Complexities of Chromosome Landing in a Highly Duplicated Genome: Toward Map-Based Cloning of a Gene Controlling Blackleg Resistance in Brassica napus

Abstract

The LmR1 locus, which controls seedling resistance to the blackleg fungus Leptosphaeria maculans in the Brassica napus cultivar Shiralee, was positioned on linkage group N7. Fine genetic mapping in a population of 2500 backcross lines identified three molecular markers that cosegregated with LmR1. Additional linkage mapping in a second population colocalized a seedling resistance gene, ClmR1, from the cultivar Cresor to the same genetic interval on N7 as LmR1. Both genes were located in a region that showed extensive inter-and intragenomic duplications as well as intrachromosomal tandem duplications. The tandem duplications seem to have occurred in the Brassica lineage before the divergence of B. rapa and B. oleracea but after the separation of Brassica and Arabidopsis from a common ancestor. Microsynteny was found between the region on N7 carrying the resistance gene and the end of Arabidopsis chromosome 1, interrupted by a single inversion close to the resistance locus. The collinear region in Arabidopsis was assayed for the presence of possible candidate genes for blackleg resistance. These data provided novel insights into the genomic structure and evolution of plant resistance loci and an evaluation of the candidate gene approach using comparative mapping with a model organism.

Genome wide identification of NBS-LRR genes in Brassica and their association with disease resistance in Brassica napus

“…LEM1 was found to confer seedling resistance to an isolate containing Avr1-2-4-7 (Ferreira et al, 1995a) and to be located within an extensive intra-chromosomal tandem duplication region (Mayerhofer et al, 2005). However, LmR1, cRLMm and cRLMrb are likely to be identical to Rlm4, and are present in the cultivars Major and Maluka (Rouxel et al, 2003b).…”

“…napus (LepR1,LmR1,CLmR1,Rlm1,Rlm3,Rlm7 and Rlm9) are mapped to genomic loci that correspond to the chromosome segment on Arabidopsis chromosome 1 harbouring AtRlm1 (Mayerhofer et al, 2005), it could be hypothesized that L. maculans resistance genes are related to the NBS-LRR protein family. Also of importance is to study the level of sequence conservation in blackleg resistance genes in Brassica species and Arabidopsis since little is known about sequence information of resistance genes identified so far.…”

“…In addition, this strategy has been used to identify blackleg resistance genes in B. napus (Mayerhofer et al, 2005, Fopa Fomeju et al, 2014 and clubroot resistance gene in B. rapa , Suwabe et al, 2012.…”

“…In addition, genetic mapping studies have shown that all blackleg resistance genes in B. napus are organised in clusters in two genomic regions: the Rlm2 resistance gene on chromosome A10 (Pilet et al, 2001) and five specific resistance genes: Rlm1, Rlm3, Rlm4, Rlm7, and Rlm9 on chromosome A7 (Delourme et al, 2004, Mayerhofer et al, 2005. It remains unclear whether these genes are a cluster of tightly linked genes, or a single gene with different alleles, or a combination of both (Delourme et al, 2004).…”

“…This QTL is located on chromosome A7 of B. napus, which also contains other resistance genes: Rlm1, Rlm3, Rlm4 and Rlm7 (Delourme et al, 2004). The identification of candidate blackleg resistance genes in B. napus has proven difficult by map-based cloning approaches due to the complex genomic structure of this polyploid species (Mayerhofer et al, 2005, Tollenaere et al, 2012). …”