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).

Investigating the effect of the mean path length on reluctance actuator output force characterization.

This paper investigates the effect of the flux's mean path length (MPL) on the reluctance actuator's analytical model. It determines the circumstances where the model neglecting the MPL is valid. The analysis is carried out for both C-Core and E-Core reluctance actuators; the analytical results are calculated by using MATrix LABoratory and then validated against a finite element model simulation by using COMputer SOLution Multiphysics.

Modeling and analysis of reluctance motion system with asymmetrical air gaps.

To achieve high throughput and efficiency, semiconductor photolithography machines need an actuation system that can meet high acceleration and precision demands on the nanoscale. One available solution is the reluctance actuator, which provides higher acceleration and force output than the standard Lorentz actuator. A floating stage with air-bearings is used to eliminate friction in the photolithography process; however, vibration transfer is not entirely eliminated, leading to potential misalignment and asymmetries between the actuator elements.

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.

Identification and Mapping of Quantitative Trait Loci Associated with Stripe Rust Resistance in Spring Club Wheat Cultivar JD.

Westend. f. sp.

Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation.

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions.

Multitrait machine- and deep-learning models for genomic selection using spectral information in a wheat breeding program.

Prediction of breeding values is central to plant breeding and has been revolutionized by the adoption of genomic selection (GS). Use of machine- and deep-learning algorithms applied to complex traits in plants can improve prediction accuracies. Because of the tremendous increase in collected data in breeding programs and the slow rate of genetic gain increase, it is required to explore the potential of artificial intelligence in analyzing the data.

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.

Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population () via Genome-Wide Association Mapping.

A previous genome-wide association study (GWAS) for leaf rust (caused by ) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by f. sp.

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).

Evaluation of the Potential for Genomic Selection to Improve Spring Wheat Resistance to Fusarium Head Blight in the Pacific Northwest.

Fusarium Head Blight (FHB) has emerged in spring wheat production in Pacific Northwest during the last decade due to factors including climate changes, crop rotations, and tillage practices. A breeding population with 170 spring wheat lines was established and screened over a 2-year period in multiple locations for FHB incidence (INC), severity (SEV), and deposition of the mycotoxin, deoxynivalenol (DON). A genome-wide association study suggested that the detectable number of genetic loci and effects are limited for marker-assisted selection.

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.

Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat.

Harnessing diversity from germplasm collections is more feasible today because of the development of lower-cost and higher-throughput genotyping methods. However, the cost of phenotyping is still generally high, so efficient methods of sampling and exploiting useful diversity are needed. Genomic selection (GS) has the potential to enhance the use of desirable genetic variation in germplasm collections through predicting the genomic estimated breeding values (GEBVs) for all traits that have been measured.

Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) 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.

Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum).

SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat.

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.

Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum).

Stripe rust, caused by Puccinia striiformis Westend. f. sp.

Novel Sources of Stripe Rust Resistance Identified by Genome-Wide Association Mapping in Ethiopian Durum Wheat ( ssp. ).

Stripe rust of wheat, caused by f. sp. (), is a global concern for wheat production, and has been increasingly destructive in Ethiopia, as well as in the United States and in many other countries.

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.

Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f. sp. tritici in elite durum wheat.

Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp.