Publications of NIPGR Scientists

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Subject: search.filters.subject.Ascochyta blight

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    Comparative genomic analysis of GARP transcription factor family in legumes and identification of stress-responsive candidate genes
    (Springer Nature Publishing AG, 2023) Singh, Ritu; Pandey, Ashutosh; Verma, Praveen K.
    The GARP transcription factors have been identified for multiple biological functions throughout the life cycle of a plant. Despite of its involvement in crucial functions, systematic study of GARPs remains obscure in plants. In this study, we explored the genomic, molecular, and evolutionary perspectives of the GARP gene family in the three major leguminous plants, namely chickpea (Cicer arietinum), soybean (Glycine max), and barrel clover (Medicago truncatula). Here, we identified 53, 56, and 107 GARP genes in Cicer, Medicago, and Glycine, respectively. They were classified into four clades and two sub-clades as per phylogenetic analysis, and the result was supported by consensus motifs, domain organization, and exon–intron structures. Detailed comparative analysis indicates conservation of the GARP gene family in plants. Identification of paralogous and orthologous gene pairs revealed that the expansion of this family occurs mainly through genome duplication in legumes. Additionally, the three-dimensional structure and functional enrichment analysis indicated their major role in signaling, growth, development, and stress processes. The chickpea GARP genes were also characterized for their transcript modulation in diverse plant organs and during pathogenic stress. Differential regulation of 24 CaGARP genes was observed during Ascochyta Blight (AB) stress. Characterization of AB-responsive genes reveals an over-representation of stress and hormone-binding elements on the promoter of CaGARPs. Additionally, interactome analysis also confirms the role of GARPs in plant stress and development. Our findings not only provide a handful of stress-responsive genes but also lay the foundation for prospective functional studies of GARPs in legumes.
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    Breeding and genomics interventions for developing ascochyta blight resistant grain legumes
    (MDPI AG, 2022) Jha, Uday C; Sharma, Kamal Dev; Nayyar, Harsh; Parida, Swarup K.; Siddique, Kadambot H M
    Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.
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    mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in ascochyta blight resistance of chickpea
    (John Wiley & Sons, 2018) Kumar, K; Purayannur, S; Kaladhar, VC; Parida, Swarup K.; Verma, Praveen K.
    Ascochyta blight (AB) caused by the fungal pathogen Ascochyta rabiei is a serious foliar disease of the legume crop chickpea (Cicer arietinum L.). Despite many genetic studies on chickpea-Ascochyta interaction, genome-wide scan of chickpea for the identification of AB associated QTLs and their gene(s) has not been accomplished. To elucidate narrow QTLs for AB resistance, here we report the use of multiple QTL-sequencing (mQTL-seq) approach on two sets of extreme AB phenotype bulks derived from Cicer intraspecific and interspecific crosses. Two major QTLs qABR4.1 and qABR4.2, and a minor QTL qABR4.3 were identified on assembled pseudomolecule 4 (Ca4). We narrowed qABR4.1 to a ‘robust ~50 kb region’ through mapping on a larger intraspecific RIL population and comparative analysis. Among four genes, the CaAHL18 gene showed higher expression under Ascochyta stress in AB resistant parent suggesting that it is the candidate gene under ‘robust qABR4.1’. Dual-luciferase assay with CaAHL18 polymorphic cis-regulatory sequences showed that higher expression is associated with an allelic variation. Thus, our findings on chickpea-Ascochyta interaction have narrowed down AB resistance associated QTLs on chickpea physical map and identified a novel QTL qABR4.3. The narrowed QTL and gene associated markers will help in biotechnological and breeding programs for chickpea improvement.