Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.)

KEY MESSAGE

Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.

Systematic characterization of multi-rust resistance genes from a 'Parula x Thatcher' population with high-density genetic map

Pyramiding multiple resistant genes has been proposed as the most effective way to control wheat rust diseases globally. Identifying the most effective pyramids is challenged by the large pool of rust resistance genes, and limited information about their mechanisms of resistance and interactions. Here, using a high-density genetic map, a double haploid population, and multi-rust field testing, we aimed to systematically characterize the most effective gene pyramids for rust resistance from the durable multi-rust resistant CIMMYT cultivar, Parula. We revealed the Parula resistance gene pyramid contains Lr34/Yr18/Sr57 (Lr34), Lr46/Yr29/Sr58 (Lr46), Lr27/Yr30/Sr2 (Sr2) and Lr68. The efficacy, magnitude of effect and interactions with each other varied for the three rust diseases. A subpopulation mapping approach was applied to characterize the complex interactions of the resistance genes by controlling for the effect of Lr34. Using this approach, we found Lr34 and Lr68 have a strong additive effect for leaf rust, while no additive effects were observed for any rusts between Lr34 and Lr46. Lr34 combined synergistically with Sr12 from Thatcher for stem rust, while the additive effect of Lr34 and Sr2 was dependent on the type of rust and environment. Two novel leaf rust QTL from Parula were identified in this study, a stable QTL QLr-7BS, and QLr-5AS, which showed Lr34 dependent expression. With these findings, we propose combining 2-3 high value genes from Canadian wheat (e.g. Sr12 from Thatcher) with a foundational multi-APR cassette for desirable and durable resistance to all three rusts in Canadian wheat.

Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

BACKGROUND

Fusarium head blight resistance genes, Fhb1 (for Type-II resistance), Fhb2 (Type-II), and Fhb5 (Type-I plus some Type-II), which originate from Sumai 3, are among the most important that confer resistance in hexaploid wheat. Near-isogenic lines (NILs), in the CDC Alsask (susceptible; n = 32) and CDC Go (moderately susceptible; n = 38) backgrounds, carrying these genes in all possible combinations were developed using flanking microsatellite markers and evaluated for their response to FHB and deoxynivalenol (DON) accumulation in eight environments. NILs were haplotyped with wheat 90 K iSelect assay to elucidate the genomic composition and confirm alleles' presence. Other than evaluating the effects of three major genes in common genetic background, the study elucidated the epistatic gene interactions as they influence FHB measurements; identified loci other than Fhb1, Fhb2, and Fhb5, in both recurrent and donor parents and examined annotated proteins in gene intervals.

RESULTS

Genotyping using 81,857 single nucleotide polymorphism (SNP) markers revealed polymorphism on all chromosomes and that the NILs carried < 3% of alleles from the resistant donor. Significant improvement in field resistance (Type-I + Type-II) resulted only among the CDC Alsask NILs, not the CDC Go NILs. The phenotypic response of NILs carrying combinations of Sumai 3 derived genes suggested non-additive responses and Fhb5 was as good as Fhb1 in conferring field resistance in both populations. In addition to Fhb1, Fhb2, and Fhb5, four to five resistance improving alleles in both populations were identified and three of five in CDC Go were contributed by the susceptible parent. The introgressed chromosome regions carried genes encoding disease resistance proteins, protein kinases, nucleotide-binding and leucine rich repeats' domains. Complex epistatic gene-gene interactions among marker loci (including Fhb1, Fhb2, Fhb5) explained > 20% of the phenotypic variation in FHB measurements.

CONCLUSIONS

Immediate Sumai 3 derivatives carry a number of resistance improving minor effect alleles, other than Fhb1, Fhb2, Fhb5. Results verified that marker-assisted selection is possible for the introgression of exotic FHB resistance genes, however, the genetic background of the recipient line and epistatic interactions can have a strong influence on expression and penetrance of any given gene.

Fungicide and Cultivar Management of Leaf Spot Diseases of Winter Wheat in Western Canada

A complex of leaf-spotting diseases-tan spot, the Septoria complex, spot blotch, and powdery mildew-are frequently observed on winter wheat in western Canada; however, there are few studies indicating varietal differences in reaction to these diseases or the benefit of fungicide application. To determine the benefit of varietal improvement and multiple fungicide treatments and application timings, field experiments were conducted at six site-years in western Canada. Two cultivars varying in reaction to leaf spot diseases were used in combination with fungicide treatments. Disease severity ranged from trace to 64% of the combined flag and penultimate leaf area diseased, differed between cultivars, and was reduced from the check by some fungicide treatments. Yield improvement by fungicide treatment varied from 3.3 to 13.2% greater than the nontreated check. At two site-years, the split application of two half rates of fungicide resulted in the greatest yield; however, in both cases, the yield benefit did not differ from a single application at the flag leaf growth stage. Cultivar selection and fungicide use under environments conducive to disease are beneficial components of an integrated leaf spot disease management program for winter wheat in western Canada.

Race Characterization of Puccinia striiformis f. sp. tritici, the Cause of Wheat Stripe Rust, in Saskatchewan and Southern Alberta, Canada and Virulence Comparison with Races from the United States

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, has been common across Saskatchewan, Canada since 2000. Fifty-nine isolates of P. striiformis f. sp. tritici, the majority of which were collected between 2011 and 2013 from Saskatchewan and southern Alberta, were analyzed for virulence frequency and diversity and compared with isolates characterized in the Pacific Northwest and Great Plains regions of the United States. In all, 31 wheat differentials, including 20 near-isogenic lines and 1 triticale variety, differentiated 59 P. striiformis f. sp. tritici isolates into 33 races, of which one race, C-PST-1, represented 31% of the isolates. None of the races were virulent on Yr5, Yr15, or YrSP. Virulence frequency ranged from 65 to 98% on YrA, Yr2, Yr8, Yr9, Yr27, Yr29, Yr32, YrSu, 'Heines VII', and 'Nord Deprez'. Race C-PST-6 was virulent on the greatest number of the differentials (n = 25) and C-PST-18 on the fewest (n = 14). Discriminant analysis of principal components and multivariate cluster analyses detected three and four major groups, respectively, which differed from each other in terms of virulence spectrum and year of collection. The diversity of the P. striiformis f. sp. tritici population in southern Alberta was greater than in Saskatchewan, which indicated that, although P. striiformis f. sp. tritici is primarily windborne over great distances and does not usually overwinter, there are detectable differences in virulence between these regions of western Canada. Comparative analyses of virulence frequency of Saskatchewan or southern Alberta isolates with isolates representing races from the Great Plains and the Pacific Northwest of the United States indicated greater similarity of Saskatchewan races to the Great Plains despite strong correlations with both parts of the United States. This suggests that the P. striiformis f. sp. tritici population in Saskatchewan is a mixture of inoculum from both parts of the United States.

Crop sequence effects on root maggot (Diptera: Anthomyiidae: Delia spp.) infestations in canola

Strong market demand for canola, Brassica napus L., has prompted some western Canadian producers to increase the frequency of this crop in rotations with other crop species, but the impact of this practice on canola insect pests has not been determined. Here, we investigate 12 cropping sequences involving canola over a 3-yr period (2008-2010 inclusive) at five locations across western Canada. Cropping sequences varied from continuous production of two herbicide-tolerant canola varieties, to production in two of 3 yr, to canola production in one of the 3 yr. Treatments analyzed were the frequency and timing of canola within the rotational sequence. Damage by larvae of root maggots (Diptera: Anthomyiidae: Delia spp.) to canola taproots increased as the study progressed, particularly in 2010 after canola had been grown continuously for 3 yr. Yield declined with continuous canola production, and differences were greatest in 2010. At mean canola crop prices for 2010, the yield reduction from continuous production amounted to economic losses of approximately Can$282-$377/ha. Crop quality, in terms of oil and protein concentrations of harvested seed, was affected more by crop variety than cropping sequence. Crop sequence effects for root maggot damage, yield, and seed quality were relatively stable in the presence of environmental (location) variation. Results of our study suggest that continuous canola production could be unsustainable over the long-term even though market forces currently provide incentive for this practice.

Identification of RAPD markers for common root rot and spot blotch (Cochliobolus sativus) resistance in barley

The identification of RAPD markers associated with genes for resistance to Cochliobolus sativus in barley would increase the efficiency of gene manipulation by reducing the number of lines that must be evaluated from a resistant by susceptible cross and by allowing selection during the off season. Two barley crosses consisting of resistant and susceptible parent genotypes ('Virden' x 'Ellice' and Fr926-77 x 'Deuce', both 2 row x 6 row crosses) and more than 140 homozygous progeny lines were rated for their reactions in field nurseries to common root rot and in a controlled environment for spot blotch. Putative RAPD markers were identified using bulked segregant analysis followed by individual progeny line analyses. Polymorphisms associated with disease reaction were detected between bulked segregant samples as differences in the band intensity of DNA fragments. The bulked segregant samples were screened against 186 RAPD primers (decamers) using the polymerase chain reaction. For the cross Fr926-77 x 'Deuce', one RAPD marker was obtained that did not segregate as expected but was associated with both diseases. For the cross 'Virden' x 'Ellice', a single RAPD marker was obtained that did not have the expected segregation ratio but was associated with spot blotch reaction. One RAPD marker linked to 2-rowed and 6-rowed spike locus was obtained in each cross, and both the marker and row type were associated with common root rot and spot blotch reactions. For the cross 'Virden' x 'Ellice', a linkage group consisting of three RAPD markers was associated with common root rot and spot blotch reaction. The genes associated with these markers condition significant levels of resistance to C. sativus and may be used to increase the speed and precision of resistance gene manipulation in barley germplasm.