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Item Genome-wide association analysis using multi model approach identified novel associations for plant architectural traits in chickpea germplasm collection(Springer Nature Publishing AG, 2026) Raiya, Rahul; Yadav, Hemant Kumar; Kumar, Kuldeep; Prakash, Nitish Ranjan; Parida, Swarup K.; Bharadwaj, Chellapilla; Hegde, Venkatraman; Tripathi, ShaileshCrop plant architecture dictates plant performance under different ecological conditions and is responsible for its establishment, development, and morphology. It plays an important role in plant breeding for yield optimization, regulating photosynthetic rate and efficiency, utilization of resources, occurrence of pests and diseases, effective mechanical harvesting, space optimization, and improving the quality of plant produce. The subtle changes in the plant’s architecture could help the plant adapt to different ecological niches and are very important, keeping in view the challenges posed due to climate change. A set of 280 diverse genotypes, which included the core collection of chickpea was evaluated during the rabi season of 2021 and 2022. A total of 10 plant architecture related traits, including plant height, first pod height, canopy width, inter-nodal length, and days to flowering were studied and significant variability was observed as per the analysis of variance (ANOVA) and phenotypic descriptors. Diversity based on π and θ estimates suggests the presence of substantial diversity, while Tajima’s D reflects balancing selection due to the abundance of shared alleles. Significant marker trait associations (MTAs) for traits like plant height (PH), first pod height (FDPH) and days to flowering were observed using trait based or BLUP estimates. In total, 97 and 51 MTAs were identified using trait based and BLUP based on multi model GWAS analysis, respectively. Among these 17 were consistent MTAs being present either across the year or were identified using more than one GWAS model. Likewise, 9 consistent MTAs were identified using the BLUP estimates. Interestingly, two genomic regions present on chromosome 5 and 7 were found to harbor multiple MTAs for PH and FPDH. The linkage disequilibrium (LD) block analysis reflects the prevalence of multiple LD blocks in these regions. The allelic effects of the MTAs reflect their additive nature in determining the phenotype. Overall, the MTAs identified in the current study are highly useful for the chickpea breeder in modulating the plant architecture, mainly PH and FPDH.Item ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality in chickpea(American Society of Plant Biologists, 2019) Basu, Udita; Upadhyaya, Hari D.; Srivastava, Rishi; Daware, Anurag; Malik, Naveen; Sharma, Akash; Bajaj, Deepak; Narnoliya, Laxmi; Thakro, Virevol; Kujur, Alice; Tripathi, Shailesh; Bharadwaj, Chellapilla; Hegde, V. S.; Pandey, Ajay K.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancing the seed yield, quality and productivity in chickpea. The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulating the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity and multiple desirable plant architecture and seed-quality traits without compromising the agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea.Item Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea(John Wiley & Sons, 2019) Basu, Udita; Bajaj, Deepak; Sharma, Akash; Malik, Naveen; Daware, Anurag; Narnoliya, Laxmi; Thakro, Virevol; Upadhyaya, Hari D.; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, QTL mapping and expression profiling. This identified 16 potential SNP loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association as well as in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding protein-coding gene and its interacting gene, Timing of CAB Expression 1, which appear to be most-promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.Item Genetic dissection of plant growth habit in chickpea(Springer, 2017) Upadhyaya, Hari D.; Bajaj, Deepak; Srivastava, Rishi; Daware, Anurag; Basu, Udita; Tripathi, Shailesh; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.