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Evaluation of Septoria Nodorum Blotch (SNB) Resistance in Glumes of Wheat (Triticum aestivum L.) and the Genetic Relationship With Foliar Disease Response.

ABSTRACT: Septoria nodorum blotch (SNB) is a necrotrophic disease of wheat prominent in some parts of the world, including Western Australia (WA) causing significant losses in grain yield. The genetic mechanisms for resistance are complex involving multiple quantitative trait loci. In order to decipher comparable or independent regulation, this study identified the genetic control for glume compared to foliar resistance across four environments in WA against 37 different isolates. High proportion of the phenotypic variation across environments was contributed by genotype (84.0% for glume response and 82.7% for foliar response) with genotype-by-environment interactions accounting for a proportion of the variation for both glume and foliar response (14.7 and 16.2%, respectively). Despite high phenotypic correlation across environments, most of the eight and 14 QTL detected for glume and foliar resistance using genome wide association analysis (GWAS), respectively, were identified as environment-specific. QTL for glume and foliar resistance neither co-located nor were in LD in any particular environment indicating autonomous genetic mechanisms control SNB response in adult plants, regulated by independent biological mechanisms and influenced by significant genotype-by- environment interactions. Known Snn and Tsn loci and QTL were compared with 22 environment-specific QTL. None of the eight QTL for glume or the 14 for foliar response were co-located or in linkage disequilibrium with Snn and only one foliar QTL was in LD with Tsn loci on the physical map. Therefore, glume and foliar response to SNB in wheat is regulated by multiple environment-specific loci which function independently, with limited influence of known NE-Snn interactions for disease progression in Western Australian environments. Breeding for stable resistance would consequently rely on recurrent phenotypic selection to capture and retain favorable alleles for both glume and foliar resistance relevant to a particular environment.

SUBMITTER: Francki MG

PROVIDER: S-EPMC8276050 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The slow rate of genetic gain for improving resistance to Septoria nodorum blotch (SNB) is due to the inherent complex interactions between host, isolates, and environments. Breeding for improved SNB resistance requires evaluation and selection of wheat genotypes consistently expressing low SNB response in different target production environments. The study focused on evaluating 232 genotypes from global origins for resistance to SNB in the flag leaf expressed in different Western Australian environments. The aim was to identify resistant donor germplasm against historical and contemporary pathogen isolates and enhance our knowledge of the genetic basis of genotype-by-environment interactions for SNB response. Australian wheat varieties, inbred lines from Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), and International Center for Agricultural Research in the Dry Areas (ICARDA), and landraces from discrete regions of the world showed low to moderate phenotypic correlation for disease response amongst genotypes when evaluated with historical and contemporary isolates at two locations across 3 years in Western Australia (WA). Significant (P < 0.001) genotype-by-environment interactions were detected regardless of same or different isolates used as an inoculum source. Joint regression analysis identified 19 genotypes that consistently expressed low disease severity under infection with different isolates in multi-locations. The CIMMYT inbred lines, 30ZJN09 and ZJN12 Qno25, were particularly pertinent as they had low SNB response and highest trait stability at two locations across 3 years. Genome wide association studies detected 20 QTL associated with SNB resistance on chromosomes 1A, 1B, 4B, 5A, 5B, 6A, 7A, 7B, and 7D. QTL on chromosomes 1B and 5B were previously reported in similar genomic regions. Multiple QTL were identified on 1B, 5B, 6A, and 5A and detected in response to SNB infection against different isolates and specific environments. Known SnTox-Snn interactions were either not evident or variable across WA environments and SNB response may involve other multiple complex biological mechanisms.

Project description:Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.

Project description:IntroductionSeptoria nodorum blotch (SNB) is a complex fungal disease of wheat caused by the Dothideomycete fungal pathogen Parastagonospora nodorum. The fungus infects through the use of necrotrophic effectors (NEs) that cause necrosis on hosts carrying matching dominant susceptibility genes. The Western Australia (WA) wheatbelt is a SNB "hot spot" and experiences significant under favorable conditions. Consequently, SNB has been a major target for breeders in WA for many years.Materials and methodsIn this study, we assembled a panel of 155 WA P. nodorum isolates collected over a 44-year period and compared them to 23 isolates from France and the USA using 28 SSR loci.ResultsThe WA P. nodorum population was clustered into five groups with contrasting properties. 80% of the studied isolates were assigned to two core groups found throughout the collection location and time. The other three non-core groups that encompassed transient and emergent populations were found in restricted locations and time. Changes in group genotypes occurred during periods that coincided with the mass adoption of a single or a small group of widely planted wheat cultivars. When introduced, these cultivars had high scores for SNB resistance. However, the field resistance of these new cultivars often declined over subsequent seasons prompting their replacement with new, more resistant varieties. Pathogenicity assays showed that newly emerged isolates non-core are more pathogenic than old isolates. It is likely that the non-core groups were repeatedly selected for increased virulence on the contemporary popular cultivars.DiscussionThe low level of genetic diversity within the non-core groups, difference in virulence, low abundance, and restriction to limited locations suggest that these populations more vulnerable to a population crash when the cultivar was replaced by one that was genetically different and more resistant. We characterize the observed pattern as a low-amplitude boom-and-bust cycle in contrast with the classical high amplitude boom-and-bust cycles seen for biotrophic pathogens where the contrast between resistance and susceptibility is typically much greater. Implications of the results are discussed relating to breeding strategies for more sustainable SNB resistance and more generally for pathogens with NEs.

Project description:Key messageWe identified allelic variation at two major loci, QSnb.nmbu-2A.1 and QSnb.nmbu-5A.1, showing consistent and additive effects on SNB field resistance. Validation of QSnb.nmbu-2A.1 across genetic backgrounds further highlights its usefulness for marker-assisted selection. Septoria nodorum blotch (SNB) is a disease of wheat (Triticum aestivum and T. durum) caused by the necrotrophic fungal pathogen Parastagonospora nodorum. SNB resistance is a typical quantitative trait, controlled by multiple quantitative trait loci (QTL) of minor effect. To achieve increased plant resistance, selection for resistance alleles and/or selection against susceptibility alleles must be undertaken. Here, we performed genetic analysis of SNB resistance using an eight-founder German Multiparent Advanced Generation Inter-Cross (MAGIC) population, termed BMWpop. Field trials and greenhouse testing were conducted over three seasons in Norway, with genetic analysis identifying ten SNB resistance QTL. Of these, two QTL were identified over two seasons: QSnb.nmbu-2A.1 on chromosome 2A and QSnb.nmbu-5A.1 on chromosome 5A. The chromosome 2A BMWpop QTL co-located with a robust SNB resistance QTL recently identified in an independent eight-founder MAGIC population constructed using varieties released in the United Kingdom (UK). The validation of this SNB resistance QTL in two independent multi-founder mapping populations, regardless of the differences in genetic background and agricultural environment, highlights the value of this locus in SNB resistance breeding. The second robust QTL identified in the BMWpop, QSnb.nmbu-5A.1, was not identified in the UK MAGIC population. Combining resistance alleles at both loci resulted in additive effects on SNB resistance. Therefore, using marker assisted selection to combine resistance alleles is a promising strategy for improving SNB resistance in wheat breeding. Indeed, the multi-locus haplotypes determined in this study provide markers for efficient tracking of these beneficial alleles in future wheat genetics and breeding activities.

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Evaluation of Septoria Nodorum Blotch (SNB) Resistance in Glumes of Wheat (Triticum aestivum L.) and the Genetic Relationship With Foliar Disease Response.

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