Browsing by Author "Mir, Reyazul Rouf"

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Deciphering cold stress resilience: multiomics insights in contrasting wheat genotypes from the western himalayas
(John Wiley & Sons, 2026) Jan, Sofora; Jan, Farkhandah; Rathore, Mukesh; Singh, Yogita; Kapoor, Prexha; Chaturvedi, Palak; Ghatak, Arindam; Ramesh, Palakurthi; Kumar, Upendra; Prasad, Manoj; Kumar, Sundeep; Rustgi, Sachin; Weckwerth, Wolfram; Kalia, Sanjay; Varshney, Rajeev Kumar; Mir, Reyazul Rouf
Cold stress threatens wheat productivity, particularly in regions with extreme climatic conditions. To elucidate the molecular mechanisms underlying wheat's response to cold stress, we performed a multiomics analysis integrating lipidomics, transcriptomics, proteomics and metabolomics. Our study focused on two wheat genotypes with contrasting cold tolerance levels, SKAU_52 (tolerant) and SKAU_4301 (susceptible) to capture genotype-specific responses under cold stress. Lipidomic analysis revealed significant changes in lipid composition, with unsaturated lipids such as digalactosyldiacyl glycerols (DGDGs) and monogalactosyldiacylglycerols (MGDGs) upregulated in response to cold stress. These lipids are associated with maintaining membrane fluidity, whereas saturated lipids were downregulated in the cold-tolerant genotype. Transcriptomics analysis provides a strong evidence that cold tolerance in wheat is governed by coordinated activation of the ICE-CBF-COR regulatory cascade, with the cold-tolerant genotype ‘SKAU_52’ showing stronger and more sustained induction across pathway tiers than the cold susceptible wheat genotype ‘SKAU_4301’. Similarly, proteomic data highlighted differential abundance of proteins involved in antioxidative defence, osmotic adjustment and signal transduction, including late embryogenesis abundant (LEA) proteins. Metabolome assessment revealed substantial alterations in carbohydrate and amino acid metabolism, with sucrose and amino acids such as hydroxyproline identified as key contributors to cold tolerance. Additionally, defence hormones such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) exhibited genotype-specific regulation with higher accumulation in cold-tolerant genotype. Overall, this integrated multi-omics approach provides novel insights into the complex molecular mechanisms underlying cold stress adaptation in wheat, supporting the development of resilient wheat varieties capable of thriving in challenging cold environments.
Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas
(John Wiley & Sons, 2023) Jan, Sofora; Kumar, Sandeep; Yousuf, Munaza; Shafi, Safoora; Majid, Ronak; Khan, M. Anwar; Jeelani, Fehim; Shikari, Asif Bashir; Kaur, Satinder; Kumar, Sundeep; Kalia, Sanjay; Singh, Kuldeep; Prasad, Manoj; Varshney, Rajeev K.; Mir, Reyazul Rouf
Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021–2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H202), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.
Editorial: Genetics and genomics to enhance crop production, towards food security
(Frontiers Media S.A., 2021) Kumar, Ajay; Mir, Reyazul Rouf; Sehgal, Deepmala; Agarwal, Pinky; Carter, Arron
Twenty first century agriculture faces many challenges including new emerging abiotic and biotic stresses and decreasing arable land. These challenges pose serious threats to food security of an ever-increasing world population. One of the solutions to meet the food demands is to develop high-yielding crop varieties with greater genetic potential and resistance/tolerance to both biotic and abiotic stresses. Just like in mid-nineteenth century, when new genes and methods resulted in the first green revolution, there is a need to combine traditional plant breeding tools with new technologies to bring another green revolution for future food security.
Genome-wide QTL analysis for pre-harvest sprouting tolerance in bread wheat
(Springer, 2009) Mohan, Amita; Kulwal, Pawan; Singh, Ravinder; Kumar, Vinay; Mir, Reyazul Rouf; Kumar, Jitendra; Prasad, Manoj; Balyan, H. S.; Gupta, P. K.
A framework linkage map comprising 214 molecular marker (SSR, AFLP, SAMPL) loci was prepared using an intervarietal recombinant inbred line (RIL) mapping population of bread wheat. The RIL population that was developed from the cross SPR8198 (red-grained and PHS tolerant geno- type) 9 HD2329 (white-grained and PHS susceptible genotype) following single seed descent segregated for pre-harvest sprouting (PHS). The RIL population and parental genotypes were evaluated in six differ- ent environments and the data on PHS were collected. Using the linkage map and PHS data, genome-wide single-locus and two-locus QTL analyses were con- ducted for PHS tolerance (PHST). Single-locus analysis following composite interval mapping (CIM) detected a total of seven QTL, located on specific arms of five different chromosome (1AS,2AL, 2DL, 3AL and 3BL). These seven QTL included two major QTL one each on 2AL and 3AL. Two of these seven QTL were also detected following two-locus analysis, which resolved a total of four main-effect QTL (M-QTL), and 12 epistatic QTL (E-QTL), the latter involved in 7 QTL 9 QTL interactions. Interestingly, none of these M-QTL and E-QTL detected by two-locus analysis was involved in Q 9 E and Q 9 Q 9 E interactions, supporting the results of ANOVA, where genotype 9 environ- ment interaction were non-significant. The QTL for PHS detected in the present study may be efficiently utilized for marker-aided selection for enhancing PHST in bread wheat.
Indian wheat genomics initiative for harnessing the potential of wheat germplasm resources for breeding disease-resistant, nutrient-dense, and climate-resilient cultivars
(Frontiers Media S.A., 2022) Kumar, Sundeep; Jacob, Sherry R.; Mir, Reyazul Rouf; Vikas, V. K.; Kulwal, Pawan; Chandra, Tilak; Kaur, Satinder; Kumar, Uttam; Kumar, Suneel; Sharma, Shailendra; Singh, Ravinder; Prasad, Sai; Singh, Anju Mahendru; Singh, Amit Kumar; Kumari, Jyoti; Saharan, M. S.; Bhardwaj, Subhash Chander; Prasad, Manoj; Kalia, Sanjay; Singh, Kuldeep
Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
(Springer, 2014) Varshney, Rajeev K.; Mir, Reyazul Rouf; Bhatia, Sabhyata; Thudi, Mahendar; Hu, Yuqin; Azam, Sarwar; Zhang, Yong; Jaganathan, Deepa; You, Frank M.; Gao, Jinliang; Riera-Lizarazu, Oscar; Luo, Ming-Cheng
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.