Indian Institute of Pulses Research

Plant architecture traits in crops are modulated through intricate interactions of various genetic pathways, which helps them to adapt to diverse environmental conditions. Key developmental pathways involved in forming plant architecture include the LAZY-TAC (Tiller Angle Control) module regulating branch and tiller angle, the CLAVATA-WUSCHEL pathway controlling shoot apical meristem fate and the GID1-DELLA pathway governing plant height and tillering in major food crops. These pathways function in concert to shape the overall architecture of plants, which is essential for optimizing light capture, resource allocation, reproductive success and eventual crop yield enhancement. Presently, plant architecture of modern crops has been shaped especially by artificial selection of natural alleles that target yield traits. Recent advances in CRISPR-Cas-based genome editing and genomics-assisted breeding strategies have enabled precise genetic manipulation of natural alleles in the functionally relevant genes regulating plant architecture traits in crops. This will assist researchers to select and introgress superior natural alleles in popular cultivars strategically for restructuring their desirable plant-types suitable for mechanical harvesting as well as enhancing the crop yield potential.

Chickpea, a vital legume crop, is highly susceptible to cold stress, especially during its reproductive phase, resulting in significant flower and pod abortions and reduced seed yield. Our previous study demonstrated that cold acclimation is effective in enhancing cold tolerance but benefits only cold-tolerant (CT) genotypes, while cold-sensitive (CS) genotypes remain unaffected. In this extended study aimed at probing the detailed mechanisms of this differential response, we further examined the expression profiles of enzymes involved in the synthesis and breakdown of osmolytes (pyrroline-5-carboxylate synthase, proline dehydrogenase (PDH), betaine aldehyde dehydrogenase) and sugars (sucrose synthase, acid invertase, trehalose-6-phosphate synthase, trehalose-6-phosphate phosphatase, and trehalase activity), along with the expression of various antioxidants (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase) in both CT and CS genotypes. Seeds of two contrasting chickpea genotypes, cold-tolerant ICC 17258 and cold-sensitive ICC 15567, were planted in pots during the first week of November in an outdoor field environment. After 40 days, the plants were transferred to walk-in growth chambers for cold acclimation at specific temperatures. Initially, the plants were exposed the plants to 25/18℃ (pre-acclimation stage; PAS) for 2 days, followed by a 21-day cold acclimation period with progressively decreasing temperatures over seven days for each cold acclimation stage (CAS): CAS1 (21/13℃), CAS2 (18/10℃), and CAS3 (15/8℃). Subsequently, the plants were subjected to cold stress at 13/7℃ for 15 days and then exposed to 30/23℃ (12 h day/night) until maturity. Our findings demonstrated that the expression of various enzymes involved in the synthesis of osmolytes and sugars in leaves, anthers, and ovules was significantly upregulated during the cold acclimation process in the CT chickpea genotypes but not in the CS genotypes. This enhanced metabolic activity, coupled with elevated levels of enzymatic antioxidants during the acclimation process, contributed to improved leaf water status, photosynthetic efficiency, and ultimately, superior reproductive performance (pollen germination, pollen viability, stigma receptivity, and ovule viability) under cold stress conditions compared to CS genotypes. The enhanced cold tolerance observed in the CT genotypes is likely attributable to their genetic predisposition and efficient stress defense mechanisms facilitated by the upregulated expression of cold-responsive enzymes.

Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.