Thrust Areas

Significant Achievements

• Agronomic evaluation of putative edited chickpea plants for Efl1 gene suggests induction of early flowering in selected plants. Molecular characterization of the progenies derived indicated mutation in the target locus.
• Bioinformatics analysis of the Ln and Sfl loci in chickpea genome to understand the structural components and allelic variation in the locus encoding number of seeds per pod (Ln) and double podding (Sfl) in chickpea germplasm is ongoing. Guide RNA specific for Sfl gene and pegRNA for Ln locus have been designed
• Evaluation of E1 seeds from independent E0 pigeonpea plants (dual guide specific to DEP1) are raised in Plant Biosafety Level 1 (PBSL1) Containment Facility. PCR analysis of 112 germinated plants resulted in identification of 29 plants (positive for the presence of Cas9 gene and cassette). Additionally, 21 primary regenerants (particle bombardment of DEP1 construct) were established in Containment facility.
• Genome editing of CaPDS gene indicated targeted mutation of PDS with shortened and pale phenotype in the regenerants
• T1 seeds ( 28 plants) were germinated from 16 T0 grasspea plants in Plant Biosafety Level 1 (PBSL1) Containment Facility and their molecular analysis is in progress. Post assessment of designed dualgRNA for LsBOS by in vitro cleavage, same is being used for genetic transformation.
• Identified gamma irradiated 76 M3 seeds and 8 electron beam irradiated M4 seeds with low ODAP content in the range of 0.01% to 0.03%.
• Genome wide identification and characterization of NHX gene family in vigna mungo was performed, and from the expression analysis, we identified five candidate Vm_NHX genes, four of which, i.e. Vm_NHX16, Vm_NHX17, Vm_NHX29 and Vm_NHX33, were localized to the vacuolar and lysosomal membrane.
• Thirty-three InDel primers spanning the chickpea QTL hotspot region (9.5-15 Mb) were designed based on in-silico polymorphisms observed from whole genome re-sequencing data of the contrasting phenotypes of ICC4958, JG16, C235, CSG8962, Dig Vijay, HC5, ICCV96030, GNG1581, JAKI9218, and DCP92-3 and validated between the chickpea drought-tolerant QTL donor (ICC4958) and recurrent genotypes for effective differentiation, thus demonstrating their potential for use in marker-assisted breeding.
• The loss of SFL (Single flower locus) governs the double-flower per node(dfpn) trait in chickpea. Most Indian chickpea cultivars with the dfpn trait are governed by the presence of a 44 kb deletion, as observed in JG62, which is used as a parental line for these cultivars. However, germplasm accessions such as ICC 14340, ICC 10919, ICC 15939, and the cultivar IPC 08-69 possess a 44 kb insertion with a missense mutation in the SFL gene, which causes the double-flower trait.
• The major QTL (qSSI_YP6.1) for salt tolerance in chickpea was fine mapped to a narrow region on chromosome 6 using QTL spanning polymorphic InDel primers between DCP92-3 and ICCV10. The QTL (qSSI_YP6.1) influences yield per plant under salt stress, with an LOD score of 4.38 and an R² value of 20.8%. These results suggest that this QTL could be applied in marker-assisted breeding, with the QTL-flanking InDel primers.
• In effort to understand the influence of codon usage bias on expression status of Short vegetative Phase (SVP) genes, 27 optimal codons were identified, the majority of which tend to end with A/T, with AGA and GTT being the most commonly used optimal codons across eleven grain legumes. The Cool season legumes and Warm season legumes differed from each other in the usage of only one optimal codon encoding for lysine. This is the first study revealing the comprehensive analysis of codon usage bias in legumes and can be used for codon optimization for heterologous expression in legumes
• Developed a fusion protein combining chickpea GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) and its modified version (with altered miRNA binding site) that is sub-cloned it in plant binary vector, pCAMBIA2300
• Identified a 1-bp substitution (non-synonymous mutation) in conserved EAR motif in CaLn (homolog of soybean Ln locus controlling number of seeds per pod and leaflet shape) specific to the wild allele (in C . cuneatumProduced Nucleus seed production of the newly developed drought tolerance MABC variety IPCL4-14 at IIPR, Kanpur and RS, Bikaner. Seeds were also given to NSC, Kanpur for multiplication.
• Identified a megaplasmid having several cry genes and a solitary VIP gene and a novel plasmid measuring 69,124 base pairs in length containing genes that are believed to be associated with virulence, ability to degrade heavy metals and resistance to antibiotics has also been identified from the novel Bt strains isolated from legume rhizospere
• Generated whole genome sequence of two Fusarium udum isolates (F16 and F17) revealing both assemblies to have 99.6% completeness and indicating the isolate’s belong to the order Hypocreales.
• Submitted eight transcriptome sequences to NCBI for blackgram-YMD infestation.
• Submitted whole genome sequences of two blackgram varieties (tolerant to YMD and tolerant to Powdery mildew) and one germplasm (tolerant to bruchids) to NCBI
• Developed cleaved amplified polymorphic sequence (CAPS) and INDEL markers based on Single nucleotide polymorphism (SNPs) identified in vegetative and reproductive QTL region for salinity stress in chickpea.
• Identified of 31,644,821 bi-allelic SNPs and 6,601,383 InDels from whole genome re-sequencing data of 195 chickpea genotypes belonging to 7 wild species
• Developed a high throughput, cost effective, reproducible and short duration hydroponics based phenotyping system that has been tested for three consecutive seasons on urdbean for salinity tolerance and found to be working well as per the requirements.
• Optimized cost effective, single seed chipping method in grasspea for testing the seeds for ODAP estimation before planting them in the field.

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