Summary: Cytokinin group of phytohormones regulate root elongation and branching during post‐embryonic development. Cytokinin‐degrading enzymes cytokinin oxidases/dehydrogenases (CKXs) have been deployed to investigate biological activities of cytokinin and to engineer root growth. We expressed chickpea cytokinin oxidase 6 (CaCKX6) under the control of a chickpea root‐specific promoter of CaWRKY31 in Arabidopsis thaliana and chickpea having determinate and indeterminate growth patterns, respectively, to study the effect of cytokinin depletion on root growth and drought tolerance. Root‐specific expression of CaCKX6 led to a significant increase in lateral root number and root biomass in Arabidopsis and chickpea without any penalty to vegetative and reproductive growth of shoot. Transgenic chickpea lines showed increased CKX activity in root. Soil‐grown advanced chickpea transgenic lines exhibited higher root‐to‐shoot biomass ratio and enhanced long‐term drought tolerance. These chickpea lines were not compromised in root nodulation and nitrogen fixation. The seed yield in some lines was up to 25% higher with no penalty in protein content. Transgenic chickpea seeds possessed higher levels of zinc, iron, potassium and copper. Our results demonstrated the potential of cytokinin level manipulation in increasing lateral root number and root biomass for agronomic trait improvement in an edible legume crop with indeterminate growth habit.

Yellow mosaic disease (YMD) caused by several begomoviruses is one of the major constraints of over a dozen leguminous crops worldwide, particularly in Asian and Southeast Asian countries. The present study aimed to investigate the distribution, diversity and prevalence of begomoviruses associated with YMD in leguminous hosts in five agro-climatic zones of India, to assess the extent of their geographical presence and develop location and crop-specific distribution maps. One hundred and seventy-four leguminous plant samples were tested from 32 locations in India to detect YMD-causing viruses. Additionally, publicly available data were incorporated into this study to provide a comprehensive overview of their distribution in India. This resulted in 581 reports on the DNA-A component representing 119 locations, which were also utilized to depict the distribution of YMD-causing viruses on a map of India. In this study, 117 full-length DNA-A and 103 DNA-B components were successfully characterized, representing the detected mungbean yellow mosaic India virus (MYMIV), mungbean yellow mosaic virus (MYMV), and horsegram yellow mosaic virus in the collected samples. Phylogenetic analysis of isolates of these species showed no differentiation based on location in India. Diversity indices revealed the abundance (55.9%) and dominance (0.56) of MYMIV across 119 locations. These findings hold significant implications for legume researchers, offering insights into disease prevalence and geographic distribution. Furthermore, the distribution of YMD-causing viruses in different agro-climatic zones will help researchers in developing zone-specific YMD-resistant cultivars of the legume crops and would facilitate effective disease management options.

Background: Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results: We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions: Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.