Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregant RNA sequencing

Fuyou Fu,W G Dilantha Fernando,Fengqun Yu,Xunjia Liu,Rui Wang,Gary Peng,Chun Zhai

doi:10.1038/s41598-019-51191-z

Fuyou Fu, W G Dilantha Fernando + Show 5 more

Open Access

https://doi.org/10.1038/s41598-019-51191-z

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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 BC1 population made from crosses of F1 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 BC1 population consisting of 1247 plants and a F2 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.

Highlights

Blackleg, caused by the ascomycete fungus Leptosphaeria maculans (Desmaz.) Ces. et De Not. [anamorph: Phoma lingam (Tode ex Fr.) Desmaz.], is one of the most important diseases of canola and rapeseed in many parts of the world[1,2]
Blackleg R genes previously mapped in B. napus are generally the dominant type, except LepR4 (Brassica A-genome), which was mapped to the B. napus linkage group A0614
All these blackleg R genes were identified through genetic mapping with a marker system, such as RFLPs, Simple Sequence Repeats (SSRs), Amplified Fragment Length Polymorphisms (AFLPs), Cleaved Amplified Polymorphic Sequences (CAPSs), or Sequence Related Amplified Polymorphisms (SRAPs)

Summary

Introduction

Blackleg (stem canker), caused by the ascomycete fungus Leptosphaeria maculans (Desmaz.) Ces. et De Not. [anamorph: Phoma lingam (Tode ex Fr.) Desmaz.], is one of the most important diseases of canola and rapeseed in many parts of the world[1,2]. The R genes BLMR1 and BLMR2 were mapped to the B. napus linkage group A10 in the B. napus cultivar Surpass 40015 All these blackleg R genes were identified through genetic mapping with a marker system, such as RFLPs, Simple Sequence Repeats (SSRs), Amplified Fragment Length Polymorphisms (AFLPs), Cleaved Amplified Polymorphic Sequences (CAPSs), or Sequence Related Amplified Polymorphisms (SRAPs). Recent data showed lower presence of AvrLm1 in L. maculans populations[28,29] due to use of Rlm[1] in canola cultivars extensively[30], Rlm[1] could still be valuable for effective control of blackleg disease in Canada as a strategy through rotation of R genes that has been recently implemented

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