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Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding

Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to whi...

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Autores principales: Majeed, Aasim, Johar, Prerna, Raina, Aamir, Salgotra, R. K., Feng, Xianzhong, Bhat, Javaid Akhter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9393495/
https://www.ncbi.nlm.nih.gov/pubmed/36003337
http://dx.doi.org/10.3389/fgene.2022.944501
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author Majeed, Aasim
Johar, Prerna
Raina, Aamir
Salgotra, R. K.
Feng, Xianzhong
Bhat, Javaid Akhter
author_facet Majeed, Aasim
Johar, Prerna
Raina, Aamir
Salgotra, R. K.
Feng, Xianzhong
Bhat, Javaid Akhter
author_sort Majeed, Aasim
collection PubMed
description Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.
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spelling pubmed-93934952022-08-23 Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding Majeed, Aasim Johar, Prerna Raina, Aamir Salgotra, R. K. Feng, Xianzhong Bhat, Javaid Akhter Front Genet Genetics Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping. Frontiers Media S.A. 2022-08-08 /pmc/articles/PMC9393495/ /pubmed/36003337 http://dx.doi.org/10.3389/fgene.2022.944501 Text en Copyright © 2022 Majeed, Johar, Raina, Salgotra, Feng and Bhat. 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
Majeed, Aasim
Johar, Prerna
Raina, Aamir
Salgotra, R. K.
Feng, Xianzhong
Bhat, Javaid Akhter
Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title_full Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title_fullStr Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title_full_unstemmed Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title_short Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
title_sort harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9393495/
https://www.ncbi.nlm.nih.gov/pubmed/36003337
http://dx.doi.org/10.3389/fgene.2022.944501
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