diversity existing among the genotypes was relatively high (41%) indicating the usefulness of cross transferability in millet