Browsing by Author "Kohli, Pawandeep Singh"

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Chickpea (Cicer arietinum) PHO1 family members function redundantly in Pi transport and root nodulation
(Elsevier B.V., 2024) Mani, Balaji; Maurya, Kanika; Kohli, Pawandeep Singh; Giri, Jitender
Phosphorus (P), a macronutrient, plays key roles in plant growth, development, and yield. Phosphate (Pi) transporters (PHTs) and PHOSPHATE1 (PHO1) are central to Pi acquisition and distribution. Potentially, PHO1 is also involved in signal transduction under low P. The current study was designed to identify and functionally characterize the PHO1 gene family in chickpea (CaPHO1s). Five CaPHO1 genes were identified through a comprehensive genome-wide search. Phylogenetically, CaPHO1s formed two clades, and protein sequence analyses confirmed the presence of conserved domains. CaPHO1s are expressed in different plant organs including root nodules and are induced by Pi-limiting conditions. Functional complementation of atpho1 mutant with three CaPHO1 members, CaPHO1, CaPHO1;like, and CaPHO1;H1, independently demonstrated their role in root to shoot Pi transport, and their redundant functions. To further validate this, we raised independent RNA-interference (RNAi) lines of CaPHO1, CaPHO1;like, and CaPHO1;H1 along with triple mutant line in chickpea. While single gene RNAi lines behaved just like WT, triple knock-down RNAi lines (capho1/like/h1) showed reduced shoot growth and shoot Pi content. Lastly, we showed that CaPHO1s are involved in root nodule development and Pi content. Our findings suggest that CaPHO1 members function redundantly in root to shoot Pi export and root nodule development in chickpea.
Dissecting chickpea genomic loci associated with the root penetration responsive traits in compacted soil
(Springer Nature Publishing AG, 2024) Donde, Ravindra; Kohli, Pawandeep Singh; Pandey, Mandavi; Sirohi, Ujjwal; Singh, Bhagat; Giri, Jitender
Soil compaction is a major concern for modern agriculture, as it constrains plant root growth, leading to reduced resource acquisition. Phenotypic variation for root system architecture (RSA) traits in compacted soils is present for various crops; however, studies on genetic associations with these traits are lacking. Therefore, we investigated RSA traits in diferent soil compaction levels and identifed signifcant genomic associations in chickpea. We conducted a Genome-Wide Association Study (GWAS) of 210 chickpea accessions for 13 RSA traits under three bulk densities (BD) (1.1BD, 1.6BD, and 1.8BD). Soil compaction decreases root exploration by reducing 12 RSA traits, except average diameter (AD). Further, AD is negatively correlated with lateral root traits, and this correlation increases in 1.8BD, suggesting the negative efect of AD on lateral root traits. Interestingly, we identifed probable candidate genes such as GLP3 and LRX for lateral root traits and CRF1-like for total length (TL) in 1.6BD soil. In heavy soil compaction, DGK2 is associated with lateral root traits. Reduction in laterals during soil compaction is mainly due to delayed seedling establishment, thus making lateral root number a critical trait. Interestingly, we also found a higher contribution of the GxE component of the number of root tips (Tips) to the total variation than the other lateral traits. We also identifed a pectin esterase, PPE8B, associated with Tips in high soil compaction and a signifcantly associated SNP with the relative change in Tips depicting a trade-of between Tips and AD. Identifed genes and loci would help develop soil-compaction-resistant chickpea varieties.
Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea
(Springer Nature Publishing AG, 2020) Kohli, Pawandeep Singh; Verma, Pankaj Kumar; Verma, Rita; Parida, Swarup K.; Thakur, Jitendra K.; Giri, Jitender
Root hairs (RHs) are single-celled elongated epidermal cells and play a vital role in nutrient absorption, particularly for immobile minerals like phosphorus (P). As an adaptive response to P deficiency, an increase in RH length enhances root-soil contact and absorptive area for P absorption. Genetic variations have been reported for RH length and its response to P deficiency in plants. However, only a few association studies have been conducted to identify genes and genetic loci associated with RH length. Here, we screened desi chickpea accessions for RH length and its plasticity under P deficiency. Further, the genome-wide association study (GWAS) was conducted to identify the genetic loci associated with RH length in P deficient and sufficient conditions. Although high variability was observed in terms of RH length in diverse genotypes, majority of the accessions showed typical response of increase in RH length in low P. Genome-wide association mapping identified many SNPs with significant associations with RH length in P-sufficient and P-deficient conditions. A few candidate genes for RH length in P deficient (SIZ1-like and HAD superfamily protein) and sufficient (RSL2-like and SMAP1-like) conditions were identified which have known roles in RH development and P deficiency response or both. Highly associated loci and candidate genes identified in this study would be useful for genomic-assisted breeding to develop P-efficient chickpea.
A lipid synthase maintains metabolic flux for jasmonate synthesis to regulate root growth and phosphate homeostasis
(Oxford University Press, 2025) Pandey, Mandavi; Verma, Lokesh; Kohli, Pawandeep Singh; Singh, Bhagat; Kochi, Abhijith; Giri, Jitender
Plants require phosphate (Pi) for proper growth and development but often face scarcity of this vital nutrient in the soil. Pi-starvation triggers membrane lipid remodeling to utilize the membrane phospholipid-bound Pi in plants. In this process, phospholipids are replaced by non-Pi-containing galactolipids (MGDG, DGDG) and sulfolipids. The galactolipids ratio (MGDG:DGDG) is suggested to influence jasmonic acid (JA) biosynthesis. However, how the MGDG:DGDG ratio, JA levels, and root growth are coordinated under Pi deficiency in rice (Oryza sativa) remains unknown. Here, we characterized DGDG synthase 1 (OsDGD1) for its role in regulating root development by maintaining metabolic flux for JA biosynthesis. We showed that OsDGD1 is responsive under low Pi and is under the direct control of Phosphate Starvation Response 2 (OsPHR2), the master regulator of low Pi adaptations. Further, OsDGD1 knockout (KO) lines showed marked phenotypic differences compared to the wild type (WT), including a significant reduction in root length and biomass, leading to reduced Pi uptake. Further, lipidome analyses revealed reduced DGDG levels in the KO line, leading to reduced membrane remodeling, thus affecting P utilization efficiency. We also observed an increase in the MGDG: DGDG ratio in KO lines, which enhanced the endogenous JA levels and signaling. This imbalance of JA in KO plants led to changes in auxin levels, causing drastic root growth inhibition. These findings indicate the critical role of OsDGD1 in maintaining optimum levels of JA during Pi deficiency for conducive root growth. Besides acting as signaling molecules and structural components, our study widens the role of lipids as metabolic flux controllers for phytohormone biosynthesis.
Physiological and genetic basis of superior phosphate uptake and utilization efficiency in the rice landrace Wazuhophek
(Oxford University Press, 2025) Kohli, Pawandeep Singh; Donde, Ravindra; Sirohi, Ujjwal; Singh, Bhagat; Anantha, M S; Bhadana, Vijai Pal; Sundaram, Raman Meenakshi; Mangrauthia, Satendra K; Giri, Jitender
Low phosphorus (P) availability due to edaphic conditions or the scarcity of P fertilizers restricts agricultural productivity. Various rice-growing regions experience poor P availability. Landraces from these regions, such as Wazuhophek in Northeast India, may provide a source of critical genetic variation needed for developing highly efficient, tolerant rice varieties. This study identifies the physiological and genetic basis of higher efficiency and tolerance in Wazuhophek. Wazuhophek displays higher shoot P content across three different P regimes (0, 15, and 200 µM P) compared to the sensitive parent, Improved Samba Mahsuri (ISM). In 0 µM, Wazuhophek’s increased shoot P content can be attributed to greater root physiological P use efficiency and improved root-to-shoot P translocation. At 15 and 200 µM P, Wazuhophek exhibited a higher crown root number and surface area, with more efficient roots than ISM, facilitating better Pi acquisition and higher shoot P. Furthermore, the genetic basis was delineated by identifying quantitative trait loci (QTLs) for critical traits. Revealing Wazuhophek’s physiological mechanism of low P tolerance provides valuable insights for developing rice varieties suited for nutrient-poor soil. Additionally, the identified QTLs for key traits offer targets for breeding more efficient low P-tolerant rice.
Rice phosphate transporter reduces the low phosphate response through jasmonate signaling
(Oxford University Press, 2026) Mani, Balaji; Maurya, Kanika; Verma, Lokesh; Gupta, Priya; Kohli, Pawandeep Singh; Gupta, Gagan; Jaskolowski, Aime; Poirier, Yves; Giri, Jitender
Phosphorus (P) is an essential macronutrient for plant growth, and its deficiency severely limits crop productivity. The PHOSPHATE1 (PHO1) protein family, defined by an N-terminal SPX domain, four transmembrane (4TM) domains, and a C-terminal EXS domain, mediates phosphate (Pi) loading into the xylem for root-to-shoot transport. In rice, OsPHO1;2 is critical for Pi export, and loss-of-function mutants exhibit severe growth retardation and Pi deficiency symptoms despite sufficient external Pi. To dissect the functional contributions of PHO1 domains beyond Pi transport, we generated CRISPR/Cas9 rice lines expressing either the EXS domain containing part of the SPX domain (S-EXS) or the 4TM+EXS domains (T-EXS) of OsPHO1;2. Phenotypic analyses under Pi-sufficient and Pi-deficient conditions revealed that S-EXS lines displayed improved early growth compared to ospho1;2 mutants, despite similar shoot Pi levels. These plants exhibited reduced jasmonic acid accumulation and attenuated phosphate starvation responses, resembling wild-type hormone profiles. In contrast, T-EXS lines mirrored the growth defects of ospho1;2 mutants. Transcriptome profiling confirmed that defense and phosphate starvation pathways were less activated in S-EXS lines relative to mutants. However, both S-EXS and T-EXS lines retained seed development defects and reduced seed phosphorus content, consistent with ospho1;2 phenotypes. Heterozygous plants carrying one functional OsPHO1;2 allele exhibited normal growth and seed development, confirming the recessive nature of the mutation. Collectively, these findings demonstrate that the S-EXS domain of OsPHO1;2 promotes plant growth independently of Pi transport by modulating jasmonate signaling and suppressing phosphate starvation responses. This highlights a signaling role for PHO1 domains, offering new insights into Pi homeostasis and potential strategies for breeding Pi-efficient crops.
Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum
(Frontiers Media S.A., 2022) Kohli, Pawandeep Singh; Pazhamala, Lekha T; Mani, Balaji; Thakur, Jitendra K.; Giri, Jitender
Root hairs (RH) are a single-cell extension of root epidermal cells. In low phosphorus (LP) availability, RH length and density increase thus expanding the total root surface area for phosphate (Pi) acquisition. However, details on genes involved in RH development and response to LP are missing in an agronomically important leguminous crop, chickpea. To elucidate this response in chickpea, we performed tissue-specific RNA-sequencing and analyzed the transcriptome modulation for RH and root without RH (Root-RH) under LP. Root hair initiation and cellular differentiation genes like RSL TFs and ROPGEFs are upregulated in Root-RH, explaining denser, and ectopic RH in LP. In RH, genes involved in tip growth processes and phytohormonal biosynthesis like cell wall synthesis and loosening (cellulose synthase A catalytic subunit, CaEXPA2, CaGRP2, and CaXTH2), cytoskeleton/vesicle transport, and ethylene biosynthesis are upregulated. Besides RH development, genes involved in LP responses like lipid and/or pectin P remobilization and acid phosphatases are induced in these tissues summarizing a complete molecular response to LP. Further, RH displayed preferential enrichment of processes involved in symbiotic interactions, which provide an additional benefit during LP. In conclusion, RH shows a multi-faceted response that starts with molecular changes for epidermal cell differentiation and RH initiation in Root-RH and later induction of tip growth and various LP responses in elongated RH.
Significance of root hairs in developing stress-resilient plants for sustainable crop production
(John Wiley & Sons, 2022) Kohli, Pawandeep Singh; Maurya, Kanika; Thakur, Jitendra K.; Bhosale, Rahul; Giri, Jitender
Root hairs represent a beneficial agronomic trait to potentially reduce fertiliser and irrigation inputs. Over the past decades, research in the plant model Arabidopsis thaliana has provided insights about root hair development, the underlying genetic framework, and the integration of environmental cues within this framework. Recent years have seen a paradigm shift, where studies are now highlighting conservation and diversification of root hair developmental programs in other plant species and the agronomic relevance of root hairs in a wider ecological context. In this review, we specifically discuss the molecular evolution of RSL (RHD Six-Like) pathway that controls root hair development and growth in land plants. We also discuss how root hairs contribute to plant performance as an active physiological rooting structure by performing resource acquisition, providing anchorage, and constructing the rhizosphere with desirable physical, chemical, and biological properties. Finally, we outline future research directions that can help achieve the potential of root hairs in developing sustainable agroecosystems.
Specific galactolipids species correlate with rice genotypic variability for phosphate utilization efficiency
(Elsevier B.V., 2021) Verma, Lokesh; Kohli, Pawandeep Singh; Maurya, Kanika; K B, Abhijith; Thakur, Jitendra K.; Giri, Jitender
Membrane lipid remodeling helps in the efficient utilization of phosphorus (P) by replacing phospholipids with galactolipids during P deficiency. Previous studies have shown lipid remodeling in rice under P deficiency; however, main lipid classes did not show association with superior P-use-efficiency in rice genotypes. Here, diverse rice genotypes were extensively phenotyped in normal (NP) and low P (LP) conditions. Based on the phenotypic response to P deficiency, genotypes were identified as tolerant and sensitive. Further, bulks were generated differing in their physiological P-use-efficiency (PPUE) during LP condition. Shoot lipidome profiling of genotypes was performed and used to correlate the abundance of various lipid classes and their constituent species with the PPUE of the genotypes. Lipid remodeling was observed as a P-starvation-induced response in all the genotypes. However, neither total galacto- and phospholipids nor the lipid classes correlated with PPUE during P deficiency. However, the difference in PPUE in the two bulks correlated with specific lipid species of galactolipids (DGDG, MGDG). Further, DGDG34:3 had the highest Mol% among the differentially accumulated lipid species between the two bulks. Our study reveals the importance of specific galactolipids species in rice adaptation to P deficient soils and thus opens new targets for future research.