scholarly journals Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

2018 ◽  
Author(s):  
Brian P. Ward ◽  
Gina Brown-Guedira ◽  
Frederic L. Kolb ◽  
David A. Van Sanford ◽  
Priyanka Tyagi ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Grain Yield ◽  
Reference Genome ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Soft Red Winter Wheat ◽  
Locus Model ◽  
Genome Wide ◽  
Red Winter Wheat

AbstractGrain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.

Genome-wide association studies for Fusarium head blight resistance and it’s trade-off with grain yield in soft red winter wheat

Plant Disease ◽  
2021 ◽  
Author(s):  
Rupesh Gaire ◽  
Gina Brown-Guedira ◽  
Yanhong Dong ◽  
Herbert Ohm ◽  
Mohsen Mohammadi
Keyword(s):  
Grain Yield ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Head Blight ◽  
Trade Off ◽  
Soft Red Winter Wheat ◽  
Genome Wide ◽  
Fhb Resistance ◽  
Red Winter Wheat

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies by using 13,784 SNP markers identified twenty-five genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q2B.1), Q7D.1, and Q7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared to other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has significant trade-off with grain yield.

scholarly journals Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0208217 ◽  
Author(s):  
Brian P. Ward ◽  
Gina Brown-Guedira ◽  
Frederic L. Kolb ◽  
David A. Van Sanford ◽  
Priyanka Tyagi ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Soft Red Winter Wheat ◽  
Genome Wide ◽  
Red Winter Wheat

scholarly journals Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 669 ◽  
Author(s):  
Peter S. Kristensen ◽  
Just Jensen ◽  
Jeppe R. Andersen ◽  
Carlos Guzmán ◽  
Jihad Orabi ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Genomic Prediction ◽  
Association Studies ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Breeding Programs ◽  
Genome Wide ◽  
Flour Yield

Use of genetic markers and genomic prediction might improve genetic gain for quality traits in wheat breeding programs. Here, flour yield and Alveograph quality traits were inspected in 635 F6 winter wheat breeding lines from two breeding cycles. Genome-wide association studies revealed single nucleotide polymorphisms (SNPs) on chromosome 5D significantly associated with flour yield, Alveograph P (dough tenacity), and Alveograph W (dough strength). Additionally, SNPs on chromosome 1D were associated with Alveograph P and W, SNPs on chromosome 1B were associated with Alveograph P, and SNPs on chromosome 4A were associated with Alveograph L (dough extensibility). Predictive abilities based on genomic best linear unbiased prediction (GBLUP) models ranged from 0.50 for flour yield to 0.79 for Alveograph W based on a leave-one-out cross-validation strategy. Predictive abilities were negatively affected by smaller training set sizes, lower genetic relationship between lines in training and validation sets, and by genotype–environment (G×E) interactions. Bayesian Power Lasso models and genomic feature models resulted in similar or slightly improved predictions compared to GBLUP models. SNPs with the largest effects can be used for screening large numbers of lines in early generations in breeding programs to select lines that potentially have good quality traits. In later generations, genomic predictions might be used for a more accurate selection of high quality wheat lines.

scholarly journals Genome‐Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

2016 ◽  
Vol 9 (2) ◽  
Author(s):  
Richard E. Boyles ◽  
Elizabeth A. Cooper ◽  
Matthew T. Myers ◽  
Zachary Brenton ◽  
Bradley L. Rauh ◽  
...  
Keyword(s):  
Grain Yield ◽  
Yield Components ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Grain Yield Components ◽  
Sorghum Germplasm

scholarly journals A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS

2021 ◽  
Vol 4 (4) ◽  
pp. e202000902 ◽  
Author(s):  
Robert A Player ◽  
Ellen R Forsyth ◽  
Kathleen J Verratti ◽  
David W Mohr ◽  
Alan F Scott ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Reference Genome ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Canis Lupus Familiaris ◽  
High Molecular Weight Dna ◽  
Short Read ◽  
Genome Wide ◽  
The Cost

Reference genome fidelity is critically important for genome wide association studies, yet most vary widely from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity. Further information is lost by economic necessity when genotyping populations, as lower resolution technologies such as genotyping arrays are commonly used. Here, we present a phased reference genome for Canis lupus familiaris using high molecular weight DNA-sequencing technologies. We tested wet laboratory and bioinformatic approaches to demonstrate a minimum workflow to generate the 2.4 gigabase genome for a Labrador Retriever. The de novo assembly required eight Oxford Nanopore R9.4 flowcells (∼23X depth) and running a 10X Genomics library on the equivalent of one lane of an Illumina NovaSeq S1 flowcell (∼88X depth), bringing the cost of generating a nearly complete reference genome to less than $10K (USD). Mapping of short-read data from 10 Labrador Retrievers against this reference resulted in 1% more aligned reads versus the current reference (CanFam3.1, P < 0.001), and a 15% reduction of variant calls, increasing the chance of identifying true, low-effect size variants in a genome-wide association studies. We believe that by incorporating the cost to produce a full genome assembly into any large-scale genotyping project, an investigator can improve study power, decrease costs, and optimize the overall scientific value of their study.

Genome‐wide association analysis of freezing tolerance in soft red winter wheat

Crop Science ◽  
2021 ◽  
Author(s):  
Juan Diego Rojas‐Gutierrez ◽  
Gwonjin Lee ◽  
Brian J Sanderson ◽  
M. Inam Jameel ◽  
Christopher G. Oakley
Keyword(s):  
Winter Wheat ◽  
Association Analysis ◽  
Freezing Tolerance ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Soft Red Winter Wheat ◽  
Genome Wide ◽  
Red Winter Wheat

scholarly journals Genome Wide Association Study of Frost Tolerance in Wheat

2021 ◽  
Author(s):  
Behnaz Soleimani ◽  
Heike Lehnert ◽  
Steve Babben ◽  
Jens Keilwagen ◽  
Michael Koch ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Negative Impact ◽  
Association Studies ◽  
Frost Tolerance ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Chromosome 5A

Abstract Winter wheat growing areas in the Northern hemisphere are regularly exposed to heavy frost. Due to the negative impact on yield, the identification of genetic factors controlling frost tolerance (FroT) and development of tools for breeding is of prime importance. Here, we detected QTL associated with FroT by genome wide association studies (GWAS) using a diverse panel of 276 winter wheat genotypes that was phenotyped at five locations in Germany and Russia in three years. The panel was genotyped using the 90K iSelect array and SNPs in FroT candidate genes. In total, 17,566 SNPs were used for GWAS resulting in the identification of 53 markers significantly associated (LOD ≥4) to FroT, corresponding to 23 QTL regions located on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B and 7D). The strongest QTL effect confirmed the importance of chromosome 5A for FroT. In addition, to our best knowledge, seven FroT QTLs were discovered for the first time in this study comprising QTLs on chromosomes 3A, 4A, 1B, and two on chromosomes 2D, 3D, and 7D. Identification of novel FroT candidate genes will help to better understand the FroT mechanism in wheat and to develop more effective combating strategies.

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