Identification of QTLs for Resistance to 10 Pathotypes of Plasmodiophora Brassicae in Brassica Oleracea Cultivar ECD11 Through Genotyping-by-sequencing

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2023 Nov 20

PMID 37982891

Authors

Md Masud Karim

Fengqun Yu

Affiliations

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Abstract

Two major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea. Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BCS lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0-65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3-23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome 'Chiifu' were searched.

Citing Articles

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References

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E . TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23(19):2633-5. DOI: 10.1093/bioinformatics/btm308. View

Ce F, Mei J, He H, Zhao Y, Hu W, Yu F . Identification of Candidate Genes for Clubroot-Resistance in Using Quantitative Trait Loci-Sequencing. Front Plant Sci. 2021; 12:703520. PMC: 8635040. DOI: 10.3389/fpls.2021.703520. View

Chu M, Song T, Falk K, Zhang X, Liu X, Chang A . Fine mapping of Rcr1 and analyses of its effect on transcriptome patterns during infection by Plasmodiophora brassicae. BMC Genomics. 2014; 15:1166. PMC: 4326500. DOI: 10.1186/1471-2164-15-1166. View

Conesa A, Gotz S, Garcia-Gomez J, Terol J, Talon M, Robles M . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21(18):3674-6. DOI: 10.1093/bioinformatics/bti610. View

Dakouri A, Zhang X, Peng G, Falk K, Gossen B, Strelkov S . Analysis of genome-wide variants through bulked segregant RNA sequencing reveals a major gene for resistance to Plasmodiophora brassicae in Brassica oleracea. Sci Rep. 2018; 8(1):17657. PMC: 6281628. DOI: 10.1038/s41598-018-36187-5. View

Dakouri A, Lamara M, Masud Karim M, Wang J, Chen Q, Gossen B . Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping. Sci Rep. 2021; 11(1):6599. PMC: 7987998. DOI: 10.1038/s41598-021-85836-9. View

Farid M, Yang R, Kebede B, Rahman H . Evaluation of accessions for resistance to and identification of genomic regions associated with resistance. Genome. 2019; 63(2):91-101. DOI: 10.1139/gen-2019-0098. View

Glazebrook J . Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol. 2005; 43:205-27. DOI: 10.1146/annurev.phyto.43.040204.135923. View

10.

Hasan M, Rahman H . Genetics and molecular mapping of resistance to Plasmodiophora brassicae pathotypes 2, 3, 5, 6, and 8 in rutabaga (Brassica napus var. napobrassica). Genome. 2016; 59(10):805-815. DOI: 10.1139/gen-2016-0034. View

11.

Hatakeyama K, Suwabe K, Tomita R, Kato T, Nunome T, Fukuoka H . Identification and characterization of Crr1a, a gene for resistance to clubroot disease (Plasmodiophora brassicae Woronin) in Brassica rapa L. PLoS One. 2013; 8(1):e54745. PMC: 3559844. DOI: 10.1371/journal.pone.0054745. View

12.

Huang Z, Peng G, Liu X, Deora A, Falk K, Gossen B . Fine Mapping of a Clubroot Resistance Gene in Chinese Cabbage Using SNP Markers Identified from Bulked Segregant RNA Sequencing. Front Plant Sci. 2017; 8:1448. PMC: 5581393. DOI: 10.3389/fpls.2017.01448. View

13.

Jiao W, Accinelli G, Hartwig B, Kiefer C, Baker D, Severing E . Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Res. 2017; 27(5):778-786. PMC: 5411772. DOI: 10.1101/gr.213652.116. View

14.

Lee J, Izzah N, Choi B, Joh H, Lee S, Perumal S . Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res. 2015; 23(1):29-41. PMC: 4755525. DOI: 10.1093/dnares/dsv034. View

15.

Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin I . The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun. 2014; 5:3930. PMC: 4279128. DOI: 10.1038/ncomms4930. View

16.

Liu Y, Li D, Yang N, Zhu X, Han K, Gu R . Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage. Int J Mol Sci. 2021; 22(8). PMC: 8074028. DOI: 10.3390/ijms22084266. View

17.

Lv H, Wang Y, Han F, Ji J, Fang Z, Zhuang M . A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics. Sci Rep. 2020; 10(1):12394. PMC: 7381634. DOI: 10.1038/s41598-020-69389-x. View

18.

McHale L, Tan X, Koehl P, Michelmore R . Plant NBS-LRR proteins: adaptable guards. Genome Biol. 2006; 7(4):212. PMC: 1557992. DOI: 10.1186/gb-2006-7-4-212. View

19.

Michael T, Jupe F, Bemm F, Motley S, Sandoval J, Lanz C . High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun. 2018; 9(1):541. PMC: 5803254. DOI: 10.1038/s41467-018-03016-2. View

20.

Nagaoka T, Doullah M, Matsumoto S, Kawasaki S, Ishikawa T, Hori H . Identification of QTLs that control clubroot resistance in Brassica oleracea and comparative analysis of clubroot resistance genes between B. rapa and B. oleracea. Theor Appl Genet. 2010; 120(7):1335-46. DOI: 10.1007/s00122-010-1259-z. View