Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg

Kumar, Vinod; Paillard, Sophie; Fopa-Fomeju, Berline; Falentin, Cyril; Deniot, Gwenaëlle; Baron, Cécile; Vallée, Patrick; Manzanares-Dauleux, Maria; Delourme, Régine

doi:10.1007/s00122-018-3103-9

Cited by 48 publications

(91 citation statements)

References 66 publications

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“…Other consistent QTL on chromosome A07 for resistance to L. maculans evaluated by ascospore shower test was localized within the marker-intervals for Rlm3 and Rlm4. QTL for field resistance on chromosome A01 was also identified within 1 Mb of previously identified QTL for QR in B. napus populations 5,35 .…”

Section: Phenotyping Environmentmentioning

confidence: 66%

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)

Raman

Diffey²,

Barbulescu

et al. 2020

Sci Rep

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Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. to identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the 'ascospore shower' test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/ or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequencebased molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross. Blackleg, caused by the fungal pathogen Leptosphaeria maculans, is a major disease of the canola (Brassica napus L., A n A n C n C n , 2n = 4× = 38) industry especially in Australia, Canada, and France. Developing new cultivars resistant to blackleg is recognized as the most economically and environmentally safe strategy to control yield losses. Traditional breeding for blackleg resistance largely relies on the selection of elite 'good looking' lines in disease nurseries where there is high disease pressure from a diverse pathogen population. Utilizing this strategy, several canola varieties have been developed and released for commercial cultivation with ratings of moderate-to highly-resistant (to blackleg) without any prior knowledge of either r...

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Section: Phenotyping Environmentmentioning

confidence: 66%

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)

Raman

Diffey²,

Barbulescu

et al. 2020

Sci Rep

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“…Together quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) can be successful in uncovering the genetic basis of complex traits [11]. GWAS is especially useful in tree crops, where generation of bi-parental populations for QTL mapping takes many years and involves high costs [12,13].…”

Section: Introductionmentioning

confidence: 99%

Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping

et al. 2020

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Walnut shell suture strength directly impacts the ability to maintain shell integrity during harvest and processing, susceptibility to insect damage and other contamination, and the proportion of kernel halves recovered during cracking. Suture strength is therefore an important breeding objective. Here, two methods of phenotyping this trait were investigated: 1) traditional, qualitative and rather subjective scoring on an interval scale by human observers, and; 2) quantitative and continuous measurements captured by a texturometer. The aim of this work was to increase the accuracy of suture strength phenotyping and to then apply two mapping approaches, quantitative trait loci (QTL) mapping and genome wide association (GWAS) models, in order to dissect the genetic basis of the walnut suture trait. Using data collected on trees within the UC Davis Walnut Improvement Program (n = 464), the genetic correlation between the texturometer method and qualitatively scored method was high (0.826). Narrow sense heritability calculated using quantitative measurements was 0.82. A major QTL for suture strength was detected on LG05, explaining 34% of the phenotypic variation; additionally, two minor QTLs were identified on LG01 and LG11. All three QTLs were confirmed with GWAS on corresponding chromosomes. The findings reported in this study are relevant for application towards a molecular breeding program in walnut.

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“…Quantitative host resistance does affect inoculum production by decreasing disease severity, as number of pseudothecia on stems increase with phoma stem canker severity (McGee & Emmett 1977;Marcroft et al, 2004a;Lô-Pelzer et al, 2009;Bousset et al, 2019). In our study, the genotypes Av, Cb, Da, Gr, Jn, Ko had higher than average levels of quantitative resistance on stem canker severity (Table S1. 2;Fopa-Fomeju et al, 2015;Kumar et al, 2018), but they did not show any specific trend regarding fruiting bodies production at a given severity class ( Fig. 4; 5).…”

Section: Discussionmentioning

confidence: 87%

Besides stem canker severity, oilseed rape host genotype matters for the production ofLeptosphaeria maculansfruiting bodies

Bousset

Vallée

Delourme

et al. 2020

Preprint

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SummaryFor fungal cyclic epidemics on annual crops, the pathogen carry-over is an important step in designing disease control strategies. However, it remains particularly difficult to estimate and predict. Plant resistance affects the pathogen development within the epidemics but we lack data on the inter-annual transmission of inoculum. We addressed this question by considering Leptosphaeria maculans on 15 oilseed rape genotypes in field during 4 growing seasons. Stem canker severity of host genotypes was visually scored at harvest while the number of fruiting bodies produced on incubated stubble was quantified using an automated image analysis framework. Our results confirm that higher severity at harvest leads to higher fruiting body production and is significantly affected by host genotype and Nitrogen supply. Most interestingly, we show that the production of fruiting bodies is significantly and substantially affected by host genotype, independently of severity at harvest. Tracking individual stems through incubation, we confirm for the first time that the oilseed rape genotype has a direct effect, not only through disease severity. While the genericity of this finding should be investigated on other fungi, this major effect of genotype on inoculum carry-over should be taken into account in models of varietal deployment strategies.

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Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg

Cited by 48 publications

References 66 publications

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)

Genetic and physical mapping of loci for resistance to blackleg disease in canola (Brassica napus L.)

Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping

Besides stem canker severity, oilseed rape host genotype matters for the production ofLeptosphaeria maculansfruiting bodies

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