Browsing by Author "Neeraj Kumar Vasistha"

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Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS
(Frontiers Media S.A., 2023) Sahadev Singh; Shailendra Singh Gaurav; Neeraj Kumar Vasistha; Uttam Kumar; Arun Kumar Joshi; Vinod Kumar Mishra; Ramesh Chand; Pushpendra Kumar Gupta
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation. Copyright © 2023 Singh, Gaurav, Vasistha, Kumar, Joshi, Mishra, Chand and Gupta.
Genome-wide association study for agronomic and yield-related traits in spring wheat (Triticum aestivum L.) germplasm
(BioMed Central Ltd, 2025) Ankita Thakur; Raman Dhariwal; Hannes Kumar Karwat; Vinod Kumar Mishra; Sandeep K. Sharma; Mukesh Kumar Singh; Sundeep Naresh Kumar; Neeraj Kumar Vasistha
Background: Common wheat (Triticum aestivum L.) is one of the most widely grown and consumed cereal crops, but its complicated genome makes it difficult to study how genes affect important agronomic and yield-related traits. Genome-wide association study (GWAS) is a useful method for finding specific loci that control complex agronomic and yield-related traits. Results: The present investigation revealed significant phenotypic variability across the genotypes examined for all traits. The broad sense heritability (H2) for all traits ranged from 0.50 to 0.71 (Env1; 2021–2022) and 0.53 to 0.81 (Env2; 2022–2023). Using two environments’ phenotypic data, and high-throughput single-nucleotide polymorphisms (SNPs) genotypic data of 20,996 markers, we discovered 114 grain-yield-related quantitative trait loci (QTLs) and 300 associated SNP markers. Eighty-five of the identified markers were stable, consistently detected across environments (Env1 and Env2) and combined environment (CE) data, and showed a significant association with 32 different QTLs. The trait with the most associated QTLs (28) was the number of fertile tillers (NFT), with 70 markers. This was followed by 20 QTLs for each, spike length (SL) and spikelet number per spike (SPS), with 69 and 82 SNPs, respectively. Conversely, six SNPs that exhibited association with multiple traits were also identified. Twenty-nine of the total 114 identified QTLs were located in chromosomal positions where at least one marker-trait association had been previously identified. Conclusion: This study has found new SNPs, and useful QTLs that may help us to understand the biological processes behind each studied trait. Further validation in various genetic backgrounds and environments is necessary to confirm the potential utility of the significant alleles found in this study for breeding wheat varieties with improved agronomic and yield-related traits. © The Author(s) 2025.
Genome-wide association study for powdery mildew resistance in CIMMYT's spring wheat germplasm
(John Wiley and Sons Inc, 2025) Deepa Bhadana; Prabhjot Kaur; Ramandeep P. Kaur; Vikas Kumar Ravat; Ashutosh; Rahul Kumar; Neeraj Kumar Vasistha
Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), is a foliar disease of wheat (Triticum aestivum) that adversely affects both grain yield and quality. Growing resistant cultivars offers an effective and environmentally sustainable solution to managing PM. However, relying on the same genetic source of resistance can lead to resistance breakdown as Bgt isolates rapidly evolve. To mitigate this, identifying novel resistance sources is crucial. In this study, 225 diverse wheat genotypes were evaluated at adult plant stage in disease nurseries over the three crop seasons (2018/2019, 2019/2020 and 2020/2021). Using disease and genotyping data from 12,160 single-nucleotide polymorphism (SNP) markers, a genome-wide association study (GWAS) was conducted to identify novel resistance loci. We identified 22 marker loci significantly (at p < 0.005) associated with PM resistance, distributed across 14 wheat chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 5D, 6A, 7A and 7B). Of these, seven loci overlap with previously identified regions, while the remaining 15 loci represent novel regions reported for the first time in this study. The identified SNP markers have significant potential for wheat breeding programmes, as they can accelerate the development of PM-resistant cultivars through marker-assisted selection. © 2024 British Society for Plant Pathology.
Genome-Wide Association Study Reveals Novel Powdery Mildew Resistance Loci in Bread Wheat
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Ramandeep Kaur; Neeraj Kumar Vasistha; Vikas Kumar Ravat; Vinod Kumar Mishra; Sandeep Sharma; Arun Kumar Joshi; Raman Dhariwal
Powdery mildew (PM), caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), significantly threatens global bread wheat production. Although the use of resistant cultivars is an effective strategy for managing PM, currently available wheat cultivars lack sufficient levels of resistance. To tackle this challenge, we conducted a comprehensive genome-wide association study (GWAS) using a diverse panel of 286 bread wheat genotypes. Over three consecutive years (2020–2021, 2021–2022, and 2022–2023), these genotypes were extensively evaluated for PM severity under field conditions following inoculation with virulent Bgt isolates. The panel was previously genotyped using the Illumina 90K Infinium iSelect assay to obtain genome-wide single-nucleotide polymorphism (SNP) marker coverage. By applying FarmCPU, a multilocus mixed model, we identified a total of 113 marker–trait associations (MTAs) located on chromosomes 1A, 1B, 2B, 3A, 3B, 4A, 4B, 5A, 5B, 6B, 7A, and 7B at a significance level of p ≤ 0.001. Notably, four novel MTAs on chromosome 6B were consistently detected in 2020–2021 and 2021–2022. Furthermore, within the confidence intervals of the identified SNPs, we identified 96 candidate genes belonging to different proteins including 12 disease resistance/host–pathogen interaction-related protein families. Among these, protein kinases, leucine-rich repeats, and zinc finger proteins were of particular interest due to their potential roles in PM resistance. These identified loci can serve as targets for breeding programs aimed at developing disease-resistant wheat cultivars. © 2023 His Majesty the King in Right of Canada.
MicroRNAs associated with spot blotch in bread wheat (Triticum aestivum)
(Academic Press, 2025) Neeraj Kumar Vasistha; Sandeep K. Sharma; Vinod Kumar Mishra; Tinku Gautam; Gautam M. Saripalli; Sunita Pal; Pushpendra Kumar Gupta
Spot blotch, caused by the fungal pathogen Bipolaris sorokiniana, poses a significant threat to wheat production worldwide, particularly in warm and humid regions. Recent advances in molecular biology have highlighted the pivotal role of microRNAs (miRNAs) in regulating plant defense responses against various biotic stresses, including fungal infections. In the present study, miRNAs in wheat were examined during spot blotch infection. High-throughput sequencing and bioinformatics analysis were employed to identify differentially expressed miRNAs in resistant and susceptible wheat genotypes (YS#54 and YS#83) following B. sorokiniana inoculation. As many as 572 conserved and 632 additional miRNAs (potentially novel) were identified; some of them were upregulated and others downregulated, suggesting their involvement in defense signaling pathways, including those targeting transcription factors and resistance-related genes. Targets for miRNAs were also identified for 467 miRNAs, which included 7937 transcripts; the expression profiles of transcripts generally had a negative correlation with miRNA expression. The results of the present study provide new insights into the miRNA-mediated regulatory networks in wheat-pathogen interactions and lay the groundwork for the development of miRNA-based markers or strategies for enhancing resistance to spot blotch disease. © 2025 Elsevier Ltd
Molecular introgression of leaf rust resistance gene Lr34 validates enhanced effect on resistance to spot blotch in spring wheat
(Springer Netherlands, 2017) Neeraj Kumar Vasistha; Arun Balasubramaniam; Vinod Kumar Mishra; Jayasudha Srinivasa; Ramesh Chand; Arun Kumar Joshi
The adult plant leaf rust resistance gene Lr34 was introduced using marker assisted selection (MAS) into an Indian wheat cultivar HUW510. Lr34 is associated with enhanced resistance to spot blotch. However, this effect has not been validated previously via introgression from one genetic background into another using MAS. The donor parent was the CIMMYT breeding line Picaflor#1. The morphological marker leaf tip necrosis (LTN+) and co-dominant STS marker csLV34 were used to track Lr34. Background selection was made with 90 simple sequence repeat (SSR) loci. BC3F3 to BC3F5 progenies were tested for spot blotch resistance. The results showed that the introgression of Lr34 can lead to enhanced resistance to spot blotch. Eleven selections retained in the cv. HUW510 background carried Lr34 and had a genetic background estimated to be as high as 95% that of the recurrent parent. The mean AUDPC for spot blotch in BC3F5 lines of Picaflor#1 × HUW510 was substantially lower (917 at timely sown conditions and 1015 under late sown conditions) than the recipient parent HUW510 (1332 at timely sown conditions and 1412 under late sown conditions). The results showed that introgression of Lr34 can lead to enhanced resistance to spot blotch. © 2017, Springer Science+Business Media B.V., part of Springer Nature.
Pyramiding of genes for grain protein content, grain quality, and rust resistance in eleven Indian bread wheat cultivars: a multi-institutional effort
(Springer Science and Business Media B.V., 2022) Pushpendra K. Gupta; Harindra S. Balyan; Parveen Chhuneja; Jai P. Jaiswal; Shubhada Tamhankar; Vinod K. Mishra; Navtej S. Bains; Ramesh Chand; Arun K. Joshi; Satinder Kaur; Harinderjeet Kaur; Gurvinder S. Mavi; Manoj Oak; Achla Sharma; Puja Srivastava; Virinder S. Sohu; Pramod Prasad; Priyanka Agarwal; Moin Akhtar; Saurabh Badoni; Reeku Chaudhary; Vijay Gahlaut; Rishi Pal Gangwar; Tinku Gautam; Vandana Jaiswal; Ravi Shekhar Kumar; Sachin Kumar; M. Shamshad; Anupama Singh; Sandhya Taygi; Neeraj Kumar Vasistha; Manish Kumar Vishwakarma
Improvement of grain protein content (GPC), loaf volume, and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcross breeding (MABB) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24, and Sr24. GPC increased by 0.8 to 3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines allowed identification of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the backgrounds of the following four cultivars: NI5439, UP2338, UP2382, and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were obtained in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621, and DBW1. The improved pre-bred lines developed following multi-institutional effort should prove a valuable source for the development of cultivars with improved nutritional quality and rust resistance in the ongoing wheat breeding programmes. © 2022, The Author(s), under exclusive licence to Springer Nature B.V.
ToxA-TSN1 interaction for spot blotch susceptibility in Indian wheat: An example of inverse gene-for-gene relationship
(American Phytopathological Society, 2020) Sudhir Navathe; Punam Singh Yadav; Ramesh Chand; Vinod Kumar Mishra; Neeraj Kumar Vasistha; Prabina Kumar Meher; Arun Kumar Joshi; Pushpendra Kumar Gupta
The ToxA-Tsn1 system is an example of an inverse gene-for-gene relationship. The gene ToxA encodes a host-selective toxin (HST) which functions as a necrotrophic effector and is often responsible for the virulence of the pathogen. The genomes of several fungal pathogens (e.g., Pyrenophora tritici-repentis, Parastagonospora nodorum, and Bipolaris sorokiniana) have been shown to carry the ToxA gene. Tsn1 is a sensitivity gene in the host, whose presence generally helps a ToxA-positive pathogen to cause spot blotch in wheat. Cultivars lacking Tsn1 are generally resistant to spot blotch; this resistance is attributed to a number of other known genes which impart resistance in the absence of Tsn1. In the present study, 110 isolates of B. sorokiniana strains, collected from the ME5A and ME4C megaenvironments of India, were screened for the presence of the ToxA gene; 77 (70%) were found to be ToxA positive. Similarly, 220 Indian wheat cultivars were screened for the presence of the Tsn1 gene; 81 (36.8%) were found to be Tsn1 positive. When 20 wheat cultivars (11 with Tsn1 and 9 with tsn1) were inoculated with ToxA-positive isolates, seedlings of only those carrying the Tsn1 allele (not tsn1) developed necrotic spots surrounded by a chlorotic halo. No such distinction between Tsn1 and tsn1 carriers was observed when adult plants were inoculated. This study suggests that the absence of Tsn1 facilitated resistance against spot blotch of wheat. Therefore, the selection of wheat genotypes for the absence of the Tsn1 allele can improve resistance to spot blotch. © 2020 The American Phytopathological Society
Transcriptome analysis for the identification of spot blotch responsive genes and miRNAs in wheat
(Academic Press, 2025) Neeraj Kumar Vasistha; Archita Tandon; Sunita Pal; Sandeep K. Sharma; Vinod Kumar Mishra; Pushpendra Kumar Gupta
Spot blotch caused by Bipolaris sorokiniana is one of the most devastating foliar diseases of wheat particularly in South Asian countries including India, Nepal, Bangladesh etc. In the present study, using whole genome transcriptome sequencing data from two contrasting genotypes for spot blotch disease (one resistant and the other susceptible), at three time points after inoculation, we identified a large number of differentially expressed genes (DEGs) and many microRNAs (miRNAs) with their target genes (in silico). The mean number of reads in six libraries were 39.8 millions with a range of 32.1–44.9 million reads per library. The reads from resistant and susceptible genotypes were aligned. The aligned reads had a mean of 32.4 million with a range of 25.0–37.1 million reads. The raw data were deposited into the National Center for Biotechnology Information (NCBI) database under the SRA accession number PRJNA1182498. The DEGs included 5294 upregulated and 4383 downregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included photosynthesis-antenna proteins, MAPK signaling pathways, plant-pathogen interactions, circadian rhythm-plant, etc. These DEGs mainly encoded proteins with leucine rich repeat (LRR) domain, F-box-like domain, non-specific serine/threonine-protein kinases (S/TPK), wall-associated receptor kinases (WAKs), etc. Many DEGs also belonged to the following families of transcription factors (TFs): ERF, NAC, WRKY, GRAS, MYB etc. Few DEGs were also associated with pathogenesis related (PR) proteins including PR 1.1, PR 1.2, PR 1.17 and PR 1.19. The results of the present study may be utilized by plant breeders, geneticists and bioinformatician for further research. © 2024 Elsevier Ltd
Zinc and iron concentration QTL mapped in a Triticum spelta × T. Aestivum cross
(Springer Verlag, 2014) Jayasudha Srinivasa; Balasubramaniam Arun; Vinod Kumar Mishra; Gyanendra Pratap Singh; Govindan Velu; Raman Babu; Neeraj Kumar Vasistha; Arun Kumar Joshi
The genetic basis of accumulation in the grain of Zn and Fe was investigated via QTL mapping in a recombinant inbred line (RIL) population bred from a cross between Triticum spelta and T. aestivum. The concentration of the two elements was measured from grain produced in three locations over two consecutive cropping seasons and from a greenhouse trial. The range in Zn and Fe concentration across the RILs was, respectively, 18.8–73.5 and 25.3–59.5 ppm, and the concentrations of the two elements were positively correlated with one another (rp =+0.79). Ten QTL (five each for Zn and Fe accumulation) were detected, mapping to seven different chromosomes. The chromosome 2B and 6A grain Zn QTL were consistently expressed across environments. The proportion of the phenotype explained (PVE) by QZn.bhu-2B was >16 %, and the locus was closely linked to the SNP marker 1101425|F|0, while QZn.bhu-6A (7.0 % PVE) was closely linked to DArT marker 3026160|F|0. Of the five Fe QTL detected, three, all mapping to chromosome 1A were detected in all seven environments. The PVE for QFe.bhu-3B was 26.0 %. © Springer-Verlag Berlin Heidelberg 2014.