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

BACKGROUND

Resistance 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).

RESULTS

Doubled-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.

CONCLUSION

Through 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.

SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.)

BACKGROUND

Field pea (Pisum sativum L.) is a self-pollinating, diploid, cool-season food legume. Crop production is constrained by multiple biotic and abiotic stress factors, including salinity, that cause reduced growth and yield. Recent advances in genomics have permitted the development of low-cost high-throughput genotyping systems, allowing the construction of saturated genetic linkage maps for identification of quantitative trait loci (QTLs) associated with traits of interest. Genetic markers in close linkage with the relevant genomic regions may then be implemented in varietal improvement programs.

RESULTS

In this study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and used to generate comprehensive linkage maps for field pea. From a set of 36,188 variant nucleotide positions detected through in silico analysis, 768 were selected for genotyping of a recombinant inbred line (RIL) population. A total of 705 SNPs (91.7%) successfully detected segregating polymorphisms. In addition to SNPs, genomic and EST-derived simple sequence repeats (SSRs) were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Sequences associated with the mapped molecular markers were used for comparative genomic analysis with other legume species. Higher levels of conserved synteny were observed with the genomes of Medicago truncatula Gaertn. and chickpea (Cicer arietinum L.) than with soybean (Glycine max [L.] Merr.), Lotus japonicus L. and pigeon pea (Cajanus cajan [L.] Millsp.). Parents and RIL progeny were screened at the seedling growth stage for responses to salinity stress, imposed by addition of NaCl in the watering solution at a concentration of 18 dS m-1. Salinity-induced symptoms showed normal distribution, and the severity of the symptoms increased over time. QTLs for salinity tolerance were identified on linkage groups Ps III and VII, with flanking SNP markers suitable for selection of resistant cultivars. Comparison of sequences underpinning these SNP markers to the M. truncatula genome defined genomic regions containing candidate genes associated with saline stress tolerance.

CONCLUSION

The SNP assays and associated genetic linkage maps developed in this study permitted identification of salinity tolerance QTLs and candidate genes. This constitutes an important set of tools for marker-assisted selection (MAS) programs aimed at performance enhancement of field pea cultivars.

Seedling and adult plant evaluation of race variability in Leptosphaeria maculans on Brassica species in Australia

Seedling and adult plant studies were used to identify the race structure of Leptosphaeria maculans (the cause of blackleg) on oilseed Brassica species in Australia. Host-pathogen interactions using a set of 12 differential host lines identified 14 seedling relationship, however, between seedling and adult plant reactions to individual isolates, indicating that seedling and adult plant resistance are under different genetic control. While non-specific adult plant resistance was observed in the B. napus line Jet Neuf, host-pathogen interactions confirmed the existence of race-specific adult plant resistances in other differential lines.

Blackleg disease on oilseed Brassica in Australia: a review

Blackleg, caused by the fungus Leptosphaeria maculans, is the major disease of canola (Brassica napus) in Australia. The development of blackleg-resistant B. napus varieties has been a major factor in the resurgence of the industry nationwide. The main sources of resistance used in Australian public breeding programs are Japanese spring varieties and French winter varieties. In these programs, all early generation material is screened in field blackleg nurseries sown on, or adjacent to, infested canola stubble from the previous season. Little is known about the genetic control of resistance, and the mechanisms responsible for generating pathogenic variability of L. maculans isolates in Australia is largely uncharacterised. Australian B. napus varieties are the most blackleg-resistant spring varieties in the world. Apart from growing blackleg-resistant varieties, other strategies that minimise infection and delay any breakdown in varietal resistance include growing canola on the same area only once every 3 years, destroying stubble, and eradicating volunteer plants between cropping seasons. Additionally, strategic use of chemicals can provide effective control to supplement varietal resistance in areas prone to severe blackleg infestation.

Evaluation of fungicides, applied at sowing, for control of blackleg in rapeseed

The effects of 4 fungicides, applied at sowing, on the severity of blackleg disease of rapeseed were studied in the field. The systemic triazole fungicide flutriafol, coated on superphosphate fertiliser and applied as an in-furrow treatment at 250 g a.i./ha, was the most effective treatment and gave appreciable disease control and markedly increased yields. The fertiliser treatment was much more effective than a fungicide-coated sand granule treatment (also at 250 g a.i./ha). When applied as fertiliser, triadimefon (250 g a.i./ha) and procymidone (2.5 kg a.i./ha) were much less effective than flutriafol (250 g a.i./ha). When applied as granules flutriafol (2 kg a.i./ha) gave the best control of disease, and increased yields over the nil fungicide treatment (4.4 v. 3.41 t/ha, P<0.05). Triadimefon (2 kg a.i./ha) was less effective than flutriafol and diniconazole (2 kg a.i./ha) had no effect on disease. Seed dressings of the 4 fungicides were phytotoxic, and had little effect on blackleg.

Variation in seed glucosinolate concentrations of Indian mustard (Brassica juncea (L.) Czern. + Coss.)

Detailed analysis of the seeds of 128 individual plants of an Indian mustard accession, PI 183117, grown at a field site with adequate soil sulfur, revealed a wide variation in both the composition and total concentrations of seed glucosinolates. An apparent somaclonal variant of the same accession is also reported. Selection of seeds from this variant resulted in the isolation of plants with significantly lower seed glucosinolate levels and a greatly reduced variability in both content and proportions of the major seed glucosinolates, compared with the parental line. Averaged over the field experiment, and 2 glasshouse experiments (the second with 2 soil sulfur levels), the reduction in total glucosinolate concentration was 22%. Neither the effect of additional sulfur, nor its interaction with the test populations, was significant. Assuming that the variation in total seed glucosinolate concentration between plants within the selection was entirely environmental, the lower limit of the broad sense heritability in the original accession was estimated as 29.5%. Additional genetic variation appears to be necessary to reduce the seed glucosinolate content to the maximum level specified under the 'Canola' standard for rapeseed.

Evaluation of rates of flutriafol for control of blackleg of rapeseed

The effect of flutriafol, applied at sowing as fungicide coated superphosphate, on the severity of blackleg disease of rapeseed was studied in the field. Fungicide rates from 50 to 200 g a.i./ha reduced disease severity and markedly increased yields. With blackleg resistant cultivars, economic yield responses were achieved even when disease severity was low.