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Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)

Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield‐limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RG...

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Autores principales: Amas, Junrey C., Bayer, Philipp E., Hong Tan, Wei, Tirnaz, Soodeh, Thomas, William J. W., Edwards, David, Batley, Jacqueline
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10502758/
https://www.ncbi.nlm.nih.gov/pubmed/37431308
http://dx.doi.org/10.1111/pbi.14116
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author Amas, Junrey C.
Bayer, Philipp E.
Hong Tan, Wei
Tirnaz, Soodeh
Thomas, William J. W.
Edwards, David
Batley, Jacqueline
author_facet Amas, Junrey C.
Bayer, Philipp E.
Hong Tan, Wei
Tirnaz, Soodeh
Thomas, William J. W.
Edwards, David
Batley, Jacqueline
author_sort Amas, Junrey C.
collection PubMed
description Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield‐limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence‐absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine‐rich repeat (TM‐LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide‐binding site leucine‐rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing‐down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
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spelling pubmed-105027582023-09-16 Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs) Amas, Junrey C. Bayer, Philipp E. Hong Tan, Wei Tirnaz, Soodeh Thomas, William J. W. Edwards, David Batley, Jacqueline Plant Biotechnol J Research Articles Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield‐limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence‐absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine‐rich repeat (TM‐LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide‐binding site leucine‐rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing‐down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives. John Wiley and Sons Inc. 2023-07-11 2023-10 /pmc/articles/PMC10502758/ /pubmed/37431308 http://dx.doi.org/10.1111/pbi.14116 Text en © 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research Articles
Amas, Junrey C.
Bayer, Philipp E.
Hong Tan, Wei
Tirnaz, Soodeh
Thomas, William J. W.
Edwards, David
Batley, Jacqueline
Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title_full Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title_fullStr Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title_full_unstemmed Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title_short Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)
title_sort comparative pangenome analyses provide insights into the evolution of brassica rapa resistance gene analogues (rgas)
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10502758/
https://www.ncbi.nlm.nih.gov/pubmed/37431308
http://dx.doi.org/10.1111/pbi.14116
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