Browsing by Author "Singh, Mohar"

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Assessing cold stress resilience in wild chickpea accessions using physiological, biochemical, and reproductive traits
(Springer Nature, 2025) Kaur, Sarbjeet; Padhiar, Deeksha; Singh, Mohar; Parida, Swarup K.; Jha, Uday C.; Sharma, Kamal Dev; Prasad, P. V. Vara; Siddique, Kadambot H. M.; Nayyar, Harsh
Domesticated chickpea (Cicer arietinum L.) exhibits high sensitivity to temperatures below 20/10 °C during its reproductive phase resulting in substantial loss of flowers, pods and crop yields. With the aim to add new sources of cold tolerance and elucidate mechanism of cold-tolerance in wild species of chickpea, the present study evaluated 36 wild accessions of three Cicer species (Cicer judaicum, Cicer pinnatifidum, Cicer reticulatum) at the reproductive stage for yield, and reproductive, physiological and biochemical traits under cold stress (15/7 °C) for two consecutive years. Cluster analysis based on yield-related traits such as pod number, seed weight, and total seed count categorized these accessions as cold-tolerant and cold-sensitive. Six C. judaicum accessions (ILWC 256, ICC 13852, ILWC 263, ILWC 20, ILWC 223, and ILWC 30) were tolerant to cold whereas the remaining ones were cold-sensitive. Under cold stress, cold-tolerant accessions exhibited lower impairment of physiological processes as compared to the cold-sensitive accessions e.g. lower tissue damage and electrolyte leakage, and higher chlorophyll content, carotenoid content, chlorophyll fluorescence, and leaf water content, thereby resulting in higher photosynthetic efficiency and carbohydrate accumulation in cold-tolerant accessions. At the biochemical level, the tolerant accessions demonstrated significantly higher amounts of cryoprotectants and enhanced activities of enzymatic and non-enzymatic antioxidants resulting in substantially lower levels of reactive oxygen species. Cold-tolerant accessions also accumulated more proline and trehalose compared to their sensitive counterparts. Slight disruptions in physiological processes, low oxidative stress and accumulation of cryoprotectants under cold stress were associated with higher pollen viability, pollen germination, pollen load, ovule receptivity, pod set, number of pods and seed yield in cold-tolerant accessions while opposite was true for cold-sensitive accessions. The wild chickpea accessions exhibiting high seed yield under cold stress are promising candidates for breeding programs aimed at cold tolerance.
Assessment of diversity in anti-nutrient profile, resistant starch, minerals and carbohydrate components in different ricebean (Vigna umbellata) accessions
(Elsevier B.V., 2023) Sharma, Paras; Goudar, Giridhar; Chandragiri, Anil Kumar; Ananthan, R; Subhash, K; Chauhan, Anitha; Longvah, T; Singh, Mohar; Bhardwaj, Rakesh; Parida, Swarup K.; Singh, Amit Kumar; Gayacharan; Chattopadhyay, Debasis
Ricebean accessions (n = 38) cultivated in India were evaluated for their comprehensive nutrient, anti-nutrients and mineral composition. Protein and total dietary fibre ranged between 23.23 and 27.33 and 12.27 to 16.69 g/100 g, respectively. Among the oligosaccharides, verbascose was not detected, however, raffinose and stachyose ranged between 47 and 186 and 117 to 5765 mg/100 g, respectively. Among the free sugars, sucrose was found dominating (up to 370 mg/100 g). Resistant starch (4.13 to 8.62 %), iron (3.49 to 7.46 mg/100 g), zinc (1.90 to 3.72 mg/100 g) and selenium (0.28 to 4.48 µg/100 g) varied significantly (p < 0.05) among ricebean samples. Phytic acid, saponin, trypsin inhibitor and oxalate analysed in ricebean accessions ranged between 303 and 760 mg/100 g, 19 to 46 mg/g, 309 to 1076 mg/100 g and 219 to 431 mg/100 g, respectively. Multivariate analysis using hierarchical clustering analysis (HCA), and principal component analysis (PCA) was employed to decipher the diversity of nutrients and anti-nutrients across the ricebean accessions. Based on HCA, dendrogram-1 (nutrients) and dendrogram-2 (minerals, anti-nutrients) were produced, having four clusters in each. In the dendrogram-1 and 2, the largest cluster had (n = 21) and (n = 15) accessions, respectively. The PCA analyse the uncorrelated set of variables (principal components) and it condenses a large set of data variables. Based on the eigenvalue >1, a total of eight PCs were formed contributing total variance of 78.8 %. The factor loading contribution in the PC1 and PC2 were from iron, fructose, glucose, raffinose and total dietary fibre, selenium (Se) and protein, respectively.
Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea
(Nature Publishing Group, 2015) Bajaj, Deepak; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66–85%) and broader natural allelic diversity (6–64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.
A high-resolution InDel (Insertion-Deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea
(Frontiers Media S.A., 2016) Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.
Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15–28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89–2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea.
An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea
(Oxford University Press, 2014) Saxena, Maneesha S.; Bajaj, Deepak; Das, Shouvik; Kujur, Alice; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.
The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6–39.8% R2 at 4.2–15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.
Interspecific hybridization using cicer microphyllum royle ex benth. for the genomic reconstruction of cultivated chickpea (Cicer arietinum L.)
(Springer Nature Publishing AG, 2026) Kumari, Pummi; Singh, Mohar; Gayacharan; Shivam; Parida, Swarup K.
Cicer microphyllum, native to cold and arid regions, offers a reservoir of beneficial alleles, including tolerance to biotic and abiotic stresses. It is a wild Cicer species from the tertiary gene pool of the cultivated chickpea. It has the potential to enhance the genetic base of cultivated species and provide useful genetic variability for crop improvement. Despite significant reproductive barriers, advancements in hybridization techniques and genomic tools have facilitated the development of viable hybrids between C. arietinum and C. microphyllum. The genomic reconstruction of the cultivated chickpea through the transfer of wild relative's genomic segments using backcrossing and molecular marker-assisted selection will help sustainable crop improvement and genetic gains.
mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea
(Oxford University Press, 2016) Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S.; Rana, Jai C.; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.
The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.
Multi-environment phenotyping of ricebean (Vigna umbellata (Thunb.) Ohwi & Ohashi) germplasm and identification of core set for accelerating the crop improvement programs
(Frontiers Media S.A., 2026) Gayacharan; Joshi, Dinesh C; Aravind, J; Wankhede, D P; Singh, Badal; Kumar, Prakash; Rajkumar, S; Parida, Swarup K; Semwal, D P; Sharma, Paras; Singh, Mohar; Chattopadhyay, Debasis; Singh, Kuldeep; Singh, G. P.; Singh, Amit Kumar
Ricebean (Vigna umbellata) is a nutrient-rich rich underutilised legume crop. It is primarily grown in the uplands of India, Nepal and China. Despite its adaptation to a wide range of agroclimatic zones and resistance to various biotic and abiotic stresses, ricebean crop improvement efforts have been slow mainly because of the low levels of genetic diversity utilised in ricebean breeding. This study presents the first multi-environment phenotyping and core collection building in ricebean with 1,589 accessions maintained at the Indian National Gene Bank. The accessions were assessed in two diverse agro-ecological regions (New Delhi and Almora), indicating significant phenotypic variations for important economic traits such as days to flowering, pod length, number of seeds per pod, and seed weight. The core subsets were sampled using MStrat, PowerCore and PCSS, and CoreHunter algorithms. The sampled coresets were evaluated using diversity indices such as genetic distance, mean difference percentage (MD%), variance difference percentage (VD%), coincidence rate (CR) and variable rate of coefficient of variation. The E-EN100 approach of CoreHunter yielded the most effective representation, resulting in a final core set with 251 accessions (14.3% from the entire collection). Diversity indices, clustering methods, QQ-plots, and distributional comparisons confirmed the representativeness of the core set. Multi-environment GGE biplot analysis identified stable and high-performing accessions for early flowering, synchronous maturity, pod and seed traits, including promising genotypes such as IC351508 and IC352944 with determinate growth habit and high yield potential. The study provides a manageable subset of the entire collection, which may play a significant role in trait discovery and ricebean cultivar development.
Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea
(PLOS, 2014) Saxena, Maneesha S.; Bajaj, Deepak; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.
Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.
The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement
(John Wiley & Sons, 2023) Francis, Aleena; Singh, Nagendra Pratap; Singh, Mohar; Sharma, Paras; Gayacharan; Kumar, Durgesh; Basu, Udita; Bajaj, Deepak; Varshney, Nidhi; Joshi, Dinesh Chandra; Semwal, Dinesh Prasad; Tyagi, Vandana; Wankhede, Dhammaprakash; Bharadwaj, Rakesh; Singh, Amit Kumar; Parida, Swarup K.; Chattopadhyay, Debasis
Ricebean [Vigna umbellata (Thunb.) Ohwi and Ohashi] (2n = 2x = 22) is a warm-season dietary pulse legume crop and was originated in the Indo-China region. It is known to provide food security to the small and marginal farmers of South and South-East Asia. Ricebean is well known for its high nutritional quality and resistance to bacterial leaf spot, Mungbean yellow mosaic virus and bruchid, which are devastating for the other Vigna family crops (Dhaliwal et al., 2022). We report a reference grade de novo genome assembly, which is anchored to the genetic linkage groups and covered almost the whole estimated genome length of ricebean and so far, the largest among the sequenced Vigna species.
Transcriptome analysis reveals key pathways and candidate genes controlling seed development and size in ricebean (Vigna umbellata)
(Frontiers Media S.A., 2022) Verma, Sachin Kumar; Mittal, Shikha; Gayacharan; Wankhede, Dhammaprakash Pandhari; Parida, Swarup K.; Chattopadhyay, Debasis; Prasad, Geeta; Mishra, Dwijesh Chandra; Joshi, Dinesh Chandra; Singh, Mohar; Singh, Kuldeep; Singh, Amit Kumar
Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development-related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development-related traits in ricebeans. A total of 51 genes encoding SCF TIR1/AFB , Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean-derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.
Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea
(Nature Publishing Group, 2016) Srivastava, Rishi; Bajaj, Deepak; Malik, Ayushi; Singh, Mohar; Parida, Swarup K.
The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement.
Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)
(BioMed Central Ltd, 2024) Sahu, Tanmaya Kumar; Verma, Sachin Kumar; Gayacharan; Singh, Nagendra Pratap; Joshi, Dinesh Chandra; Wankhede, D. P.; Singh, Mohar; Bhardwaj, Rakesh; Singh, Badal; Parida, Swarup K.; Chattopadhyay, Debasis; Singh, Gyanendra Pratap; Singh, Amit Kumar
Background: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. Results: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo–keto-reductase with flowering and maturity were revealed. Conclusion: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.