Browsing by Author "Siddique, Kadambot H M"

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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.
A chickpea genetic variation map based on the sequencing of 3,366 genomes
(Springer Nature Publishing AG, 2021) Varshney, Rajeev K; Roorkiwal, Manish; Sun, Shuai; Bajaj, Prasad; Chitikineni, Annapurna; Thudi, Mahendar; Singh, Narendra P; Du, Xiao; Upadhyaya, Hari D; Khan, Aamir W; Wang, Yue; Garg, Vanika; Fan, Guangyi; Cowling, Wallace A; Crossa, José; Gentzbittel, Laurent; Voss-Fels, Kai Peter; Valluri, Vinod Kumar; Sinha, Pallavi; Singh, Vikas K; Ben, Cécile; Rathore, Abhishek; Punna, Ramu; Singh, Muneendra K; Tar'an, Bunyamin; Bharadwaj, Chellapilla; Yasin, Mohammad; Pithia, Motisagar S; Singh, Servejeet; Soren, Khela Ram; Kudapa, Himabindu; Jarquín, Diego; Cubry, Philippe; Hickey, Lee T; Dixit, Girish Prasad; Thuillet, Anne-Céline; Hamwieh, Aladdin; Kumar, Shiv; Deokar, Amit A; Chaturvedi, Sushil K; Francis, Aleena; Howard, Réka; Chattopadhyay, Debasis; Edwards, David; Lyons, Eric; Vigouroux, Yves; Hayes, Ben J; Wettberg, Eric von; Datta, Swapan K; Yang, Huanming; Nguyen, Henry T; Wang, Jian; Siddique, Kadambot H M; Mohapatra, Trilochan; Bennetzen, Jeffrey L; Xu, Xun; Liu, Xin
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
Differential resilience of chickpea's reproductive organs to cold stress across developmental stages: insights into antioxidant strategies for enhanced fertility
(Frontiers Media S.A., 2025) Padhiar, Deeksha; Kaur, Sarbjeet; Jha, Uday Chand; Prasad, P. V. Vara; Sharma, Kamal Dev; Kumar, Sanjeev; Parida, Swarup Kumar; Siddique, Kadambot H M; Nayyar, Harsh
Chickpea is highly sensitive to cold stress during its reproductive stages, leading to significant reductions in potential pod formation due to decreased reproductive success. This study aimed to investigate the specific responses of anthers and ovules to cold stress, explore the role of oxidative stress and antioxidant mechanisms, and understand the relationship between oxidative stress and reproductive function to enhance our understanding of chickpea responses to cold stress. Chickpea seeds of contrasting genotypes—cold-tolerant (ICC 17258, ICC 16349) and cold-sensitive (ICC 15567, GPF 2)—were sown outdoors in early November under optimal conditions (25.5/15.4°C mean day/night temperatures). At 50 days after sowing, plants were subjected to 13/7°C cold stress (12 h light/dark in walk-in growth chambers. Cold stress significantly increased membrane damage and reduced cellular viability in anthers and ovules, particularly in cold-sensitive (CS) genotypes. Oxidative damage was more pronounced in anthers, particularly at anthesis (stage 2), as indicated by elevated malondialdehyde and hydrogen peroxide levels. Cold-tolerant (CT) genotypes exhibited increased antioxidant activity under stress, especially at pre-anthesis (stage 1), followed by declines at later stage, although responses varied by genotype. Anthers exhibited higher overall antioxidants activity than ovules, while ovules demonstrated notably high catalase activity. Among the antioxidants studied, ascorbate peroxidase and glutathione reductase were most prominent in the CT genotype, along with higher levels of ascorbate (AsA) and glutathione (GSH), highlighting the critical role of the AsA–GSH cycle in conferring cold tolerance to chickpea. Exogenous supplementation with 1 mM ascorbate (AsA) and glutathione (GSH) significantly stimulated pollen germination in cold-stressed plants under in vitro conditions, with a greater effect observed in CS genotypes. Furthermore, antioxidant activity strongly correlated with key reproductive traits such as pollen germination and ovule viability. This study revealed that the anthers and ovules exhibited distinct responses to cold stress, with significant genotypic differences across key reproductive stages. These insights provide a deeper understanding of cold tolerance mechanisms in chickpea and provide vital clues for breeding strategies to enhance resilience and reproductive success under cold stress.
Genotypic variability and trait associations for cold stress tolerance in cultivated chickpea (Cicer arietinum L.) during the reproductive stage
(PLOS, 2026) Padhiar, Deeksha; Kaur, Sarbjeet; Parida, Swarup K.; Jha, Uday C; Shama, Kamal Dev; Prasad, Pagadala Venkat Vara; Siddique, Kadambot H M; Nayyar, Harsh
Chickpea (Cicer arietinum L.), a major winter legume in northern South Asia and Australia, frequently encounters low temperatures (0–15 °C) during reproduction, causing substantial yield losses. The present study involved screening two independent sets of 100 genotypes over consecutive winters to identify sources of reproductive-stage cold tolerance and to elucidate the underlying mechanisms. Following outdoor establishment, plants were exposed to controlled cold stress (15/7 °C day/night) during flowering and pod development (15 d) in walk-in growth chambers. Ten representative cold-tolerant (CT) and ten cold-sensitive (CS) genotypes were selected each year based on integrated performance across yield, physiological, biochemical, and reproductive traits for a detailed mechanistic analysis. Cold-sensitive genotypes exhibited severe dysfunction, characterized by high electrolyte leakage (50−59% above CT) and malondialdehyde (39−51% above CT), indicating membrane damage. Reduced chlorophyll content (21−23%), photosystem II efficiency (23−29%), and stomatal conductance (40−43%) impaired photosynthesis. Inadequate cryoprotectants (reduced by 25−58%) and antioxidants (reduced by 38−55%) caused oxidative damage. Reproductive collapse followed, with pollen viability and germination declining by 24−46%, stigma receptivity and ovule viability decreasing by 41−68%, and seed yields falling by 85−95%. Cold-tolerant genotypes-maintained homeostasis through integrated protection in terms of superior membrane stability, enhanced compatible solutes, and elevated antioxidant activities, which sustained photosynthesis and reproductive success, achieving better yields under cold stress. Principal component analysis revealed cold tolerance as an integrated system (PC1:72.6–81.3% variance), clearly separating the CT from the CS genotypes. Membrane stability, photosynthetic efficiency, and pollen viability emerged as diagnostic traits (r = 0.85–0.91 with yield, p < 0.001; heritability 70−99%). Tolerance operated independently of maturity (R² = 0.10–0.18), enabling donor identification across maturity classes. Twenty cold-tolerant genotypes were identified, spanning the early, medium, and late maturity groups, respectively. These findings establish a mechanistic understanding of reproductive-stage cold tolerance, provide vital selection markers, and identify genetic resources for breeding cold-resilient chickpea cultivars.