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Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01

Plasmodiophora brassicae causes clubroot disease in brassica crops worldwide. Brassica rapa, a progenitor of Brassica napus (canola), possesses important sources for resistance to clubroot. A doubled haploid (DH) population consisting of 84 DH lines were developed from a Backcross2 (BC(2)) plant thr...

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Autores principales: Yu, Fengqun, Zhang, Yan, Wang, Jinghe, Chen, Qilin, Karim, Md. Masud, Gossen, Bruce D., Peng, Gary
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8790046/
https://www.ncbi.nlm.nih.gov/pubmed/35095960
http://dx.doi.org/10.3389/fpls.2021.785989
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author Yu, Fengqun
Zhang, Yan
Wang, Jinghe
Chen, Qilin
Karim, Md. Masud
Gossen, Bruce D.
Peng, Gary
author_facet Yu, Fengqun
Zhang, Yan
Wang, Jinghe
Chen, Qilin
Karim, Md. Masud
Gossen, Bruce D.
Peng, Gary
author_sort Yu, Fengqun
collection PubMed
description Plasmodiophora brassicae causes clubroot disease in brassica crops worldwide. Brassica rapa, a progenitor of Brassica napus (canola), possesses important sources for resistance to clubroot. A doubled haploid (DH) population consisting of 84 DH lines were developed from a Backcross2 (BC(2)) plant through an interspecific cross of B. rapa turnip cv. ECD01 (resistant, R) with canola line DH16516 (susceptible, S) and then backcrossed with DH16516 as the recurrent parent. The DH lines and their parental lines were tested for resistance to four major pathotypes (3A, 3D, 3H, and 5X) of P. brassicae identified from canola. The R:S segregation ratio for pathotype 3A was 1:3, and 3:1 for pathotypes 3D, 3H, and 5X. From genotyping by sequencing (GBS), a total of 355.3 M short reads were obtained from the 84 DH lines, ranging from 0.81 to 11.67 M sequences per line. The short reads were aligned into the A-genome of B. napus “Darmor-bzh” version 4.1 with a total of 260 non-redundant single-nucleotide polymorphism (SNP) sites. Two quantitative trait loci (QTLs), Rcr10(ECD01) and Rcr9(ECD01), were detected for the pathotypes in chromosomes A03 and A08, respectively. Rcr10(ECD01) and Rcr9(ECD01) were responsible for resistance to 3A, 3D, and 3H, while only one QTL, Rcr9(ECD01), was responsible for resistance to pathotype 5X. The logarithm of the odds (LOD) values, phenotypic variation explained (PVE), additive (Add) values, and confidence interval (CI) from the estimated QTL position varied with QTL, with a range of 5.2–12.2 for LOD, 16.2–43.3% for PVE, 14.3–25.4 for Add, and 1.5–12.0 cM for CI. The presence of the QTLs on the chromosomes was confirmed through the identification of the percentage of polymorphic variants using bulked-segregant analysis. There was one gene encoding a disease resistance protein and 24 genes encoding proteins with function related to plant defense response in the Rcr10(ECD01) target region. In the Rcr9(ECD01) region, two genes encoded disease resistance proteins and 10 genes encoded with defense-related function. The target regions for Rcr10(ECD01) and Rcr9(ECD01) in B. napus were homologous to the 11.0–16.0 Mb interval of chromosome A03 and the 12.0–14.5 Mb interval of A08 in B. rapa “Chiifu” reference genome, respectively.
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spelling pubmed-87900462022-01-27 Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01 Yu, Fengqun Zhang, Yan Wang, Jinghe Chen, Qilin Karim, Md. Masud Gossen, Bruce D. Peng, Gary Front Plant Sci Plant Science Plasmodiophora brassicae causes clubroot disease in brassica crops worldwide. Brassica rapa, a progenitor of Brassica napus (canola), possesses important sources for resistance to clubroot. A doubled haploid (DH) population consisting of 84 DH lines were developed from a Backcross2 (BC(2)) plant through an interspecific cross of B. rapa turnip cv. ECD01 (resistant, R) with canola line DH16516 (susceptible, S) and then backcrossed with DH16516 as the recurrent parent. The DH lines and their parental lines were tested for resistance to four major pathotypes (3A, 3D, 3H, and 5X) of P. brassicae identified from canola. The R:S segregation ratio for pathotype 3A was 1:3, and 3:1 for pathotypes 3D, 3H, and 5X. From genotyping by sequencing (GBS), a total of 355.3 M short reads were obtained from the 84 DH lines, ranging from 0.81 to 11.67 M sequences per line. The short reads were aligned into the A-genome of B. napus “Darmor-bzh” version 4.1 with a total of 260 non-redundant single-nucleotide polymorphism (SNP) sites. Two quantitative trait loci (QTLs), Rcr10(ECD01) and Rcr9(ECD01), were detected for the pathotypes in chromosomes A03 and A08, respectively. Rcr10(ECD01) and Rcr9(ECD01) were responsible for resistance to 3A, 3D, and 3H, while only one QTL, Rcr9(ECD01), was responsible for resistance to pathotype 5X. The logarithm of the odds (LOD) values, phenotypic variation explained (PVE), additive (Add) values, and confidence interval (CI) from the estimated QTL position varied with QTL, with a range of 5.2–12.2 for LOD, 16.2–43.3% for PVE, 14.3–25.4 for Add, and 1.5–12.0 cM for CI. The presence of the QTLs on the chromosomes was confirmed through the identification of the percentage of polymorphic variants using bulked-segregant analysis. There was one gene encoding a disease resistance protein and 24 genes encoding proteins with function related to plant defense response in the Rcr10(ECD01) target region. In the Rcr9(ECD01) region, two genes encoded disease resistance proteins and 10 genes encoded with defense-related function. The target regions for Rcr10(ECD01) and Rcr9(ECD01) in B. napus were homologous to the 11.0–16.0 Mb interval of chromosome A03 and the 12.0–14.5 Mb interval of A08 in B. rapa “Chiifu” reference genome, respectively. Frontiers Media S.A. 2022-01-12 /pmc/articles/PMC8790046/ /pubmed/35095960 http://dx.doi.org/10.3389/fpls.2021.785989 Text en Copyright © 2022 Yu, Zhang, Wang, Chen, Karim, Gossen and Peng. 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 Plant Science
Yu, Fengqun
Zhang, Yan
Wang, Jinghe
Chen, Qilin
Karim, Md. Masud
Gossen, Bruce D.
Peng, Gary
Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title_full Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title_fullStr Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title_full_unstemmed Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title_short Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01
title_sort identification of two major qtls in brassica napus lines with introgressed clubroot resistance from turnip cultivar ecd01
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8790046/
https://www.ncbi.nlm.nih.gov/pubmed/35095960
http://dx.doi.org/10.3389/fpls.2021.785989
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