Investigation and Genome-Wide Association Analysis of Fusarium Seedling Blight Resistance in Chinese Elite Wheat Lines

Fusarium seedling blight (FSB) is an important disease of wheat occurring as part of the Fusarium disease complex consisting also of Fusarium head blight (FHB). 240 Chinese elite cultivars and lines were evaluated in greenhouse experiments for FSB resistance and genotyped using the wheat 90 K single nucleotide polymorphism arrays. Among them, 23 accessions had an average lesion length of less than 0.6 cm, exhibiting potential for breeding for FSB resistance in wheat. Jingfumai 1 and Yangmai 11 had a relatively high resistance to both FSB and FHB simultaneously. Six relatively stable quantitative trait loci (QTLs) were detected on chromosome arms 1DL, 3AS, 3BL, 6BL, 7AL, and Un using the mixed linear model approach, interpreting 4.83–7.53% of phenotypic variation. There was a negative correlation between the average FSB lesion length and the BLUE FHB index with a low coefficient, and resistance to both diseases appeared to be conferred by different QTLs across the same population. Four KASP markers were detected on 1DL, 3AS, 3BL, and 6BL in QTLs to facilitate marker-assisted selection. Combined with transcriptome data analysis, eight defense-related genes were considered as candidates for mapping QTLs. The resistant elite germplasm, mapped QTLs, and KASP markers developed in this study are useful resources for enhancing Fusarium seedling blight in wheat breeding.

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Automatic Evaluation of Wheat Resistance to Fusarium Head Blight Using Dual Mask-RCNN Deep Learning Frameworks in Computer Vision

Remote Sensing ◽

10.3390/rs13010026 ◽

2020 ◽

Vol 13 (1) ◽

pp. 26

Author(s):

Wen-Hao Su ◽

Jiajing Zhang ◽

Ce Yang ◽

Rae Page ◽

Tamas Szinyei ◽

...

Keyword(s):

Fusarium Head Blight ◽

Ground Truth ◽

Wheat Breeding ◽

Head Blight ◽

Detection Rates ◽

Ground Truth Data ◽

Resistant Cultivars ◽

Feature Pyramid ◽

Rater Error ◽

Wheat Lines

In many regions of the world, wheat is vulnerable to severe yield and quality losses from the fungus disease of Fusarium head blight (FHB). The development of resistant cultivars is one means of ameliorating the devastating effects of this disease, but the breeding process requires the evaluation of hundreds of lines each year for reaction to the disease. These field evaluations are laborious, expensive, time-consuming, and are prone to rater error. A phenotyping cart that can quickly capture images of the spikes of wheat lines and their level of FHB infection would greatly benefit wheat breeding programs. In this study, mask region convolutional neural network (Mask-RCNN) allowed for reliable identification of the symptom location and the disease severity of wheat spikes. Within a wheat line planted in the field, color images of individual wheat spikes and their corresponding diseased areas were labeled and segmented into sub-images. Images with annotated spikes and sub-images of individual spikes with labeled diseased areas were used as ground truth data to train Mask-RCNN models for automatic image segmentation of wheat spikes and FHB diseased areas, respectively. The feature pyramid network (FPN) based on ResNet-101 network was used as the backbone of Mask-RCNN for constructing the feature pyramid and extracting features. After generating mask images of wheat spikes from full-size images, Mask-RCNN was performed to predict diseased areas on each individual spike. This protocol enabled the rapid recognition of wheat spikes and diseased areas with the detection rates of 77.76% and 98.81%, respectively. The prediction accuracy of 77.19% was achieved by calculating the ratio of the wheat FHB severity value of prediction over ground truth. This study demonstrates the feasibility of rapidly determining levels of FHB in wheat spikes, which will greatly facilitate the breeding of resistant cultivars.

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Genome-Wide Association Analysis of Fusarium Head Blight Resistance in Chinese Elite Wheat Lines

Frontiers in Plant Science ◽

10.3389/fpls.2020.00206 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 7

Author(s):

Zhanwang Zhu ◽

Ling Chen ◽

Wei Zhang ◽

Lijun Yang ◽

Weiwei Zhu ◽

...

Keyword(s):

Fusarium Head Blight ◽

Association Analysis ◽

Fusarium Head Blight Resistance ◽

Genome Wide Association ◽

Blight Resistance ◽

Head Blight ◽

Genome Wide Association Analysis ◽

Genome Wide ◽

Wheat Lines

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Disease Resistance Evaluation of Elite CIMMYT Wheat Lines Containing the Coupled Fhb1 and Sr2 Genes

Plant Disease ◽

10.1094/pdis-02-20-0369-re ◽

2020 ◽

Vol 104 (9) ◽

pp. 2369-2376

Author(s):

Xinyao He ◽

Gurcharn S. Brar ◽

David Bonnett ◽

Susanne Dreisigacker ◽

Jessica Hyles ◽

...

Keyword(s):

Stem Rust ◽

Selection Process ◽

Recombinant Inbred Lines ◽

Resistance Breeding ◽

Wheat Breeding ◽

Head Blight ◽

Phenotypic Marker ◽

Repulsion Phase ◽

Speed Up ◽

Wheat Lines

Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide. Fhb1 is the most widely utilized and the only isolated gene for FHB resistance, while Sr2 is a durable stem rust resistance gene used in rust-prone areas. The two loci are closely linked on the short arm of chromosome 3B and the two genes are in repulsion phase among cultivars. With climate change and the shift in Fusarium populations, it is imperative to develop wheat cultivars resistant to both diseases. The present study was dedicated to developing wheat germplasm combining Fhb1 and Sr2 resistance alleles in the International Maize and Wheat Improvement Center (CIMMYT)’s elite cultivars’ backgrounds. Four recombinant inbred lines (RILs) in Hartog background that have the resistant Fhb1 and Sr2 alleles in coupled phase linkage were crossed with seven CIMMYT bread wheat lines, resulting in 208 lines. Molecular markers for both genes were employed in addition to the use of pseudo-black chaff (PBC) as a phenotypic marker for the selection of Sr2. At various stages of the selection process, progeny lines were assessed for FHB index, Fusarium damaged kernels (FDK), stem rust, and PBC expression as well as other diseases of interest (stripe rust and leaf spotting diseases). The 25 best lines were selected for CIMMYT’s wheat breeding program. In addition to expressing resistance to FHB, most of these 25 lines have an acceptable level of resistance to other tested diseases. These lines will be useful for wheat breeding programs worldwide and potentially speed up the resistance breeding efforts against FHB and stem rust.

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Visual Assessment of the Severity of Fusarium Seedling Blight (FSB) and Fusarium Head Blight (FHB) Disease in Barley

BIO-PROTOCOL ◽

10.21769/bioprotoc.1507 ◽

2015 ◽

Vol 5 (12) ◽

Cited By ~ 1

Author(s):

Shahin Ali ◽

Lokanadha Gunupuru ◽

Fiona Doohan

Keyword(s):

Fusarium Head Blight ◽

Visual Assessment ◽

Seedling Blight ◽

Head Blight ◽

Fusarium Seedling Blight

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A Genome-Wide Association Study for Partial Resistance to Maize Common Rust

Phytopathology ◽

10.1094/phyto-11-15-0305-r ◽

2016 ◽

Vol 106 (7) ◽

pp. 745-751 ◽

Cited By ~ 19

Author(s):

Bode A. Olukolu ◽

William F. Tracy ◽

Randall Wisser ◽

Brian De Vries ◽

Peter J. Balint-Kurti

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Quantitative Resistance ◽

Mixed Linear Model ◽

Genome Wide Association ◽

Cell Wall Modification ◽

Single Nucleotide ◽

Puccinia Sorghi ◽

Genome Wide ◽

A Genome

Quantitative resistance to maize common rust (causal agent Puccinia sorghi) was assessed in an association mapping population of 274 diverse inbred lines. Resistance to common rust was found to be moderately correlated with resistance to three other diseases and with the severity of the hypersensitive defense response previously assessed in the same population. Using a mixed linear model accounting for the confounding effects of population structure and flowering time, genome-wide association tests were performed based at 246,497 single-nucleotide polymorphism loci. Three loci associated with maize common rust resistance were identified. Candidate genes at each locus had predicted roles, mainly in cell wall modification. Other candidate genes included a resistance gene and a gene with a predicted role in regulating accumulation of reactive oxygen species.

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Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize

International Journal of Molecular Sciences ◽

10.3390/ijms21197386 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7386

Author(s):

Ashok Babadev Jagtap ◽

Yogesh Vikal ◽

Gurmukh Singh Johal

Keyword(s):

Heat Stress ◽

Stress Tolerance ◽

Cost Effective ◽

Genetic Dissection ◽

Rna Seq ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Genome Wide ◽

Heat Stress Tolerance ◽

Kasp Markers

Maize is the third most important cereal crop worldwide. However, its production is vulnerable to heat stress, which is expected to become more and more severe in coming years. Germplasm resilient to heat stress has been identified, but its underlying genetic basis remains poorly understood. Genomic mapping technologies can fill the void, provided robust markers are available to tease apart the genotype-phenotype relationship. In the present investigation, we used data from an RNA-seq experiment to identify single nucleotide polymorphisms (SNPs) between two contrasting lines, LM11 and CML25, sensitive and tolerant to heat stress, respectively. The libraries for RNA-seq were made following heat stress treatment from three separate tissues/organs, comprising the top leaf, ovule, and pollen, all of which are highly vulnerable to damage by heat stress. The single nucleotide variants (SNVs) calling used STAR mapper and GATK caller pipelines in a combined approach to identify highly accurate SNPs between the two lines. A total of 554,423, 410,698, and 596,868 SNVs were discovered between LM11 and CML25 after comparing the transcript sequence reads from the leaf, pollen, and ovule libraries, respectively. Hundreds of these SNPs were then selected to develop into genome-wide Kompetitive Allele-Specific PCR (KASP) markers, which were validated to be robust with a successful SNP conversion rate of 71%. Subsequently, these KASP markers were used to effectively genotype an F2 mapping population derived from a cross of LM11 and CML25. Being highly cost-effective, these KASP markers provide a reliable molecular marker toolkit to not only facilitate the genetic dissection of the trait of heat stress tolerance but also to accelerate the breeding of heat-resilient maize by marker-assisted selection (MAS).

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

Phytopathology ◽

10.1094/phyto-02-17-0073-r ◽

2017 ◽

Vol 107 (12) ◽

pp. 1486-1495 ◽

Cited By ~ 16

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.

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