scholarly journals High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 145-149 ◽  
Author(s):  
Michael G. Francki ◽  
Esther Walker ◽  
Dora A. Li ◽  
Kerrie Forrest
Keyword(s):  
Average Distance ◽  
Flag Leaf ◽  
Snp Markers ◽  
Genetic Maps ◽  
Stagonospora Nodorum ◽  
Adult Plant ◽  
Stagonospora Nodorum Blotch ◽  
Snp Mapping ◽  
Marker Loci ◽  
Genomic Regions

The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex, consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, and 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074, and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. The SSR- and DArT-based genetic maps had an average distance of 6.5, 7.8, and 9.7 cM between marker loci for populations EGA/Millewa, P92201D5/P91193D1, and 6HRWSN125/WAWHT2074, respectively. This study used single nucleotide polymorphism (SNP) markers from the iSelect Infinium 90K genotyping array to fine-map genomic regions harbouring QTL for flag leaf and glume SNB resistance, reducing the average distance between markers to 2.9, 3.3, and 3.4 cM for populations P92201D5/P91193D1, EGA/Millewa, and 6HRWSN125/WAWHT2074, respectively. Increasing the marker density of the genetic maps with SNPs did not identify any new QTL for SNB resistance but discriminated previously identified co-located QTL into separate but closely linked QTL.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

2020 ◽  
Vol 3 (2) ◽  
pp. 28 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Trait Loci ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

scholarly journals Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jyotirmoy Halder ◽  
Jinfeng Zhang ◽  
Shaukat Ali ◽  
Jagdeep S. Sidhu ◽  
Harsimardeep S. Gill ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Fusarium Head Blight ◽  
Tan Spot ◽  
Stagonospora Nodorum ◽  
Head Blight ◽  
Sources Of Resistance ◽  
Stagonospora Nodorum Blotch ◽  
Valuable Source ◽  
Race 1 ◽  
Genomic Regions

Abstract Background In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB). Results A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms. Conclusion Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.

scholarly journals Pre-breeding for disease resistance in wheat – the stagonospora nodorum blotch example

2012 ◽  
Vol 33 (1) ◽  
pp. 6
Author(s):  
Manisha Shankar ◽  
Michael Francki ◽  
Rob Loughman
Keyword(s):  
Molecular Markers ◽  
Disease Resistance ◽  
Adult Plant Resistance ◽  
Stagonospora Nodorum ◽  
Genetic Enhancement ◽  
Adult Plant ◽  
Genetic Knowledge ◽  
Breeding Programs ◽  
Stagonospora Nodorum Blotch ◽  
Resistance Expression

?Pre-breeding? is an alternative term used for ?genetic enhancement?, and in recent times it has become an essential, planned part of all plant breeding activities. The main objectives of pre-breeding for disease resistance are to increase the efficiency of breeding by providing breeding programs with (i) molecular markers linked to effective disease resistance genes, (ii) improved germplasm and associated genetic knowledge that enhance resistance expression and diversity, (iii) improved parental stocks which can be readily utilised within breeding programs and (iv) improved selection methodologies. This article discusses the various activities involved in a pre-breeding program targeting disease resistance with recent outcomes of genetic enhancement for adult plant resistance to stagonospora nodorum blotch in wheat.

scholarly journals A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

2021 ◽  
pp. 1-7
Author(s):  
Prashant Bhandari ◽  
Tong Geon Lee
Keyword(s):  
Genetic Map ◽  
Recombination Frequency ◽  
Average Distance ◽  
Genetic Research ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphism ◽  
Fresh Market ◽  
Crop Breeding ◽  
Single Nucleotide

Genetic maps saturated with genetic markers are useful for genetic research and crop breeding; however, the genetic map for the large-fruited fresh-market tomato (Solanum lycopersicum) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. We constructed a novel fresh-market tomato genetic map by using 3614 single nucleotide polymorphism (SNP) markers and a 93 F2 segregating progeny derived from a cross between two United States large-fruited fresh-market tomato lines. The average distance between markers was less than 1 cM, and substantial recombination densities between markers were observed across the approximate centromere locations. A linkage panel for large-fruited fresh-market tomato was also established using the combined dataset of the genetic map and 58 SNP-genotyped core tomato lines. The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches.

scholarly journals New Quantitative Trait Loci in Wheat for Flag Leaf Resistance to Stagonospora nodorum Blotch

2011 ◽  
Vol 101 (11) ◽  
pp. 1278-1284 ◽  
Author(s):  
M. G. Francki ◽  
M. Shankar ◽  
E. Walker ◽  
R. Loughman ◽  
H. Golzar ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Flag Leaf ◽  
Stagonospora Nodorum ◽  
Stagonospora Nodorum Blotch ◽  
Leaf Resistance ◽  
Trait Loci ◽  
Compare And Contrast ◽  
Wheat Parent

Stagonospora nodorum blotch (SNB) is a significant disease in some wheat-growing regions of the world. Resistance in wheat to Stagonospora nodorum is complex, whereby genes for seedling, flag leaf, and glume resistance are independent. The aims of this study were to identify alternative genes for flag leaf resistance, to compare and contrast with known quantitative trait loci (QTL) for SNB resistance, and to determine the potential role of host-specific toxins for SNB QTL. Novel QTL for flag leaf resistance were identified on chromosome 2AS inherited from winter wheat parent ‘P92201D5’ and chromosome 1BS from spring wheat parent ‘EGA Blanco’. The chromosomal map position of markers associated with QTL on 1BS and 2AS indicated that they were unlikely to be associated with known host–toxin insensitivity loci. A QTL on chromosome 5BL inherited from EGA Blanco had highly significant association with markers fcp001 and fcp620 based on disease evaluation in 2007 and, therefore, is likely to be associated with Tsn1-ToxA insensitivity for flag leaf resistance. However, fcp001 and fcp620 were not associated with a QTL detected based on disease evaluation in 2008, indicating two linked QTL for flag leaf resistance with multiple genes residing on 5BL. This study identified novel QTL and their effects in controlling flag leaf SNB resistance.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

2019 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Genome Wide ◽  
Trait Loci ◽  
Ssr And Snp Markers ◽  
Gene Scanning ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.

scholarly journals Genome Wide Association Study of Resistance to PstS2 and Warrior Races of Stripe (Yellow) Rust in Bread Wheat Landraces

2020 ◽  
Author(s):  
Muhammad Massub Tehseen ◽  
Fatma Aykut Tonk ◽  
Muzaffer Tosun ◽  
Ahmed Amri ◽  
Carolina P. Sansaloni ◽  
...  
Keyword(s):  
Association Study ◽  
Resistance Genes ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Adult Plant ◽  
Mapping Panel ◽  
Genome Wide ◽  
Genomic Regions ◽  
Trait Associations

ABSTRACTStripe rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and new emerging aggressive races of stripe rusts are causing serious concerns in all main wheat growing areas of the world. To search for new sources of resistance genes and associated QTL for effective utilization in future breeding programs an association mapping panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the association mapping panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study are far away from any previously reported Yr gene or QTL hence, tagging novel genomic regions. The In-silico analysis of the novel QTL regions identified candidate resistance genes encoding proteins putative to plants disease resistance and defense mechanism.

scholarly journals Identification and Mapping of Adult Plant Resistance Loci to Leaf Rust and Stripe Rust in Common Wheat Cultivar Kundan

Plant Disease ◽  
2017 ◽  
Vol 101 (3) ◽  
pp. 456-463 ◽  
Author(s):  
Y. Ren ◽  
R. P. Singh ◽  
B. R. Basnet ◽  
C. X. Lan ◽  
J. Huerta-Espino ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Stripe Rust ◽  
Plant Resistance ◽  
Adult Plant Resistance ◽  
Average Distance ◽  
Recombinant Inbred Lines ◽  
Interval Mapping ◽  
Snp Markers ◽  
Adult Plant ◽  
Additive Interaction

Leaf rust (LR) and stripe rust (YR) are important diseases of wheat worldwide. We used 148 recombinant inbred lines (RIL) from the cross of Avocet × Kundan for determining and mapping the genetic basis of adult plant resistance (APR) loci. The population was phenotyped LR and YR for three seasons in field trials conducted in Mexico and genotyped with the diversity arrays technology sequencing (DArT-Seq) and simple sequence repeat markers. The final genetic map was constructed using 2,937 polymorphic markers with an average distance of 1.29 centimorgans between markers. Inclusive composite interval mapping identified two co-located APR quantitative trait loci (QTL) for LR and YR, two LR QTL, and three YR QTL. The co-located resistance QTL on chromosome 1BL corresponded to the pleiotropic APR gene Lr46/Yr29. QLr.cim-2BL, QYr.cim-2AL, and QYr.cim-5AS could be identified as new resistance loci in this population. Lr46/Yr29 contributed 49.5 to 65.1 and 49.2 to 66.1% of LR and YR variations, respectively. The additive interaction between detected QTL showed that LR severities for RIL combining four QTL ranged between 5.3 and 25.8%, whereas the lowest YR severities were for RIL carrying QTL on chromosomes 1BL + 2AL + 6AL. The high-density DArT-Seq markers across chromosomes can be used in fine mapping of the targeted loci and development SNP markers.

scholarly journals Quantitative Trait Loci for Seedling and Adult Plant Resistance to Stagonospora nodorum in Wheat

2008 ◽  
Vol 98 (8) ◽  
pp. 886-893 ◽  
Author(s):  
M. Shankar ◽  
E. Walker ◽  
H. Golzar ◽  
R. Loughman ◽  
R. E. Wilson ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Grain Yield ◽  
Plant Resistance ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Adult Plant Resistance ◽  
Flag Leaf ◽  
Grain Weight ◽  
Stagonospora Nodorum ◽  
Adult Plant

Stagonospora nodorum blotch (SNB) caused by Stagonospora nodorum is a severe disease of wheat (Triticum aestivum) in many areas of the world. S. nodorum affects both seedling and adult plants causing necrosis of leaf and glume tissue, inhibiting photosynthetic capabilities, and reducing grain yield. The aims of this study were to evaluate disease response of 280 doubled haploid (DH) individuals derived from a cross between resistant (6HRWSN125) and susceptible (WAWHT2074) genotypes, compare quantitative trait loci (QTL) for seedling and adult plant resistance in two consecutive years, and assess the contribution of QTL on grain weight. Flag leaves and glumes of individuals from the DH population were inoculated with mixed isolates of S. nodorum at similar maturity time to provide accurate disease evaluation independent of morphological traits and identify true resistance for QTL analysis. Fungicide protected and inoculated plots were used to measure relative grain weight (RGW) as a yield-related trait under pathogen infection. The lack of similar QTL and little or no correlation in disease scores indicate different genes control seedling and adult plant disease and independent genes control flag leaf and glume resistance. This study consistently identified a QTL on chromosome 2DL for flag leaf resistance (QSnl.daw-2D) and 4BL for glume resistance (QSng.daw-4B) from the resistant parent, 6HRWSN125, explaining 4 to 19% of the phenotypic variation at each locus. A total of 5 QTL for RGW were consistently detected, where two were in the same marker interval for QSnl.daw-2D and QSng.daw-4B indicating the contribution of these QTL to yield related traits. Therefore, RGW measurement in QTL analysis could be used as a reliable indicator of grain yield affected by S. nodorum infection.

scholarly journals A Model for Predicting Onset of Stagonospora nodorum Blotch in Winter Wheat Based on Preplanting and Weather Factors

2017 ◽  
Vol 107 (6) ◽  
pp. 635-644 ◽  
Author(s):  
L. K. Mehra ◽  
C. Cowger ◽  
P. S. Ojiambo
Keyword(s):  
Logistic Regression ◽  
Winter Wheat ◽  
Flag Leaf ◽  
Disease Onset ◽  
The United States ◽  
Stagonospora Nodorum ◽  
Stagonospora Nodorum Blotch ◽  
Model Based ◽  
Leaf Emergence ◽  
Disease Occurrence

Stagonospora nodorum blotch (SNB) caused by Parastagonospora nodorum is a serious disease of wheat worldwide. In the United States, the disease is prevalent on winter wheat in many eastern states, and its management relies mainly on fungicide application after flag leaf emergence. Although SNB can occur prior to flag leaf emergence, the relationship between the time of disease onset and yield has not been determined. Such a relationship is useful in identifying a threshold to facilitate prediction of disease onset in the field. Disease occurred in 390 of 435 disease cases that were recorded across 11 counties in North Carolina from 2012 to 2014. Using cases with disease occurrence, the effect of disease onset on yield was analyzed to identify a disease onset threshold that related time of disease onset to yield. Regression analysis showed that disease onset explained 32% of the variation in yield (P < 0.0001) and from this relationship, day of year (DOY) 102 was identified as the disease onset threshold. Below-average yield occurred in 87% of the disease cases when disease onset occurred before DOY 102 but in only 28% of those cases when onset occurred on or after DOY 102. Subsequently, binary logistic regression models were developed to predict the occurrence and onset of SNB using preplanting factors and cumulative daily infection values (cDIV) starting 1 to 3 weeks prior to DOY 102. Logistic regression showed that previous crop, latitude, and cDIV accumulated 2 weeks prior to DOY 102 (cDIV.2) were significant (P < 0.0001) predictors of disease occurrence, and wheat residue, latitude, longitude, and cDIV.2 were significant (P < 0.0001) predictors of disease onset. The disease onset model had a correct classification rate of 0.94 and specificity and sensitivity rates >0.90. Performance of the disease onset model based on the area under the receiver operating characteristic curve (AUC), κ, and the true skill statistic (TSS) was excellent, with prediction accuracy values >0.88. Similarly, internal validation of the disease onset model based on AUC, κ, and TSS indicated good performance, with accuracy values >0.88. This disease onset prediction model could serve as a useful decision support tool to guide fungicide applications to manage SNB in wheat.

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