Comparing performances of different statistical models and multiple threshold methods in a nested association mapping population of wheat.

Nested association mapping (NAM) populations emerged as a multi-parental strategy that combines the high statistical power of biparental linkage mapping with greater allelic richness of association mapping. Several statistical models have been developed for marker-trait associations (MTAs) in genome-wide association studies (GWAS), which ranges from simple to increasingly complex models. These statistical models vary in their performance for detecting real association with the avoidance of false positives and false negatives.

LMA or vivipary? Wheat grain can germinate precociously during grain maturation under the cool conditions used to induce late maturity alpha-amylase (LMA).

Introduction: This study found that wheat () grain can germinate precociously during the maturation phase of grain development, a phenomenon called vivipary that was associated with alpha-amylase induction. Farmers receive severe discounts for grain with low falling number (FN), an indicator that grain contains sufficiently elevated levels of the starch-digesting enzyme alpha-amylase to pose a risk to end-product quality. High grain alpha-amylase can result from: preharvest sprouting (PHS)/germination when mature wheat is rained on before harvest, or from late maturity alpha-amylase (LMA) when grain experiences cool temperatures during the soft dough stage of grain maturation (Zadoks growth stage 85).

Biogenic VOCs Emission Profiles Associated with Plant-Pest Interaction for Phenotyping Applications.

Pest attacks on plants can substantially change plants' volatile organic compounds (VOCs) emission profiles. Comparison of VOC emission profiles between non-infected/non-infested and infected/infested plants, as well as resistant and susceptible plant cultivars, may provide cues for a deeper understanding of plant-pest interactions and associated resistance. Furthermore, the identification of biomarkers-specific biogenic VOCs-associated with the resistance can serve as a non-destructive and rapid tool for phenotyping applications.

Reliable DNA Markers for a Previously Unidentified, Yet Broadly Deployed Hessian Fly Resistance Gene on Chromosome 6B in Pacific Northwest Spring Wheat Varieties.

Hessian fly [ (Say)] is a major pest of wheat ( L.) throughout the United States and in several other countries. A highly effective and economically feasible way to control Hessian fly is with resistant cultivars.

Combining Genomic and Phenomic Information for Predicting Grain Protein Content and Grain Yield in Spring Wheat.

Genomics and high throughput phenomics have the potential to revolutionize the field of wheat ( L.) breeding. Genomic selection (GS) has been used for predicting various quantitative traits in wheat, especially grain yield.

Deep Learning for Predicting Complex Traits in Spring Wheat Breeding Program.

Genomic selection (GS) is transforming the field of plant breeding and implementing models that improve prediction accuracy for complex traits is needed. Analytical methods for complex datasets traditionally used in other disciplines represent an opportunity for improving prediction accuracy in GS. Deep learning (DL) is a branch of machine learning (ML) which focuses on densely connected networks using artificial neural networks for training the models.

Introgression of a Novel Ug99-Effective Stem Rust Resistance Gene into Wheat and Development of Chromosome-Specific Markers via Genotyping-by-Sequencing (GBS).

is a wild relative of common wheat ( L.) with resistance to f. , the causal agent of stem rust, including the highly virulent race TTKSK (Ug99).

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping.

Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO).

A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat.

Stem rust of wheat caused by the fungal pathogen f. sp. historically caused major yield losses of wheat worldwide.

Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions.

Background: The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments.

Multi-Locus Mixed Model Analysis Of Stem Rust Resistance In Winter Wheat.

Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f.

Virulence Characterization of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Ethiopia and Evaluation of Ethiopian Wheat Germplasm for Resistance to Races of the Pathogen from Ethiopia and the United States.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases of wheat in Ethiopia.

Association mapping of leaf rust resistance loci in a spring wheat core collection.

We identified 15 potentially novel loci in addition to previously characterized leaf rust resistance genes from 1032 spring wheat accessions. Targeted AM subset panels were instrumental in revealing interesting loci. Leaf rust is a common disease of wheat, consistently reducing yields in many wheat-growing regions of the world.

Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight.

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease of wheat and barley that leads to reduced yield and mycotoxin contamination of grain, making it unfit for human consumption. FHB is a global problem, with outbreaks in the United States, Canada, Europe, Asia and South America. In the United States alone, total direct and secondary economic losses from 1993 to 2001 owing to FHB were estimated at $7.

Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars.

Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat.

Aegilops tauschii, the diploid progenitor of the wheat D genome, is a readily accessible germplasm pool for wheat breeding as genes can be transferred to elite wheat cultivars through direct hybridization followed by backcrossing. Gene transfer and genetic mapping can be integrated by developing mapping populations during backcrossing. Using direct crossing, two genes for resistance to the African stem rust fungus race TTKSK (Ug99), were transferred from the Ae.

Spring Wheat Tolerance and Resistance to Heterodera avenae in the Pacific Northwest.

The cereal cyst nematode Heterodera avenae reduces wheat yields in the Pacific Northwest. Previous evaluations of cultivar resistance had been in controlled environments. Cultivar tolerance had not been evaluated.

Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat.

Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as 'Ug99') race group.

Development and characterization of a compensating wheat-Thinopyrum intermedium Robertsonian translocation with Sr44 resistance to stem rust (Ug99).

The emergence of the highly virulent Ug99 race complex of the stem rust fungus (Puccinia graminis Pers. f. sp.

Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculata and characterization of spontaneous translocation stocks with reduced alien chromatin.

This study reports the discovery and molecular mapping of a resistance gene effective against stem rust races RKQQC and TTKSK (Ug99) derived from Aegilops geniculata (2n = 4x = 28, U(g)U(g)M(g)M(g)). Two populations from the crosses TA5599 (T5DL-5M(g)L·5M(g)S)/TA3809 (ph1b mutant in Chinese Spring background) and TA5599/Lakin were developed and used for genetic mapping to identify markers linked to the resistance gene. Further molecular and cytogenetic characterization resulted in the identification of nine spontaneous recombinants with shortened Ae.

Development and characterization of wheat-Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust.

The emergence of a new highly virulent race of stem rust (Puccinia graminis tritici), Ug99, rapid evolution of new Ug99 derivative races overcoming resistance of widely deployed genes, and spread towards important wheat growing areas now potentially threaten world food security. Exploiting novel genes effective against Ug99 from wild relatives of wheat is one of the most promising strategies for the protection of the wheat crop. A new source of resistance to Ug99 was identified in the short arm of the Aegilops searsii chromosome 3S(s) by screening wheat- Ae.

Complex microcolinearity among wheat, rice, and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat.

A major quantitative trait locus (QTL), Qfhs.ndsu-3BS, for resistance to Fusarium head blight (FHB) in wheat has been identified and verified by several research groups. The objectives of this study were to construct a fine genetic map of this QTL region and to examine microcolinearity in the QTL region among wheat, rice, and barley.