Hima Kudapa

Hima Kudapa
International Crops Research Institute for Semi Arid Tropics | ICRISAT · Genetic Gains

PhD

About

118
Publications
25,039
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2,803
Citations
Citations since 2017
52 Research Items
2191 Citations
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20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500

Publications

Publications (118)
Article
Full-text available
Chickpea (Cicer arietinum L.) production is highly susceptible to heat stress (day/night temperatures above 32/20 °C). Identifying the molecular mechanisms and potential candidate genes underlying heat stress response is important for increasing chickpea productivity. Here, we used an RNA-seq approach to investigate the transcriptome dynamics of 48...
Article
Full-text available
Pearl millet ( Pennisetum glaucum L.), an important source of iron (Fe) and zinc (Zn) for millions of families in dryland tropics, helps in eradicating micronutrient malnutrition. The crop is rich in Fe and Zn, therefore, identification of the key genes operating the mineral pathways is an important step to accelerate the development of biofortifie...
Article
Full-text available
The ever-changing climate and the current COVID-19 pandemic compound the problems and seriously impact agriculture production, resulting in socio-economic insecurities and imposing health implications globally. Most of the poor and malnourished population in the developing countries depends on agriculture for food, income, and employment. Impact of...
Article
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Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In th...
Article
Full-text available
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of “QTL‐hotspot”, a genomic region controlling chickpea growth with positive consequences on crop production under drought. We re...
Article
Full-text available
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources ¹ . So far, few chickpea ( Cicer arietinum ) germplasm accessions have been characterized at the genome sequence level ² . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessio...
Article
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The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea ( Cicer arietinum ). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (...
Article
Full-text available
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 r...
Article
Full-text available
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 bio...
Article
Full-text available
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 i...
Article
Full-text available
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...
Preprint
Full-text available
Background: Chickpea, pigeonpea, and groundnut are the primary crop legumes 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...
Article
Full-text available
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...
Article
Full-text available
The present study reports profiling of the elevated CO2 concentration responsive global transcriptome in chickpea along with a combinatorial approach for exploring interlinks of physiological and transcriptional changes, important for the climate change scenario. Various physiological parameters were recorded from chickpea cultivars (JG 11 and KAK...
Article
Full-text available
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 p...
Data
Figure S1 Length distribution of unique small RNAs in twenty small RNA libraries. Figure S2 The 5′ nucleotide composition of identified miRNAs in chickpea and other species. Figure S3 Gene ontology enrichment of miRNA targets. Figure S4 Pathway annotation of targets using KEGG database. Figure S5 T‐plots and miRNA‐mRNA alignments validated by d...
Data
Table S1 Details of identified miRNAs (known and novel), their targets and annotation. Table S2 Statistics of degradome sequencing and splicing sites identified in each sample. Table S3 List of primers used for qRT‐PCR experiments.
Article
Full-text available
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 susceptib...
Article
Full-text available
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 conditi...
Data
Drought responsive genes in the shoot tissues. (XLS)
Data
Drought responsive genes encoding TFs in the root tissues. (XLS)
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Drought responsive genes encoding TFs in the shoot tissues. (XLS)
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Distribution of 20 top TF families identified in 4572 DEGs. (DOC)
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Drought responsive genes in the root tissues. (XLS)
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Stress-related annotations for differentially expressed genes between the genotypes under drought stress. The genes were also annotated for some important characteristics involved in various stresses. (DOC)
Data
Number of up and down-regulated genes for 12 comparative combinations of the samples. (DOC)
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DEGs in “QTL-hotspot” reported in Kale et al. 2015. (DOC)
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GO analysis of 4572 differentially expressed genes in the experiment. (DOC)
Data
Differentially expressed genes identified in the “QTL-hotspot_a” and “QTL-hotspot_b” in the present study. The genes corresponding to the present DEGs are indicated with the red arrows. (DOC)
Article
Full-text available
Chickpea is one of the world's largest cultivated food legume 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 a...
Article
Full-text available
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 I...
Article
Full-text available
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 m...
Data
Identification and characterization of domains and motifs, exon-intron structure of the identified DCL genes in (A) chickpea; (B) pigeonpea; and (C) groundnut (A. duranensis and A. ipaensis). In domain organization, roman numbers I, II, III, IV, V, and VI represent DEAD, Helicase-C, Dicer-dimer, PAZ, RNAase III, and dsrm domain, respectively.
Data
List of the cis-regulatory elements identified upstream of the AGO genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
Data
List of the cis-regulatory elements identified upstream of the RDR genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Identification of miRNAs targeting the AGO genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Identification of miRNAs targeting the RDR genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Identification and characterization of domains and motifs, exon-intron structure of the identified RDR genes in (A) chickpea; (B) pigeonpea; and (C) groundnut (A. duranensis and A. ipaensis).
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Interaction network of DCL, AGO, and RDR proteins in (A,B) chickpea; (C,D) pigeonpea; and (E,F) groundnut (A. duranensis and A. ipaensis). In (A,C,E), thicker lines suggest stronger associations while in (B,D,F) red colored nodes indicate genes involved in defense response.
Data
List of primers used for qRT-PCR studies in chickpea, pigeonpea, and groundnut.
Data
Identification of miRNAs targeting the DCL genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
Data
Identification and characterization of domains and motifs, exon-intron structure of the identified AGO genes in (A) chickpea; (B) pigeonpea; and (C) groundnut (A. duranensis and A. ipaensis).
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List of paralogs of the identified DCL, AGO, and RDR genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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List of orthologs of the identified DCL, AGO, and RDR genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis) in Medicago and soybean.
Data
List of the cis-regulatory elements identified upstream of the DCL genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Gene ontology annotation of the DCL genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Gene ontology annotation of the AGO genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
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Gene ontology annotation of the RDR genes in chickpea, pigeonpea, and groundnut (A. duranensis and A. ipaensis).
Data
Figure S1 Genome‐wide distribution of AP2/ERF and HSP90 genes in chickpea. A total of 128 AP2/ERF and three HSP90 genes were found to be anchored onto the pseudomolecules, while the remaining (19 AP2/ERF and two HSP90) genes were localized on the scaffolds. Clusters of tandemly duplicated genes are highlighted in green and those linked with lines r...
Data
Figure S7 Phylogenetic tree based on conserved domain sequence of AP2/ERF protein in Medicago. The unrooted tree was divided into 12 groups, ERF (marked in green), DREB (marked in red), AP2 (marked in blue), RAV (marked in pink) and soloist (marked in teak). Legends on the right represent the respective subfamily members. Only bootstrap values grea...
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Appendix S1 Experimental procedures, results and discussion.
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Figure S3 Genome‐wide distribution of AP2/ERF and HSP90 genes in Medicago.
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Figure S6 Pie chart representation of DREB (A1–A6) and ERF (B1–B6) genes in five legumes.
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Figure S11 Putative motif prediction in chickpea using MEME.
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Figure S2 Genome‐wide distribution of AP2/ERF and HSP90 genes in pigeonpea. A total of 93 AP2/ERF and three HSP90 genes were found to be anchored onto the pseudomolecules, while the remaining (83 AP2/ERF and four HSP90) genes were localized on the scaffolds. Clusters of tandemly duplicated genes are highlighted in green and those linked with lines...
Data
Figure S4 Genome‐wide distribution of AP2/ERF and HSP90 genes in common bean.
Data
Figure S8 Phylogenetic tree based on conserved domain sequence of AP2/ERF protein in common bean. The unrooted tree was divided into 12 groups, ERF (marked in green), DREB (marked in red), AP2 (marked in blue), RAV (marked in pink) and soloist (marked in teak). Legends on the right represent the respective subfamily members. Only bootstrap values g...
Data
Figure S12 Putative motif prediction in pigeonpea using MEME.
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Figure S16 Gene ontology assignment to the AP2/ERF sequences identified in the five legumes.
Data
Figure S5 Genome‐wide distribution of AP2/ERF and HSP90 genes in Lotus.
Data
Figure S9 Phylogenetic tree based on conserved domain sequence of AP2/ERF protein in Lotus. The unrooted tree was divided into 12 groups, ERF (marked in green), DREB (marked in red), AP2 (marked in blue), RAV (marked in pink) and soloist (marked in teak). Legends on the right represent the respective subfamily members. Only bootstrap values greater...
Data
Figure S10 Phylogenetic relationships, gene structures and motif composition of HSP90 genes in chickpea (Ca), pigeonpea (Cc), common bean (Pv), Medicago (Mt) and Lotus (Lj). (a) Phylogenetic tree constructed using MEGA 5.0 by neighbour‐joining (NJ) method with 1000 bootstrap replicates. Bootstrap support is indicated at each node. (b) Exon/intron s...
Data
Figure S13 Putative motif prediction in Medicago using MEME.
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Figure S14 Putative motif prediction in common bean using MEME.
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Figure S15 Putative motif prediction in Lotus using MEME.
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Table S1 Physio‐chemical and structural properties of the identified AP2/ERF members in chickpea. Table S2 Physio‐chemical and structural properties of the identified AP2/ERF members in pigeonpea. Table S3 Physio‐chemical and structural properties of the identified AP2/ERF members in Medicago. Table S4 Physio‐chemical and structural properties o...
Article
Full-text available
Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gain 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 sequencin...
Article
Full-text available
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 sequenci...
Article
Full-text available
The main objective of the present study was to isolate and characterize actinomycetes for their plant growth-promotion in chickpea. A total of 89 actinomycetes were screened for their antagonism against fungal pathogens of chickpea by dual culture and metabolite production assays. Four most promising actinomycetes were evaluated for their physiolog...
Article
Full-text available
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 com...