Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus

Abstract

BackgroundResistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS).ResultsDoubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response.ConclusionThrough multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0877-2) contains supplementary material, which is available to authorized users.

Single R Gene Introgression Lines for Accurate Dissection of the Brassica - Leptosphaeria Pathosystem

“…The remaining A07 R gene, Rlm1 , was localized to a region 3.8 Mb below the Rlm3 / Rlm4 map interval, positioned in an interval of approximately 920 kb (163 predicted genes) between the markers sN9539 and Ind07-02 (Figure 1). The physical location for Rlm3 and Rlm4 are in agreement with our own previous lower-resolution mapping of these genes (Larkan et al, 2016). …”

“…Seven lines were confirmed to carry Rlm4 , including two varieties not previously defined as Rlm4 varieties. Of particular note is the Australian variety Trigold, which is included as a susceptible control in some field-based disease nurseries (Raman et al, 2012b; Larkan et al, 2016). No lines were detected to carry both Rlm3 and Rlm4 , though Tapidor DH, which we have previously shown to carry Rlm2 (Larkan et al, 2015), appears to additionally contain Rlm9 .…”

“…napus variety lines and previously-reported R gene content. References: 1, (Larkan et al, 2013); 2, (Rouxel et al, 2003b); 3, (Mayerhofer et al, 1997); 4, (Delourme et al, 2006); 5, (Marcroft et al, 2012); 6, (Van De Wouw et al, 2009); 7, (van de Wouw et al, 2014); 8, (Zhang et al, 2015); 9, (Mayerhofer et al, 2005); 10, (Kutcher et al, 2007); 11, (Moreno-Rico et al, 2001); 12, (Dion et al, 1995); 13, (Ferreira et al, 1995); 14, (Rouxel et al, 2003b); 15, (Raman et al, 2012b); 16, (Yu et al, 2012); 17, (Balesdent et al, 2002); 18, (Li et al, 2004); 19, (Dusabenyagasani and Fernando, 2008); 20, (Balesdent et al, 2005); 21, (Kutcher et al, 2010); 22, (Larkan et al, 2016); 23, (Gout et al, 2006); 24, (Ghanbarnia et al, 2015); 25, (Light et al, 2011). …”

“…Six of the isolates (98-15s, 00-100s, WA30s, 89-12s, 2367s, and 3R11s) have previously been fully-characterized via whole-genome resequencing (Ghanbarnia et al, 2015). Transgenic isolates 3R11: AvrLm1 (Larkan et al, 2013), 2367: AvrLm4-7 and 2367: AvrLm7 (Larkan et al, 2016) have been described previously, as has the genomic AvrLm2 construct used to produce 3R11: AvrLm2 (Ghanbarnia et al, 2015). The remaining transgenic isolates (2367: AvrLm3 and 3R11: AvrLm6 ) were produced by introducing genomic avirulence allele constructs, including approximately 1 kb 5′ and 500 bp 3′ of the CDS (Supplementary Table 2) using the same Agrobacterium transformation method (Utermark and Karlovsky, 2008) and the fungal transformation vector (Larkan et al, 2013) as described previously.…”

“…Nineteen R genes, identified in several Brassica species, have been reported to convey race-specific resistance against L. maculans (reviewed in Raman et al, 2013). Twelve of these R genes have been positioned in the A genome of B. napus or B. rapa ( Rlm1, Rlm2, Rlm3, Rlm4, Rlm7, Rlm9, LepR1, LepR2, LepR3, LepR4 ) or the B genome of B. juncea ( LmJR1, LmJR2 ) via linkage mapping (Delourme et al, 2004; Yu et al, 2005, 2007, 2012; Christianson et al, 2006; Long et al, 2011; Raman et al, 2012a,b; Larkan et al, 2013, 2014, 2016), while two more have been assigned to B genome chromosomes of B. juncea and/or B. nigra ( Rlm6, Rlm10 ) through marker-based assessment of recombinant or chromosome addition lines (Chèvre et al, 1996, 1997; Eber et al, 2011). RlmS , identified in the B. napus variety Surpass 400 (Van De Wouw et al, 2009) likely corresponds to the BlmR2 locus mapped to chromosome A10 (Long et al, 2011; Larkan et al, 2013).…”