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This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1265-1) contains supplementary material, which is available to authorized users.

Fungal pathogens and plant parasitic nematodes are prominent in causing diseases in legume crops. Chemical control of nematodes and fungi are not very effective and also cause product contamination. Molecular biology has made it possible to identify and clone genes associated with pathogenesis related proteins, anti-fungal proteins and compounds, phytoalexins and enzymes controlling oxidative burst, etc. which lead to a number of transgenic plant developments. It has also been possible to overexpress them constitutively in several transgenic crop systems. In a majority of cases it was proved that these anti-fungal proteins are very effective against various fungal pathogens. RFLP (Restriction Fragment Length Polymorphism) has made it possible to generate high-density maps of various commercially important crops including peas. However, progress of molecular mapping and gene tagging is limited due to availability of low degree of polymorphism using conventional DNA markers like RAPD and RFLP. In recent years, development of microsatellite based markers and AFLP has produced adequate polymorphism in a number of grain legumes like chickpea which otherwise was shown to be low polymorphic. Besides, there are also some successful examples of gene tagging using these markers for fungal diseases and nematode resistance in grain legumes.

Protease inhibitors are natural defense proteins that inhibit the proteolytic activity of proteases. Legume protease inhibitors are diverse in their molecular mechanism and many of them have successfully been deployed in crop plants to confer resistance against insect pests. Nine combinations of degenerated primers,designed, based on “multiple aligned” gene sequences from NCBI Gene bank database were used to amplify the protease inhibitor genes in of ten different legume crops (two varieties each)viz.fieldpea,chickpea, lentil, lathyrus, pigeonpea , frenchbean,mungbean ,clusterbean , horsegramand cowpea .The primer combination BBF2/BBR2 amplified the expectedamplicon of 800 bp invarities ofmungbean,horsegramand cowpea. These amplicons obtained from each genotype were further ligated to the pJET1.2/blunt vector and transformed into XL1 blue strain of E.coli. Out of 41 clones sequenced, two clone sequences obtained from cowpea (DCS 6) showed homology with substilisin-like serine protease inhibitor of Desulfovibria vulgaris and serine/threonine protein kinase of Epichlocfastucae.These genes can be transformed into Agrobacterium based binary vectors and used for transformation of crops. Therefore these findings offer new genes for transgenic development against lepidopteron pests.

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.