scholarly journals Deep Learning Genome-wide Linkage Association Study for Wheat Fusarium Head Blight Resistance Genes Discovery

2021 ◽  
Author(s):  
Wayne Xu ◽  
Andriy Bilichak ◽  
Raman Dhariwal ◽  
Maria Henriquez ◽  
Harpinder Randhawa
Keyword(s):  
Deep Learning ◽  
Association Study ◽  
Fusarium Head Blight ◽  
Marker Genes ◽  
Parental Population ◽  
Head Blight ◽  
Gene Markers ◽  
Genome Wide ◽  
Fhb Resistance ◽  
Linkage Association

Background: Fusarium head blight (FHB) is one of the most devastating diseases of wheat worldwide and artificial intelligence can assist with understanding resistance to the disease. Considering different sample populations, marker types, reference maps, and statistical methods, we developed a Deep Learning Genome-wide Linkage Association Study (dpGLAS) of FHB resistance in wheat. Results: The dpGLAS was first applied to two bi-parental population datasets in which the cultivar AC Barrie was a common parent for FHB resistance. Eight candidate gene markers were discovered in the one AC Barrie population and 10 in the other associated with FHB resistance. Eight of these markers were also supported by the conventional QTL mapping. Most of these candidate marker genes were found associated with the Reactive Oxygen Species (ROS) and Abscisic acid (ABA) axes. These ROS and ABA pathways were further supported by RNA-seq transcriptome data of FHB resistant cv. AAC Tenacious, a parent of the third bi-parental population. In this dataset, the ROS-centered Panther protein families were significantly enriched in those genes that had most different response to FHB when compared the resistance Tenacious and the susceptible Roblin. Conclusions: This study developed the framework of dpGLAS and identified candidate genes for FHB resistance in the Canadian spring wheat cultivars AC Barrie and AAC Tenacious.

scholarly journals Evaluation of Genomic Prediction for Fusarium Head Blight Resistance with a Multi-Parental Population

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 756
Author(s):  
Wentao Zhang ◽  
Kerry Boyle ◽  
Anita Brule-Babel ◽  
George Fedak ◽  
Peng Gao ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Genomic Selection ◽  
Fusarium Head Blight Resistance ◽  
Breeding Value ◽  
Minor Effect ◽  
Parental Population ◽  
Head Blight ◽  
Training Population ◽  
Environment Model ◽  
Fhb Resistance

Fusarium head blight (FHB) resistance is quantitatively inherited, controlled by multiple minor effect genes, and highly affected by the interaction of genotype and environment. This makes genomic selection (GS) that uses genome-wide molecular marker data to predict the genetic breeding value as a promising approach to select superior lines with better resistance. However, various factors can affect accuracies of GS and better understanding how these factors affect GS accuracies could ensure the success of applying GS to improve FHB resistance in wheat. In this study, we performed a comprehensive evaluation of factors that affect GS accuracies with a multi-parental population designed for FHB resistance. We found larger sample sizes could get better accuracies. Training population designed by CDmean based optimization algorithms significantly increased accuracies than random sampling approach, while mean of predictor error variance (PEVmean) had the poorest performance. Different genomic selection models performed similarly for accuracies. Including prior known large effect quantitative trait loci (QTL) as fixed effect into the GS model considerably improved the predictability. Multi-traits models had almost no effects, while the multi-environment model outperformed the single environment model for prediction across different environments. By comparing within and across family prediction, better accuracies were obtained with the training population more closely related to the testing population. However, achieving good accuracies for GS prediction across populations is still a challenging issue for GS application.

scholarly journals Genome-Wide Association Mapping of Fusarium Head Blight Resistance in Spring Wheat Lines Developed in the Pacific Northwest and CIMMYT

2017 ◽  
Vol 107 (12) ◽  
pp. 1486-1495 ◽  
Author(s):  
Rui Wang ◽  
Jianli Chen ◽  
James A. Anderson ◽  
Junli Zhang ◽  
Weidong Zhao ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Pacific Northwest ◽  
Spring Wheat ◽  
Genome Wide Association ◽  
Head Blight ◽  
Genome Wide ◽  
The Pacific ◽  
Fhb Resistance ◽  
Wheat Lines ◽  
Sumai 3

Fusarium head blight (FHB) is a destructive disease of wheat in humid and semihumid areas of the world. It has emerged in the Pacific Northwest (PNW) in recent years because of changing climate and crop rotation practices. Our objectives in the present study were to identify and characterize quantitative trait loci (QTL) associated with FHB resistance in spring wheat lines developed in the PNW and the International Maize and Wheat Improvement Center. In total, 170 spring wheat lines were evaluated in field and greenhouse trials in 2015 and 2016. Fourteen lines showing consistent resistance in multiple environments were identified. These lines are valuable resources in wheat variety improvement of FHB resistance because they have no Sumai 3 or Sumai 3-related background. The 170 lines were genotyped using a high-density Illumina 90K single-nucleotide polymorphisms (SNP) assay and 10 other non-SNP markers. A genome-wide association analysis was conducted with a mixed model (Q+K). Consistent, significant SNP associations with multiple traits were found on chromosomes 1B, 2B, 4B, 5A, 5B, and 6A. The locus on chromosome 5B for reduced deoxynivalenol content may be novel. The identified QTL are being validated in additional mapping studies and the identified resistant lines are being used in variety development for FHB resistance and facilitated by marker-assisted selection.

scholarly journals Genome-Wide Association Study and QTL Mapping Revealed Genetic Loci for Fusarium Head Blight Resistance in Chinese Hexaploid Wheat

2021 ◽  
Author(s):  
Chaonan Shi ◽  
Junyou Geng ◽  
Yan Ren ◽  
Yueting Zheng ◽  
Chunyi Liu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Wheat Yield ◽  
Fusarium Head Blight Resistance ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genetic Loci ◽  
Head Blight ◽  
Genome Wide ◽  
Fhb Resistance

Abstract Fusarium Head Blight (FHB) greatly affects wheat yield worldwide and could also downgrade quality. In this study, a total of 406 wheat cultivars were investigated for FHB disease index (DI). Results indicated that the FHB DI of 95% of the tested cultivars showed more than scale 2. Genome-wide association study (GWAS) identified 321 SNPs significantly related to FHB resistance on all chromosomes with 2.71–13.32% phenotypic variance explained (PVE). An important genetic locus gFHB-5A (329,828,930 to 595,372,995 bp) was identified to modulate FHB resistance in two panels, and the incidence of resistant alleles at the gFHB-5A1a locus were increasing with time in the tested cultivars. Two loci of gFHB-2B (9,740,162 to 68,200,954 bp) with PVE values of 2.73–3.57% and gFHB-7A (515,126,041 to 537,557,064 bp) with PVE values of 2.71–7.04% were identified to be significantly associated with FHB resistance. Linkage analysis in a bi-parental population identified the QTL FHB.hau-4D flanked by markers wPt-8836 and wPt-4572 with PVE value of 8.9%. This study identified new genetic loci to control FHB resistance and provided useful information of marker-assist selection in wheat FHB resistance breeding.

Screening of an EMS mutagenized population of a wheat cultivar susceptible to Fusarium head blight identifies resistant variants

Plant Disease ◽  
2021 ◽  
Author(s):  
Bhavit Chhabra ◽  
Lovepreet Singh ◽  
Sydney Wallace ◽  
Adam Schoen ◽  
Yanhong Dong ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Wheat Cultivar ◽  
Genetic Resistance ◽  
Field Testing ◽  
Head Blight ◽  
Point Of Sale ◽  
Alternative Approaches ◽  
Small Grains ◽  
Fhb Resistance ◽  
Mutant Lines

Fusarium head blight (FHB) primarily caused by Fusarium graminearum is a key disease of small grains. Diseased spikes show symptoms of premature bleaching shortly after infection and have aborted or shriveled seeds, resulting in reduced yields. The fungus also deteriorates quality and safety of the grain due to production of mycotoxins, especially deoxynivalenol (DON), which can result in grain being docked or rejected at the point of sale. Genetic host resistance to FHB is quantitative and no complete genetic resistance against this devastating disease is available. Alternative approaches to develop new sources of FHB resistance are needed. In this study, we performed extensive forward genetic screening of the M4 generation of an EMS induced mutagenized population of cultivar Jagger to isolate variants with FHB resistance. In field testing, 74 mutant lines were found to have resistance against FHB spread and 30 lines out of these also had low DON content. Subsequent testing over two years in controlled greenhouse conditions revealed ten M6 lines showing significantly lower FHB spread. Seven and six lines out of those 10 lines also had reduced DON content and lower FDKs, respectively. Future endeavors will include identification of the mutations that led to resistance in these variants.

scholarly journals Alien chromatin but not Fhb7 confers Fusarium head blight resistance in wheat breeding

2021 ◽  
Author(s):  
Xianrui Guo ◽  
Qinghua Shi ◽  
Jing Yuan ◽  
Mian Wang ◽  
Jing Wang ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Fusarium Head Blight Resistance ◽  
Resistance Breeding ◽  
Wheat Breeding ◽  
Glutathione S Transferase ◽  
Head Blight ◽  
Fhb Resistance ◽  
Translocation Lines ◽  
High Level ◽  
Thinopyrum Elongatum

AbstractFusarium head blight (FHB), caused by Fusarium species, seriously threaten global wheat production. Three wheat-Th.elongatum FHB resistant translocation lines have been developed and used for breeding. Transcriptomic analysis identified a derivative glutathione S-transferase transcript T26102, which was homologous to Fhb7 and induced dramatically by Fusarium graminearum. Homologs of Fhb7 were detected in several genera in Triticeae, including Thinopyrum, Elymus, Leymus, Pseudoroegeria and Roegeria. Several wheat-Thinopyrum translocation lines carrying Fhb7 remain susceptible to FHB, and transgenic plants overexpressing the T26102 on different backgrounds did not improve the FHB resistance. Taken as a whole, we show the application of the chromatin derived from diploid Thinopyrum elongatum successfully conferring wheat with high level FHB resistance independent of the Fhb7.One Sentence SummaryThinopyrum elongatum chromatin from 7EL was successfully applied to wheat FHB resistance breeding, but the resistant gene other than the reported Fhb7 remained unknown.

scholarly journals Identification of a Novel Genomic Region Associated With Resistance to Fusarium Head Blight in Chinese Winter Wheat

2021 ◽  
Author(s):  
Yunzhe Zhao ◽  
Xinying Zhao ◽  
Mengqi Ji ◽  
Wenqi Fang ◽  
Hong Guo ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Fusarium Head Blight ◽  
Genome Wide Association Study ◽  
Wheat Breeding ◽  
Scab Resistance ◽  
Yield Reduction ◽  
Transferase Activity ◽  
Head Blight ◽  
A Genome ◽  
Fhb Resistance

Abstract Background: Fusarium head blight (FHB) is a disease affecting wheat spikes caused by Fusarium species, which leads to cases of severe yield reduction and seed contamination. Therefore, identifying resistance genes from various sources is always of importance to wheat breeders. In this study, a genome-wide association study (GWAS) focusing on FHB using a high-density genetic map constructed with 90K single nucleotide polymorphism (SNP) arrays in a panel of 205 elite winter wheat accessions, was conducted in 3 environments. Results: Sixty-six significant marker–trait associations (MTAs) were identified (P<0.001) on fifteen chromosomes explaining 5.4–11.2% of the phenotypic variation therein. Some important new genomic regions involving FHB resistance were found on chromosomes 2A, 3B, 5B, 6A, and 7B. On chromosome 7B, 6 MTAs at 92 genetic positions were found in 2 environments. Moreover, there were 11 MTAs consistently associated with diseased spikelet rate and diseased rachis rate as pleiotropic effect loci. Eight new candidate genes of FHB resistance were predicated in wheat. Of which, three genes: TraesCS5D01G006700, TraesCS6A02G013600, and TraesCS7B02G370700 on chromosome 5DS, 6AS, and 7BL, respectively, were important in defending against FHB by regulating chitinase activity, calcium ion binding, intramolecular transferase activity, and UDP-glycosyltransferase activity in wheat. In addition, a total of six excellent alleles associated with wheat scab resistance were discovered. Conclusion: These results provide important genes/loci for enhancing FHB resistance in wheat breeding populations by marker-assisted selection.

Genome‐wide analysis and prediction of Fusarium head blight resistance in soft red winter wheat

Crop Science ◽  
2020 ◽  
Vol 60 (6) ◽  
pp. 2882-2900 ◽  
Author(s):  
Dylan L. Larkin ◽  
Amanda L. Holder ◽  
R. Esten Mason ◽  
David E. Moon ◽  
Gina Brown‐Guedira ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Fusarium Head Blight ◽  
Fusarium Head Blight Resistance ◽  
Blight Resistance ◽  
Head Blight ◽  
Genome Wide Analysis ◽  
Soft Red Winter Wheat ◽  
Genome Wide ◽  
Red Winter Wheat

scholarly journals Mapping of QTL associated with Fusarium head blight in spring wheat RL4137

2009 ◽  
Vol 44 (No. 4) ◽  
pp. 147-159 ◽  
Author(s):  
Srinivasachary ◽  
N. Gosman ◽  
A. Steed ◽  
S. Faure ◽  
R. Bayles ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Resistant Variety ◽  
Resistant Line ◽  
Head Blight ◽  
Resistance Qtl ◽  
Multiple Trials ◽  
Fhb Resistance ◽  
Positive Effect

Fusarium head blight (FHB) is a destructive disease of wheat worldwide. We aimed to map QTL for FHB resistance in RL4137, a FHB resistant line derived from Frontana using 90 recombinant inbred lines (RIL) from a cross between RL4137 and the moderately FHB resistant variety Timgalen. A total of seven putative FHB resistance QTL (1B, 2B, 3A, 6A, 6B, 7A and 7D) were identified and in all but one instance, the alleles from RL4137 had a positive effect on FHB resistance. The QTL, Qfhs.jic-2band Qfhs.jic-6b contributed by the alleles from RL4137 and Timgalen, respectively were detected in multiple trials. Our study also identified three QTL for plant height (2B, 4A and 5B), two QTL for weight of infected spikelets from infected ears (2B and 6A) and one QTL for &ldquo;awns&rdquo; (2B). The QTL mapped on 2B for PH, WIS and awns co-localized with Qfhs.jic-2b. The FHB QTL on 1B and 6B were not associated with PH QTL and that the minor PH QTL on 4A and 5B, did not co-localise with any other FHB resistance QTL.

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