N. Nadarajan

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

Genomics‑assisted breeding in four major pulse crops of developing countries: present status and prospects

Key messageGiven recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.AbstractThe global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

A protocol for high-quality genomic DNA extraction from legumes.

Current DNA extraction protocols, which require liquid nitrogen, lyophilization and considerable infrastructure in terms of instrumentation, often impede the application of biotechnological tools in less researched crops in laboratories in developing countries. We modified and optimized the existing CTAB method for plant genomic DNA extraction by avoiding liquid nitrogen usage and lyophilization. DNA was extracted directly from freshly harvested leaves ground in pre-heated CTAB buffer. Chloroform:isoamyl alcohol (24:1) and RNase treatments followed by single-purification step decontaminated the samples thereby paving way for selective extraction of DNA. High molecular weight DNA yield in the range of 328 to 4776 ng/μL with an average of 1459 ng/μL was obtained from 45 samples of cultivated and wild Cajanus species. With an absorbance ratio at 260 to 280 nm, a range of 1.66 to 2.20, and a mean of 1.85, very low levels of protein and polysaccharide contamination were recorded. Forty samples can be extracted daily at a cost between 1.8 and US

Novel genic microsatellite markers from Cajanus scarabaeoides and their comparative efficiency in revealing genetic diversity in pigeonpea

2.0 per plant sample. This modified method is suitable for most plants especially members of the Leguminosae. Apart from Cajanus, it has been extensively applied in DNA extraction from Cicer and Vigna species.

Identification, Characterization, and Phylogenetic analysis of Pigeon pea (Cajanus cajan L. Mill sp.) Resistance Gene Analogs using PCR cloning and in silico methods

Paucity of molecular markers is hindering molecular breeding programmes for genetic improvement in pigeonpea, which is considered to be among the richest source of dietary protein in Asia and Africa. At the time of the start of this study, only 156 microsatellite markers were available in pigeonpea (Burns et al. 2001; Odeny et al. 2007, 2009). Recently with the publication of draft genome sequence and deep transcriptome studies, the stage has been set to enrich genomic resources to aid molecular breeding in pigeonpea (Dutta et al. 2011; Singh et al. 2012; Varshney et al. 2012). Genic microsatellites or EST-SSRs (simple sequence repeats) derived from expressed sequence tags (ESTs) are useful because these are inexpensive to develop, represent transcribed genes, and often a putative function can be assigned to them. Compared with genomic sequences, genic SSRs have several advantages as genetic markers. First, if an EST marker is found to be genetically associated with a trait of interest, it may represent the gene affecting the trait directly (Chen et al. 2001; Thiel et al. 2003). Therefore, EST-derived markers can provide opportunities for gene discovery and enhance the role of genetic markers by assaying variation in transcribed and known-function genes. Second, EST-derived

Data on draft genome sequence of chickpea (Cicer arietinum)

Pigeon Pea (Cajanus cajan), an important grain legume, is susceptible to Fusarium wilt (FW), sterility mosaic disease (SMD), and Phytophthora blight. Identification of resistance gene analogs (RGAs) is important for development of resistant varieties. In this study, degenerate primers targeting nucleotide binding sites (NBS) of known resistance (R) genes were used to amplify RGAs from two Pigeon Pea genotypes with differing disease resistance profiles. The translated cloned RGAs had high amino acid identity (68–71%) with putative disease resistance proteins in Glycine Max. Five RGA open reading frames were found in the whole Pigeon Pea genome after BLASTN analysis with the cloned sequences. Translated RGA proteins contained several characteristic features such as the NB-ARC domain (characteristic of death-related disease resistance genes) and four NBS motifs. A tryptophan residue at the kinase-2 motif was indicative of the non-TIR-NBS class of proteins. Phylogenetic analysis revealed two major clusters. The seven Pigeon Pea RGAs were in a non-TIR group alongside wilt resistance proteins from tomato. Specific primers were designed against the RGAs identified by BLASTN, and these successfully amplified sequences from all eight Pigeon Pea genotypes. The 40 resultant sequences were combined according to genotype and subjected to phylogenetic analysis. Genotypes clustered according to breeding pedigree. Multiple alignments of the 40 sequences revealed several single nucleotide polymorphisms (SNPs) that are useful in identifying candidate resistance genes associated with FW and SMD.

Ontogeny of in vitro shoot organogenesis from axillary meristem explants in chickpea (Cicer arietinum L.)

The dataset contains genome sequence of the ~738 Mb chickpea genome from CDC Frontier, a kabuli variety, which contains an estimated 28,269 genes. Re-sequencing and analysis of 90 cultivated and wild genotypes from 10 different countries identifies both targets of breeding-associated genetic sweeps and targets of breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main classes of cultivated chickpea- desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding, and provide insights into both genome diversity and domestication. GBrowse Visualization Links: Chickpea genome at LIS Research Article

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

Chickpea (Cicer arietinum L.) is a major food legume crops for the tropics and sub-tropical regions and is the main dietary protein source for vegetarians in developing countries. Besides several abiotic factors, its production is constrained by insect pests, as well as many fungal diseases. The success of any attempt to produce resistant varieties through genetic engineering to a large extent depends on the availability of efficient and reproducible regeneration and transformation procedures. Further, the transformation techniques can be more successfully applied if the ontogeny of shoot development is well understood. Ontogeny of shoot development from axillary meristem explants (AME) in chickpea has been studied with the optimization of conditions for high-frequency multiple shoot induction. Preculture of seeds in TDZ significantly enhances the frequency of multiple shoot induction from the explants. Ontogeny and early events of multiple shoot induction revealed direct adventitious origin of the shoots. The understanding of the regeneration process could be further utilized in the designing of efficient transformation methods.