How plants cope with temperature stress

A cold night can follow a hot day, and because they cannot move, plants subjected to such temperature fluctuations must acclimate on the basis mainly of pre-existing proteins. Zhang et al. report in a paper in BMC Plant Biology, however, that heat-induced cell death results from transcriptional activation of a kinase related to disease resistance factors and leading to a localized hypersensitive response. This specialized response reflects the failure of adaptations that normally enable plants to survive over a remarkable temperature range, by mechanisms that are not fully understood

Development of cost-effective SNP assays for chickpea genome analysis and breeding

A total of 1499 ESTs generated from 26 different Cicer species, available in the public domain at the time of analysis, were used for in silico identification of SNPs using the bioinformatic tools developed at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) (http://hpc.icrisat.org/PBSWeb). Cluster analysis provided a total of 118 clusters, of which 11 clusters contained sequences from more than one Cicer species. Further, these clusters were assembled into 19 contigs and 184 putative SNPs were identified in 15 contigs. However, only 73 SNPs involved restriction enzyme sites for development of the CAPS assays as identified through the SNP2CAPs program. Primer pairs were designed for only 8 contigs (CL3a, CL3c, CL3d, CL3e, CL4a, CL10, CL20 and CL99) which had SNPs, resulting in putative recognition sites to commonly used restriction enzymes. Results of the demonstrates the utility of Cicer EST resources and the availability of bioinformatics analysis pipelines for the large-scale identification of SNPs on the HPC (High Performance Computer) at ICRISAT and the development of costeffective CAPS assay for SNP genotyping. It is anticipated that the availability of large number of ESTs from more than one genotype of cultivated chickpea (C. arietinum) in the near future will make it possible to develop larger number of SNPs in cultivated chickpea germplasm for genome analysis and breeding application

A database of annotated tentative orthologs from crop abiotic stress transcripts

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

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

Large variation in gravimetric TE exists in wild and cultivated groundnut germplasm

Transpiration efficiency is considered as one trait that can contribute to achieving higher yields under conditions of limited water, and variations for TE exist in groundnut. We have measured TE gravimetrically in 440 genotypes, encompassing the mini-core collection of groundnut, and have found a 4-fold range of variation for TE (0.62-2.75 g biomass kg-1 water transpired). The relation between the TE values measured under well-watered and water stress conditions was significant, but the correlation coefficient was weak (r=0.23). The surrogate traits for TE, SLA and SCMR, did not show any significant relation with TE, regardless of water regime. By contrast, we found that the rate of water loss per unit of leaf area was inversely related to TE. We also measured TE under well-watered conditions in 21 accessions of peanut wild relative and 10 accessions of cultivated groundnut. TE varied 1.99-4.93 g.kg-1 in the wild and 2.27-3.50 g.kg-1 in the cultivated. On average, TE was higher in the wild peanut than the cultivated. We found that the rate of water loss per unit of leaf area was lower in the wild peanut, and was well and negatively related to TE (r = 0.56)

Using genetic and genomic resources to broaden the genetic base of cultivated groundnut

Groundnut is highly self-pollinated tetraploid crop with 2n = 40 chromosomes and ~2800 Mb genome. ICRISAT genebank at Patancheru, India has the largest collection: 14,968 cultivated accessions from 92 countries and 451 wild relative accessions representing nine sections and 44 species. For enhancing the use of germplasm, core and mini core collections were developed that when evaluated identified several new sources of variation for agronomic traits and resistance to biotic and abiotic stresses. Further, a composite collection of 1000 accessions, which also included 184 mini core accessions, has been molecularly profiled using 21 SSRs and formed a reference set of 300 most diverse accessions (http//www.generationcp.org). Genetic populations are being developed for mapping of genes associated with beneficial traits. These are useful resources to analyze genetic relationships and identify marker trait associations using linkage disequilibrium and association mapping. Unlike past, several genomic resources are now available to research community: high throughput platforms including DArT technology, SSRs, BAC libraries, ESTs, and genetic linkage maps

Bioinformatics platform for ICRISAT's global research needs

Scientists in ICRISAT’s Global Theme on Biotechnology employ a range of modern genomic technologies in their efforts to enhance the efficiency and effectiveness of crop improvement. These include high-throughput genotyping technologies. The rate-limiting step in genomics is no longer data generation but rather the speed, at which data is captured, validated, analyzed and turned into useful knowledge. The role of Bioinformatics is to remove this rate-limiting step through the development of software platforms for handling large volumes of data generated and facilitate its analysis. The term ‘platform’ implies all those vital services and technologies that are needed to support genomics research projects at all of ICRISAT locations. Bioinformatics at ICRISAT functions both as a research and research support unit. Research efforts in Bioinformatics at ICRISAT focus on two major areas. One relates to infrastructure development which includes: (a) the development of appropriate software and efficient protocols for data capture, storage, retrieval and dissemination.........

Molecular characterization of pigeonpea [Cajanus cajan (L.) Millspaugh] composite collection

Pigeonpea is diploid (2n = 22) and primarily grown for food (dry seeds or green vegetables) • Sixth most important food legume crop and good source of protein; enriches soil; provides fodder and fuel wood; and arrests soil erosion • Grown in over 82 countries worldwide as a field and/or backyard crop • As a regular crop, grown only in 19 countries on 4.6 million ha producing 3.5 million tons of grain (FAOSTAT, 2005)......................

Testing public Bt maize events for control of stem borers in the first confined field trials in Kenya

Transgenic maize (Zea mays L), developed using modified genes from the bacterium Bacillus thuringiensis (Bt), controls stem borers without observable negative effects to humans, livestock or the environment, and is now sown on 134 million hectares globally. Bt maize could contribute to increasing maize production in Kenya. Nine public Bt maize events of cry1Ab and cry1Ba genes were tested in confined field trials site (CFTs) to assess the control of four major Kenyan stem borer species. Leaf damage rating, number of exit holes and tunnel length were scored in the field evaluations. Leaf area consumed and mortality rates among stem borers were scored in the leaf bioassays in a Biosafety Level II laboratory, located at the Kenya Agricultural Research Institute (KARI), National Agricultural Research Laboratories (NARL). Field evaluations showed that Bt maize controlled Chilo partellus with mean damage scores of 1.2 against 2.7 for the non-Bt CML216 control. Laboratory bioassays showed high control for Eldana saccharina and Sesamia calamistis, with mean larval mortality of 64 and 92%, respectively. However, substantial control was not observed for Busseola fusca. These results showed that Bt maize could control three of the four major stem borers in Kenya with mortality records of 52.7% for B. fusca, 62.3% for E. saccharina and 85.8% for S. calamistis. Additional Bt genes need to be sought and tested for effective stem borer control in all maize growing ecologies in Kenya

Genotyping Finger Millet Germplasm –Developing a Composite Collection

Finger millet [Eleusine coracana (L.) Gaertn.] belongs to family Poaceae. It is a tetraploid species with 2n=36, and selfpollinating. • Cultivated in 23 countries on 3.38 million ha producing 3.76 m t mainly in Africa and Asia. • A very important crop in Uganda, Nepal, Kenya, Ethiopia, Eritrea and India. • Nutritionally rich in protein, minerals and metionine amino acid..