Publications by authors named "Himabindu Kudapa"

34 Publications

Regulatory non-coding RNAs: a new frontier in regulation of plant biology.

Funct Integr Genomics 2021 May 20. Epub 2021 May 20.

Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.
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http://dx.doi.org/10.1007/s10142-021-00787-8DOI Listing
May 2021

Systems biology for crop improvement.

Plant Genome 2021 May 5:e20098. Epub 2021 May 5.

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India.

In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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http://dx.doi.org/10.1002/tpg2.20098DOI Listing
May 2021

Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops.

BMC Genomics 2021 Apr 21;22(1):289. Epub 2021 Apr 21.

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.

Background: Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops.

Results: In this study, genome-wide NAC proteins - 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes.

Conclusion: As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.
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http://dx.doi.org/10.1186/s12864-021-07602-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8059324PMC
April 2021

Can omics deliver temperature resilient ready-to-grow crops?

Crit Rev Biotechnol 2021 Apr 7:1-24. Epub 2021 Apr 7.

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.

Plants are extensively well-thought-out as the main source for nourishing natural life on earth. In the natural environment, plants have to face several stresses, mainly heat stress (HS), chilling stress (CS) and freezing stress (FS) due to adverse climate fluctuations. These stresses are considered as a major threat for sustainable agriculture by hindering plant growth and development, causing damage, ultimately leading to yield losses worldwide and counteracting to achieve the goal of "zero hunger" proposed by the Food and Agricultural Organization (FAO) of the United Nations. Notably, this is primarily because of the numerous inequities happening at the cellular, molecular and/or physiological levels, especially during plant developmental stages under temperature stress. Plants counter to temperature stress via a complex phenomenon including variations at different developmental stages that comprise modifications in physiological and biochemical processes, gene expression and differences in the levels of metabolites and proteins. During the last decade, omics approaches have revolutionized how plant biologists explore stress-responsive mechanisms and pathways, driven by current scientific developments. However, investigations are still required to explore numerous features of temperature stress responses in plants to create a complete idea in the arena of stress signaling. Therefore, this review highlights the recent advances in the utilization of omics approaches to understand stress adaptation and tolerance mechanisms. Additionally, how to overcome persisting knowledge gaps. Shortly, the combination of integrated omics, genome editing, and speed breeding can revolutionize modern agricultural production to feed millions worldwide in order to accomplish the goal of "zero hunger."
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http://dx.doi.org/10.1080/07388551.2021.1898332DOI Listing
April 2021

Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet.

Sci Rep 2020 11 10;10(1):19473. Epub 2020 Nov 10.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India.

Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32-120 mg kg, Zn: 19-87 mg kg, PC: 8-16%), heritability (h ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, 'Late embryogenesis abundant protein', 'Myb domain', 'pentatricopeptide repeat', and 'iron ion binding' coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.
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http://dx.doi.org/10.1038/s41598-020-76230-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655845PMC
November 2020

Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement.

Funct Integr Genomics 2020 Nov 21;20(6):739-761. Epub 2020 Oct 21.

Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.

Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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http://dx.doi.org/10.1007/s10142-020-00756-7DOI Listing
November 2020

Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations.

Plant Cell Physiol 2020 Aug;61(8):1449-1463

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India.

The present study reports profiling of the elevated carbon dioxide (CO2) concentration responsive global transcriptome in chickpea, along with a combinatorial approach for exploring interlinks between physiological and transcriptional changes, important for the climate change scenario. Various physiological parameters were recorded in two chickpea cultivars (JG 11 and KAK 2) grown in open top chambers under ambient [380 parts per million (ppm)] and two stressed/elevated CO2 concentrations (550 and 700 ppm), at different stages of plant growth. The elevated CO2 concentrations altered shoot and root length, nodulation (number of nodules), total chlorophyll content and nitrogen balance index, significantly. RNA-Seq from 12 tissues representing vegetative and reproductive growth stages of both cultivars under ambient and elevated CO2 concentrations identified 18,644 differentially expressed genes including 9,687 transcription factors (TF). The differential regulations in genes, gene networks and quantitative real-time polymerase chain reaction (qRT-PCR) -derived expression dynamics of stress-responsive TFs were observed in both cultivars studied. A total of 138 pathways, mainly involved in sugar/starch metabolism, chlorophyll and secondary metabolites biosynthesis, deciphered the crosstalk operating behind the responses of chickpea to elevated CO2 concentration.
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http://dx.doi.org/10.1093/pcp/pcaa077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7434580PMC
August 2020

An integrated research framework combining genomics, systems biology, physiology, modelling and breeding for legume improvement in response to elevated CO under climate change scenario.

Curr Plant Biol 2020 Jun;22:100149

Research Program- Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.

How unprecedented changes in climatic conditions will impact yield and productivity of some crops and their response to existing stresses, abiotic and biotic interactions is a key global concern. Climate change can also alter natural species' abundance and distribution or favor invasive species, which in turn can modify ecosystem dynamics and the provisioning of ecosystem services. Basic anatomical differences in C and C plants lead to their varied responses to climate variations. In plants having a C pathway of photosynthesis, increased atmospheric carbon dioxide (CO) positively regulates photosynthetic carbon (C) assimilation and depresses photorespiration. Legumes being C plants, they may be in a favorable position to increase biomass and yield through various strategies. This paper comprehensively presents recent progress made in the physiological and molecular attributes in plants with special emphasis on legumes under elevated CO conditions in a climate change scenario. A strategic research framework for future action integrating genomics, systems biology, physiology and crop modelling approaches to cope with changing climate is also discussed. Advances in sequencing and phenotyping methodologies make it possible to use vast genetic and genomic resources by deploying high resolution phenotyping coupled with high throughput multi-omics approaches for trait improvement. Integrated crop modelling studies focusing on farming systems design and management, prediction of climate impacts and disease forecasting may also help in planning adaptation. Hence, an integrated research framework combining genomics, plant molecular physiology, crop breeding, systems biology and integrated crop-soil-climate modelling will be very effective to cope with climate change.
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http://dx.doi.org/10.1016/j.cpb.2020.100149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233140PMC
June 2020

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.

Plant Biotechnol J 2019 05 1;17(5):914-931. Epub 2018 Dec 1.

Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India.

Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post-transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.
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http://dx.doi.org/10.1111/pbi.13026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472043PMC
May 2019

RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.).

PLoS One 2018 28;13(6):e0199774. Epub 2018 Jun 28.

Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.

Drought is the most important constraint that effects chickpea production globally. RNA-Seq has great potential to dissect the molecular mechanisms of tolerance to environmental stresses. Transcriptome profiles in roots and shoots of two contrasting Iranian kabuli chickpea genotypes (Bivanij and Hashem) were investigated under water-limited conditions at early flowering stage using RNA-Seq approach. A total of 4,572 differentially expressed genes (DEGs) were identified. Of these, 261 and 169 drought stress responsive genes were identified in the shoots and the roots, respectively, and 17 genes were common in the shoots and the roots. Gene Ontology (GO) analysis revealed several sub-categories related to the stress, including response to stress, defense response and response to stimulus in the tolerant genotype Bivanij as compared to the sensitive genotype Hashem under drought stress. In addition, several Transcription factors (TFs) were identified in major metabolic pathways such as, ABA, proline and flavonoid biosynthesis. Furthermore, a number of the DEGs were observed in "QTL-hotspot" regions which were reported earlier in chickpea. Drought tolerance dissection in the genotypes revealed that the genes and the pathways involved in shoots of Bivanij were the most important factor to make a difference between the genotypes for drought tolerance. The identified TFs in the experiment, particularly those which were up-regulated in shoots of Bivanij during drought stress, were potential candidates for enhancing tolerance to drought.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199774PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6023194PMC
December 2018

The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development.

Plant Cell Environ 2018 09 16;41(9):2209-2225. Epub 2018 May 16.

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.

Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 samples at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated.
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http://dx.doi.org/10.1111/pce.13210DOI Listing
September 2018

Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea.

Sci Rep 2018 03 19;8(1):4855. Epub 2018 Mar 19.

School of Science, The Pangenomics Group, RMIT University, Melbourne, Australia.

Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR, phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance.
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http://dx.doi.org/10.1038/s41598-018-23116-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859185PMC
March 2018

Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops.

Front Plant Sci 2017 25;8:488. Epub 2017 Apr 25.

Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India.

Biotic stress in legume crops is one of the major threats to crop yield and productivity. Being sessile organisms, plants have evolved a myriad of mechanisms to combat different stresses imposed on them. One such mechanism, deciphered in the last decade, is small RNA (sRNA) mediated defense in plants. Small RNAs (sRNAs) have emerged as one of the major players in gene expression regulation in plants during developmental stages and under stress conditions. They are known to act both at transcriptional and post-transcriptional levels. Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDR) constitute the major components of sRNA biogenesis machinery and are known to play a significant role in combating biotic and abiotic stresses. This study is, therefore, focused on identification and characterization of sRNA biogenesis proteins in three important legume crops, namely chickpea, pigeonpea, and groundnut. Phylogenetic analysis of these proteins between legume species classified them into distinct clades and suggests the evolutionary conservation of these genes across the members of Papillionidoids subfamily. Variable expression of sRNA biogenesis genes in response to the biotic stresses among the three legumes indicate the possible existence of specialized regulatory mechanisms in different legumes. This is the first ever study to understand the role of sRNA biogenesis genes in response to pathogen attacks in the studied legumes.
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http://dx.doi.org/10.3389/fpls.2017.00488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404147PMC
April 2017

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects.

Front Plant Sci 2016 2;7:455. Epub 2016 May 2.

International Crops Research Institute for the Semi-Arid TropicsHyderabad, India; The University of Western AustraliaCrawley, WA, Australia.

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.
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http://dx.doi.org/10.3389/fpls.2016.00455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852475PMC
May 2016

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea.

Plant Biotechnol J 2016 07 23;14(7):1563-77. Epub 2016 Jan 23.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.

APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea.
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http://dx.doi.org/10.1111/pbi.12520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066796PMC
July 2016

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.

Sci Rep 2016 Jan 13;6:19228. Epub 2016 Jan 13.

Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.

Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
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http://dx.doi.org/10.1038/srep19228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725360PMC
January 2016

Gene Expression and Yeast Two-Hybrid Studies of 1R-MYB Transcription Factor Mediating Drought Stress Response in Chickpea (Cicer arietinum L.).

Front Plant Sci 2015 24;6:1117. Epub 2015 Dec 24.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia.

Drought stress has been one of the serious constraints affecting chickpea productivity to a great extent. Genomics-assisted breeding has a potential to accelerate breeding precisely and efficiently. In order to do so, understanding the molecular mechanisms for drought tolerance and identification of candidate genes are crucial. Transcription factors (TFs) have important roles in the regulation of plant stress related genes. In this context, quantitative real time-PCR (qRT-PCR) was used to study the differential gene expression of selected TFs, identified from large-scale expressed sequence tags (ESTs) analysis, in contrasting drought responsive genotypes. Root tissues of ICC 4958 (tolerant), ICC 1882 (sensitive), JG 11 (elite), and JG 11+ (introgression line) were used for the study. Subsequently, a candidate single repeat MYB (1R-MYB) transcript that was remarkably induced in the drought tolerant genotypes under drought stress was cloned (coding sequence region for the 1R-MYB protein) and subjected to yeast two-hybrid (Y2H) analysis. The screening of a root cDNA library with Y2H using the 1R-MYB bait protein, identified three CDS encoding peptides namely, galactinol-sucrose galactosyltransferase 2, CBL (Calcineurin B-like)-interacting serine/threonine-protein kinase 25, and ABA responsive 17-like, which were confirmed by co-transformation in yeast. These findings provide preliminary insights into the ability of this 1R-MYB transcription factor to co-regulate drought tolerance mechanism in chickpea.
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http://dx.doi.org/10.3389/fpls.2015.01117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689849PMC
January 2016

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement.

Front Plant Sci 2015 24;6:1116. Epub 2015 Dec 24.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia.

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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http://dx.doi.org/10.3389/fpls.2015.01116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689856PMC
January 2016

Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.).

Sci Rep 2015 Oct 19;5:15296. Epub 2015 Oct 19.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.

A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot_a" (15 genes) and "QTL-hotspot_b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.
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http://dx.doi.org/10.1038/srep15296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609953PMC
October 2015

High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea.

Plant Sci 2015 Jun 9;235:46-57. Epub 2015 Mar 9.

Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA. Electronic address:

Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.
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http://dx.doi.org/10.1016/j.plantsci.2015.03.002DOI Listing
June 2015

The extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum Streptomyces sp. in chickpea.

Springerplus 2015 23;4:31. Epub 2015 Jan 23.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 Telangana India.

The physiological and molecular responses of five strains of Streptomyces sp. (CAI-17, CAI-68, CAI-78, KAI-26 and KAI-27), with their proven potential for charcoal rot disease control in sorghum and plant growth-promotion (PGP) in sorghum and rice, were studied to understand the mechanisms causing the beneficial effects. In this investigation, those five strains were evaluated for their PGP capabilities in chickpea in the 2012-13 and 2013-14 post-rainy seasons. All of the Streptomyces sp. strains exhibited enhanced nodule number, nodule weight, root weight and shoot weight at 30 days after sowing (DAS) and pod number, pod weight, leaf area, leaf weight and stem weight at 60 DAS in both seasons over the un-inoculated control. At crop maturity, the Streptomyces strains had enhanced stover yield, grain yield, total dry matter and seed number plant(-1) in both seasons over the un-inoculated control. In the rhizosphere, the Streptomyces sp. also significantly enhanced microbial biomass carbon, dehydrogenase activity, total nitrogen, available phosphorous and organic carbon in both seasons over the un-inoculated control. Of the five strains of Streptomyces sp., CAI-17, CAI-68 and CAI-78 were superior to KAI-26 and KAI-27 in terms of their effects on root and shoot development, nodule formation and crop productivity. Scanning electron microscopy (SEM) micrographs had revealed the success in colonization of the chickpea roots by all five strains. Quantitative real-time PCR (qRT-PCR) analysis of selected PGP genes of actinomycetes revealed the selective up-regulation of indole-3-acetic acid (IAA)-related and siderophore-related genes by CAI-68 and of β-1,3-glucanase genes by KAI-26.
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http://dx.doi.org/10.1186/s40064-015-0811-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310830PMC
February 2015

Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.).

Theor Appl Genet 2014 Dec 21;127(12):2663-78. Epub 2014 Oct 21.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Hyderabad, India.

Key Message: We report a likely candidate gene, CcTFL1, for determinacy in pigeonpea through candidate gene sequencing analysis, mapping, QTL analysis together with comparative genomics and expression profiling. Pigeonpea (Cajanus cajan) is the sixth most important legume crop grown on ~5 million hectares globally. Determinacy is an agronomically important trait selected during pigeonpea domestication. In the present study, seven genes related to determinacy/flowering pattern in pigeonpea were isolated through a comparative genomics approach. Single nucleotide polymorphism (SNP) analysis of these candidate genes on 142 pigeonpea lines found a strong association of SNPs with the determinacy trait for three of the genes. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a likely candidate for determinacy in pigeonpea since it explained 45-96 % of phenotypic variation for determinacy, 45 % for flowering time and 77 % for plant height. Comparative genomics analysis of CcTFL1 with the soybean (Glycine max) and common bean (Phaseolus vulgaris) genomes at the micro-syntenic level further enhanced our confidence in CcTFL1 as a likely candidate gene. These findings have been validated by expression analysis that showed down regulation of CcTFL1 in a determinate line in comparison to an indeterminate line. Gene-based markers developed in the present study will allow faster manipulation of the determinacy trait in future breeding programs of pigeonpea and will also help in the development of markers for these traits in other related legume species.
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http://dx.doi.org/10.1007/s00122-014-2406-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236620PMC
December 2014

Genomics-assisted breeding for drought tolerance in chickpea.

Funct Plant Biol 2014 Oct;41(11):1178-1190

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.

Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.
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http://dx.doi.org/10.1071/FP13318DOI Listing
October 2014

Genome-based analysis of the transcriptome from mature chickpea root nodules.

Front Plant Sci 2014 11;5:325. Epub 2014 Jul 11.

Institute for Molecular BioSciences, Goethe University Frankfurt am Main Frankfurt am Main, Germany ; GenXPro GmbH, Frankfurt Biotechnology Innovation Center (FIZ) Frankfurt am Main, Germany.

Symbiotic nitrogen fixation (SNF) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. A successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. Although some of these processes are well understood today many of the molecular mechanisms underlying SNF, especially in chickpea, remain unclear. Here, we reannotated our previously published transcriptome data generated by deepSuperSAGE (Serial Analysis of Gene Expression) to the recently published draft genome of chickpea to assess the root- and nodule-specific transcriptomes of the eukaryotic host cells. The identified gene expression patterns comprise up to 71 significantly differentially expressed genes and the expression of twenty of these was validated by quantitative real-time PCR with the tissues from five independent biological replicates. Many of the differentially expressed transcripts were found to encode proteins implicated in sugar metabolism, antioxidant defense as well as biotic and abiotic stress responses of the host cells, and some of them were already known to contribute to SNF in other legumes. The differentially expressed genes identified in this study represent candidates that can be used for further characterization of the complex molecular mechanisms underlying SNF in chickpea.
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http://dx.doi.org/10.3389/fpls.2014.00325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4093793PMC
July 2014

Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.

PLoS One 2014 23;9(1):e86039. Epub 2014 Jan 23.

Research Program on Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India ; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, Mexico DF, Mexico.

A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086039PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900451PMC
November 2014

Functional genomics to study stress responses in crop legumes: progress and prospects.

Funct Plant Biol 2013 Dec;40(12):1221-1233

International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India.

Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.
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http://dx.doi.org/10.1071/FP13191DOI Listing
December 2013

Legume biology: the basis for crop improvement.

Funct Plant Biol 2013 Dec;40(12):v-viii

Legumes represent the most valued food sources in agriculture after cereals. Despite the advances made in breeding food legumes, there is a need to develop and further improve legume productivity to meet increasing food demand worldwide. Several biotic and abiotic stresses affect legume crop productivity throughout the world. The study of legume genetics, genomics and biology are all important in order to understand the limitations of yield of legume crops and to support our legume breeding programs. With the advent of huge genomic resources and modern technologies, legume research can be directed towards precise understanding of the target genes responsible for controlling important traits for yield potential, and for resistance to abiotic and biotic stresses. Programmed and systematic research will lead to developing high yielding, stress tolerant and early maturing varieties. This issue of Functional Plant Biology is dedicated to 'Legume Biology' research covering part of the work presented at VI International Conference on Legume Genetics and Genomics held at Hyderabad, India, in 2012. The 13 contributions cover recent advances in legume research in the context of plant architecture and trait mapping, functional genomics, biotic stress and abiotic stress.
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http://dx.doi.org/10.1071/FPv40n12_FODOI Listing
December 2013

A putative candidate for the recessive gall midge resistance gene gm3 in rice identified and validated.

Theor Appl Genet 2014 Jan 22;127(1):113-24. Epub 2013 Oct 22.

Directorate of Rice Research, Rajendranagar, Hyderabad, 500030, Andhra Pradesh, India.

Key Message: We report here tagging and fine-mapping of gm3 gene, development of a functional marker for it and its use in marker-assisted selection. The recessive rice gall midge resistance gene, gm3 identified in the rice breeding line RP2068-18-3-5 confers resistance against five of the seven Indian biotypes of the Asian rice gall midge Orseolia oryzae. We report here tagging and fine-mapping of gm3 gene, development of a functional marker for it and demonstrated its use in marker-assisted selection (MAS). A mapping population consisting of 302 F10 recombinant inbred lines derived from the cross TN1 (susceptible)/RP2068-18-3-5, was screened against gall midge biotype 4 (GMB4) and analyzed with a set of 89 polymorphic SSR markers distributed uniformly across the rice genome. Two SSR markers, RM17480 and gm3SSR4, located on chromosome 4L displayed high degree of co-segregation with the trait phenotype and flanked the gene. In silico analysis of the genomic region spanning these two markers contained 62 putatively expressed genes, including a gene encoding an NB-ARC (NBS-LRR) domain containing protein. A fragment of this gene was amplified with the designed marker, NBcloning 0.9 Kb from the two susceptible TN1, Improved Samba Mahsuri (B95-1) and two resistant cultivars, RP 2068-18-3-5 and Phalguna (with Gm2 gene). The amplicons were observed to be polymorphic between the susceptible and resistant genotypes and hence were cloned and sequenced. A new primer, gm3del3, which was designed based on sequence polymorphism, amplified fragments with distinct size polymorphism among RP2068-18-3-5, Phalguna and TN1 and B95-1 and displayed no recombination in the entire mapping population. Expression of the candidate NB-ARC gene in the susceptible TN1 and the resistant RP2068-18-3-5 plants following infestation with GMB4 was analyzed, through real-time reverse transcription PCR. Results showed twofold enhanced expression in RP2068-18-3-5 plants, but not in TN1 plants, 120 h after infestation. Amino acid sequence and structure analysis of the proteins coded by different alleles of gm3 gene showed deletion of eight amino acids due to an early stop codon in RP2068-18-3-5 resulting in a change in the functional domain of the protein. The gm3del3 was used as a functional marker for introgression of gm3 gene into the genetic background of the elite bacterial blight resistant cultivar Improved Samba Mahsuri (B95-1) through MAS.
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http://dx.doi.org/10.1007/s00122-013-2205-7DOI Listing
January 2014

Evaluation of Streptomyces strains isolated from herbal vermicompost for their plant growth-promotion traits in rice.

Microbiol Res 2014 Jan 19;169(1):40-8. Epub 2013 Sep 19.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India. Electronic address:

Six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140, CAI-155 and KAI-180, isolated from six different herbal vermi-composts were characterized for in vitro plant growth-promoting (PGP) properties and further evaluated in the field for PGP activity in rice. Of the six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140 and CAI-155 produced siderophores; CAI-13, CAI-93, CAI-155 and KAI-180 produced chitinase; CAI-13, CAI-140, CAI-155 and KAI-180 produced lipase; CAI-13, CAI-93, CAI-155 and KAI-180 produced protease; and CAI-13, CAI-85, CAI-140 and CAI-155 produced ß-1-3-glucanase whereas all the six actinomycetes produced cellulase, hydrocyanic acid and indole acetic acid (IAA). The actinomycetes were able to grow in NaCl concentrations of up to 8%, at pH values between 7 and 11, temperatures between 20 and 40 °C and compatible with fungicide bavistin at field application levels. In the rice field, the actinomycetes significantly enhanced tiller numbers, panicle numbers, filled grain numbers and weight, stover yield, grain yield, total dry matter, root length, volume and dry weight over the un-inoculated control. In the rhizosphere, the actinomycetes also significantly enhanced total nitrogen, available phosphorous, % organic carbon, microbial biomass carbon and nitrogen and dehydrogenase activity over the un-inoculated control. Sequences of 16S rDNA gene of the actinomycetes matched with different Streptomyces species in BLAST analysis. Of the six actinomycetes, CAI-85 and CAI-93 were found superior over other actinomycetes in terms of PGP properties, root development and crop productivity. qRT-PCR analysis on selected plant growth promoting genes of actinomycetes revealed the up-regulation of IAA genes only in CAI-85 and CAI-93.
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http://dx.doi.org/10.1016/j.micres.2013.09.008DOI Listing
January 2014

Suppressive subtraction hybridization reveals that rice gall midge attack elicits plant-pathogen-like responses in rice.

Plant Physiol Biochem 2013 Feb 28;63:122-30. Epub 2012 Nov 28.

Directorate of Rice Research, Rajendranagar, Hyderabad 500030, Andhra Pradesh, India.

The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructive insect pest of rice (Oryza sativa L.). Till date, 11 gall midge resistance gene loci have been characterized in different rice varieties. To elucidate molecular basis of incompatible (hypersensitive response plus [HR+] type) and compatible rice-gall midge interactions, two suppressive subtraction hybridization cDNA libraries were constructed. These were enriched for differentially expressed transcripts after gall midge infestation in two rice varieties (resistant Suraksha and susceptible TN1). In total, 2784 ESTs were generated and sequenced from the two libraries, of which 1536 were from the resistant Suraksha and 1248 were from the susceptible TN1. Majority (80%) of the ESTs was non-redundant sequences with known functions and was classified into three principal gene ontology (GO) categories and 12 groups. Upregulation of NBS-LRR, Cytochrome P450, heat shock proteins, phenylalanine ammonia lyase and OsPR10α genes from the Suraksha library, as revealed by real-time PCR, indicated that R gene mediated, salicylic acid related defense pathway is likely to be involved in gall midge resistance. Present study suggested that resistance in Suraksha against gall midge is similar in nature to the resistance observed in plants against pathogens. However, in TN1, genes related to primary metabolism and redox were induced abundantly. Results suggested that genes encoding translationally controlled tumor protein and NAC domain proteins are likely to be involved in the gall midge susceptibility.
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http://dx.doi.org/10.1016/j.plaphy.2012.11.021DOI Listing
February 2013