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SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security

The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone l...

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Autores principales: Saxesena, Ravi Ranjan, Mishra, Vinod Kumar, Chand, Ramesh, Kumar, Uttam, Chowdhury, Apurba Kumar, Bhati, Jyotika, Budhlakoti, Neeraj, Joshi, Arun Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016274/
https://www.ncbi.nlm.nih.gov/pubmed/35450212
http://dx.doi.org/10.3389/fgene.2022.859676
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author Saxesena, Ravi Ranjan
Mishra, Vinod Kumar
Chand, Ramesh
Kumar, Uttam
Chowdhury, Apurba Kumar
Bhati, Jyotika
Budhlakoti, Neeraj
Joshi, Arun Kumar
author_facet Saxesena, Ravi Ranjan
Mishra, Vinod Kumar
Chand, Ramesh
Kumar, Uttam
Chowdhury, Apurba Kumar
Bhati, Jyotika
Budhlakoti, Neeraj
Joshi, Arun Kumar
author_sort Saxesena, Ravi Ranjan
collection PubMed
description The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.
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spelling pubmed-90162742022-04-20 SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security Saxesena, Ravi Ranjan Mishra, Vinod Kumar Chand, Ramesh Kumar, Uttam Chowdhury, Apurba Kumar Bhati, Jyotika Budhlakoti, Neeraj Joshi, Arun Kumar Front Genet Genetics The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism. Frontiers Media S.A. 2022-04-05 /pmc/articles/PMC9016274/ /pubmed/35450212 http://dx.doi.org/10.3389/fgene.2022.859676 Text en Copyright © 2022 Saxesena, Mishra, Chand, Kumar, Chowdhury, Bhati, Budhlakoti and Joshi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Saxesena, Ravi Ranjan
Mishra, Vinod Kumar
Chand, Ramesh
Kumar, Uttam
Chowdhury, Apurba Kumar
Bhati, Jyotika
Budhlakoti, Neeraj
Joshi, Arun Kumar
SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title_full SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title_fullStr SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title_full_unstemmed SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title_short SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security
title_sort snp discovery using bsr-seq approach for spot blotch resistance in wheat (triticum aestivum l.), an essential crop for food security
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016274/
https://www.ncbi.nlm.nih.gov/pubmed/35450212
http://dx.doi.org/10.3389/fgene.2022.859676
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