Browsing by Author "Pushpendra Kumar Gupta"

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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.
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
QTL mapping for some grain traits in bread wheat (Triticum aestivum L.)
(Springer, 2018) Supriya Kumari; Vandana Jaiswal; Vinod Kumar Mishra; Rajneesh Paliwal; Harindra Singh Balyan; Pushpendra Kumar Gupta
Grain traits are important agronomic attributes with the market value as well as milling yield of bread wheat. In the present study, quantitative trait loci (QTL) regulating grain traits in wheat were identified. Data for grain area size (GAS), grain width (GWid), factor form density (FFD), grain length-width ratio (GLWR), thousand grain weight (TGW), grain perimeter length (GPL) and grain length (GL) were recorded on a recombinant inbred line derived from the cross of NW1014 × HUW468 at Meerut and Varanasi locations. A linkage map of 55 simple sequence repeat markers for 8 wheat chromosomes was used for QTL analysis by Composite interval mapping. Eighteen QTLs distributed on 8 chromosomes were identified for seven grain traits. Of these, five QTLs for GLWR were found on chromosomes 1A, 6A, 2B, and 7B, three QTLs for GPL were located on chromosomes 4A, 5A and 7B and three QTLs for GAS were mapped on 5D and 7D. Two QTLs were identified on chromosomes 4A and 5A for GL and two QTLs for GWid were identified on chromosomes 7D and 6A. Similarly, two QTLs for FFD were found on chromosomes 1A and 5D. A solitary QTL for TGW was identified on chromosome 2B. For several traits, QTLs were also co-localized on chromosomes 2B, 4A, 5A, 6A, 5D, 7B and 7D. The QTLs detected in the present study may be validated for specific crosses and then used for marker-assisted selection to improve grain quality in bread wheat. © 2018, Prof. H.S. Srivastava Foundation for Science and Society.
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