Fine Mapping of Brassica Napus Blackleg Resistance Gene Rlm1 Through Bulked Segregant RNA Sequencing

Overview

Journal Sci Rep

Specialty Science

Date 2019 Oct 12

PMID 31601933

Citations 11

Authors

Fuyou Fu

Xunjia Liu

Rui Wang

Chun Zhai

Gary Peng

Fengqun Yu

W G Dilantha Fernando

Affiliations

Soon will be listed here.

Abstract

The fungal pathogen Leptosphaeria maculans causes blackleg disease on canola and rapeseed (Brassica napus) in many parts of the world. A B. napus cultivar, 'Quinta', has been widely used for the classification of L. maculans into pathogenicity groups. In this study, we confirmed the presence of Rlm1 in a DH line (DH24288) derived from B. napus cultivar 'Quinta'. Rlm1 was located on chromosome A07, between 13.07 to 22.11 Mb, using a BC population made from crosses of F plants of DH16516 (a susceptible line) x DH24288 with bulked segregant RNA Sequencing (BSR-Seq). Rlm1 was further fine mapped in a 100 kb region from 19.92 to 20.03 Mb in the BC population consisting of 1247 plants and a F population consisting of 3000 plants using SNP markers identified from BSR-Seq through Kompetitive Allele-Specific PCR (KASP). A potential resistance gene, BnA07G27460D, was identified in this Rlm1 region. BnA07G27460D encodes a serine/threonine dual specificity protein kinase, catalytic domain and is homologous to STN7 in predicted genes of B. rapa and B. oleracea, and A. thaliana. Robust SNP markers associated with Rlm1 were developed, which can assist in introgression of Rlm1 and confirm the presence of Rlm1 gene in canola breeding programs.

Citing Articles

Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield.

Wang H, Li X, Meng B, Fan Y, Khan S, Qian M Plant Biotechnol J. 2024; 22(7):1897-1912.

PMID: 38386569 PMC: 11182599. DOI: 10.1111/pbi.14309.

Identification of a Branch Number Locus in Soybean Using BSA-Seq and GWAS Approaches.

Dai D, Huang L, Zhang X, Zhang S, Yuan Y, Wu G Int J Mol Sci. 2024; 25(2).

PMID: 38255945 PMC: 10815202. DOI: 10.3390/ijms25020873.

Detection of Blackleg Resistance Gene Rlm1 in Double-Low Rapeseed Accessions from Sichuan Province, by Kompetitive Allele-Specific PCR.

Chai L, Zhang J, Fernando W, Li H, Huang X, Cui C Plant Pathol J. 2021; 37(2):194-199.

PMID: 33866761 PMC: 8053842. DOI: 10.5423/PPJ.OA.10.2020.0204.

Genome-wide transcriptome reveals mechanisms underlying Rlm1-mediated blackleg resistance on canola.

Zhai C, Liu X, Song T, Yu F, Peng G Sci Rep. 2021; 11(1):4407.

PMID: 33623070 PMC: 7902848. DOI: 10.1038/s41598-021-83267-0.

Recent Findings Unravel Genes and Genetic Factors Underlying Resistance in and Its Relatives.

Cantila A, Saad N, Amas J, Edwards D, Batley J Int J Mol Sci. 2021; 22(1).

PMID: 33396785 PMC: 7795555. DOI: 10.3390/ijms22010313.

References

Schonberg A, Rodiger A, Mehwald W, Galonska J, Christ G, Helm S . Identification of STN7/STN8 kinase targets reveals connections between electron transport, metabolism and gene expression. Plant J. 2017; 90(6):1176-1186. DOI: 10.1111/tpj.13536. View

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R . InterProScan: protein domains identifier. Nucleic Acids Res. 2005; 33(Web Server issue):W116-20. PMC: 1160203. DOI: 10.1093/nar/gki442. View

Li P, Quan X, Jia G, Xiao J, Cloutier S, You F . RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. BMC Genomics. 2016; 17(1):852. PMC: 5093994. DOI: 10.1186/s12864-016-3197-x. View

Yu F, Gugel R, Randy Kutcher H, Peng G, Rimmer S . Identification and mapping of a novel blackleg resistance locus LepR4 in the progenies from Brassica napus × B. rapa subsp. sylvestris. Theor Appl Genet. 2012; 126(2):307-15. DOI: 10.1007/s00122-012-1919-2. 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

Larkan N, Lydiate D, Parkin I, Nelson M, Epp D, Cowling W . The Brassica napus blackleg resistance gene LepR3 encodes a receptor-like protein triggered by the Leptosphaeria maculans effector AVRLM1. New Phytol. 2012; 197(2):595-605. DOI: 10.1111/nph.12043. View

Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M . AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995; 23(21):4407-14. PMC: 307397. DOI: 10.1093/nar/23.21.4407. View

Dion Y, Gugel R, Rakow G, Seguin-Swartz G, Landry B . RFLP mapping of resistance to the blackleg disease [causal agent, Leptosphaeria maculans (Desm.) Ces. et de Not.] in canola (Brassica napus L.). Theor Appl Genet. 2013; 91(8):1190-4. DOI: 10.1007/BF00220928. View

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

10.

Fu F, Liu L, Chai Y, Chen L, Yang T, Jin M . Localization of QTLs for seed color using recombinant inbred lines of Brassica napus in different environments. Genome. 2007; 50(9):840-54. DOI: 10.1139/g07-068. View

11.

Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I . Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet. 2005; 111(8):1514-23. DOI: 10.1007/s00122-005-0080-6. View

12.

Delourme R, Pilet-Nayel M, Archipiano M, Horvais R, Tanguy X, Rouxel T . A Cluster of Major Specific Resistance Genes to Leptosphaeria maculans in Brassica napus. Phytopathology. 2008; 94(6):578-83. DOI: 10.1094/PHYTO.2004.94.6.578. View

13.

Sela I, Ashkenazy H, Katoh K, Pupko T . GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. 2015; 43(W1):W7-14. PMC: 4489236. DOI: 10.1093/nar/gkv318. View

14.

Saitou N, Nei M . The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25. DOI: 10.1093/oxfordjournals.molbev.a040454. View

15.

Parkin I, Sharpe A, Keith D, Lydiate D . Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome. 1995; 38(6):1122-31. DOI: 10.1139/g95-149. View

16.

Ferreira M, Williams P, Osborn T . RFLP mapping of Brassica napus using doubled haploid lines. Theor Appl Genet. 2013; 89(5):615-21. DOI: 10.1007/BF00222456. View

17.

Mayerhofer R, Wilde K, Mayerhofer M, Lydiate D, Bansal V, Good A . Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus. Genetics. 2005; 171(4):1977-88. PMC: 1456120. DOI: 10.1534/genetics.105.049098. View

18.

Li H . A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27(21):2987-93. PMC: 3198575. DOI: 10.1093/bioinformatics/btr509. View

19.

Trapnell C, Pachter L, Salzberg S . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. PMC: 2672628. DOI: 10.1093/bioinformatics/btp120. View

20.

Larkan N, Ma L, Borhan M . The Brassica napus receptor-like protein RLM2 is encoded by a second allele of the LepR3/Rlm2 blackleg resistance locus. Plant Biotechnol J. 2015; 13(7):983-92. DOI: 10.1111/pbi.12341. View