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Improving Marker Assisted Selection In Soft Winter Wheat For Fusarium Head Blight Resistance With Qtl Validation Genome Wide Association And Genomic Selection
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Book Synopsis Improving Marker Assisted Selection in Soft Winter Wheat for Fusarium Head Blight Resistance with QTL Validation, Genome-Wide Association, and Genomic Selection by : Jared Howell Benson
Download or read book Improving Marker Assisted Selection in Soft Winter Wheat for Fusarium Head Blight Resistance with QTL Validation, Genome-Wide Association, and Genomic Selection written by Jared Howell Benson and published by . This book was released on 2011 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat by : Dennis Nicuh Bulusan Lozada
Download or read book Association Mapping and Genomic Selection for Yield and Agronomic Traits in Soft Winter Wheat written by Dennis Nicuh Bulusan Lozada and published by . This book was released on 2018 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tools such as genome-wide association study (GWAS) and genomic selection (GS) have expedited the development of crops with improved genetic potential. While GWAS aims to identify significant markers associated with a trait of interest, the goal of GS is to utilize all marker effects to predict the performance of new breeding lines prior to testing. A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft winter wheat (SWW) lines evaluated in eight site-years in Arkansas and Oklahoma. Broad sense heritability of GY (H2=0.48) was moderate compared to other traits including plant height (H2=0.81) and kernel weight (H2=0.77). Markers associated with multiple traits on chromosomes 1A, 2D, 3B, and 4B serve as potential targets for marker assisted breeding to select for GY improvement. Validation of GY-related loci using spring wheat from the International Maize and Wheat Improvement Center (CIMMYT) in Mexico confirmed the effects of three loci in chromosomes 3A, 4B, and 6B. Lines possessing the favorable allele at all three loci (A-C-G allele combination) had the highest mean GY of possible haplotypes. The same population of 239 lines was used in a GS study as a training population (TP) to determine factors that affect the predictability of GY. The TP size had the greatest effect on predictive ability across the measured traits. Adding covariates in the GS model was more advantageous in increasing prediction accuracies under single population cross validations than in forward predictions. Forward validation of the prediction models on two new populations resulted in a maximum accuracy of 0.43 for GY. Genomic selection was "superior" to marker-assisted selection in terms of response to selection and combining phenotypic selection with GS resulted in the highest response. Results from this study can be used to accelerate the process of GY improvement and increase genetic gains in wheat breeding programs.
Book Synopsis Advances in breeding for quantitative disease resistance by : Valerio Hoyos-Villegas
Download or read book Advances in breeding for quantitative disease resistance written by Valerio Hoyos-Villegas and published by Frontiers Media SA. This book was released on 2023-02-28 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat and Its Wild Relatives by : Sampurna Bartaula
Download or read book Genome-Wide Association Studies Combined with Genomic Selection as a Tool to Increase Fusarium Head Blight Resistance in Wheat and Its Wild Relatives written by Sampurna Bartaula and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Fusarium head blight (FHB) is a devastating wheat (Triticum aestivum L.) disease worldwide. Presently, there is insufficient FHB resistance in the Canadian wheat germplasm. Genome-wide association study (GWAS) and genomic selection (GS) can be utilized to identify sources of resistance that could benefit wheat breeding. To define the genetic architecture of FHB resistance, association panels from a spring and a winter collection were evaluated using the Wheat Illumina Infinium 90K array. A total of 206 accessions from the spring panel and 73 from the winter panel were evaluated in field trials for 3-4 years at two locations, namely Morden (Manitoba) and Ottawa (Ontario). These accessions were phenotyped for FHB incidence (INC), severity (SEV), visual rating index (VRI), and deoxynivalenol (DON) content. Significant (p
Book Synopsis Genomic selection and characterization in cereals by : Muhammad Abdul Rehman Rashid
Download or read book Genomic selection and characterization in cereals written by Muhammad Abdul Rehman Rashid and published by Frontiers Media SA. This book was released on 2023-05-10 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genetic and Genomic Studies on Wheat Pre-harvest Sprouting Resistance by : Meng Lin
Download or read book Genetic and Genomic Studies on Wheat Pre-harvest Sprouting Resistance written by Meng Lin and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, "Tutoumai A" and "Siyang 936", contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from "Tutoumai A" and "AUS1408" into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.
Book Synopsis Genomic Approaches for Mapping and Predicting Disease Resistance in Wheat (Triticum Aestivum L.) by : Cristiano Lemes Da Silva
Download or read book Genomic Approaches for Mapping and Predicting Disease Resistance in Wheat (Triticum Aestivum L.) written by Cristiano Lemes Da Silva and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat diseases cause significant economic losses every year. To ensure global food security, newly released cultivars must possess increased levels of broadly-effective resistance against wheat pathogens, acceptable end-use quality, and high yield potential. Genetic host resistance stands out from other management strategies as the most viable option for controlling diseases. New genotyping platforms allow whole genome marker discovery at a relatively low cost, favoring the identification of novel loci underlying traits of interest. The work presented here describes genomic approaches for mapping and predicting the resistance to Fusarium head blight (FHB) and wheat rusts. The first study used biparental mapping to identify quantitative trait loci (QTL) associated with Fusarium head blight (FHB) resistance. A doubled haploid population (DH) was originated from a cross of Everest and WB-Cedar, which are widely grown wheat cultivars in Kansas with moderately resistant and moderately susceptible reactions to FHB, respectively. We confirmed that neither of the parents carry known large-effect QTLs, suggesting that FHB resistance is native. Eight small-effect QTLs were identified as associated with multiple mechanisms of FHB resistance. All QTLs had additive effects, providing significant improvements in levels of resistance when they were found in combinations within DH lines. In the second study, a genome-wide association mapping (GWAS) and genomic selection (GS) models were applied for FHB resistance in a panel of 962 elite lines from the K-State Wheat Breeding Program. Significant single nucleotide polymorphisms (SNPs) associated with the percentage of symptomatic spikelets were identified but not reproducible across breeding panels tested in each year. Accuracy of predictions ranged from 0.25 to 0.51 depending on GS model, indicating that it can be a useful tool to increase levels of FHB resistance. GWAS and GS approaches were also applied to a historical dataset to identify loci underlying resistance to leaf and stem rust at seedling stage in a panel of elite winter wheat lines. Infection types of multiple races of wheat rusts from the last sixteen years of the Southern Regional Performance Nursery (SRPN) were used in this study. A total of 533 elite lines originating from several breeding programs were tested in the SRPN during this period of time. GWAS identified significant SNP-trait associations for wheat rusts, confirming the effectiveness of already known genes and revealing potentially novel loci associated with resistance.
Book Synopsis Assessing Genome Wide Breeding Strategies for Economic Traits in Soft Winter Wheat and Their Impact on Genetic Architecture by : Amber L. Hoffstetter
Download or read book Assessing Genome Wide Breeding Strategies for Economic Traits in Soft Winter Wheat and Their Impact on Genetic Architecture written by Amber L. Hoffstetter and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: With next generation sequencing technology, such as genotyping-by-sequencing (GBS), breeders can now genotype large populations with thousands of markers. This technology can be coupled with statistical methods such as genome-wide association studies (GWAS) and genomic selection (GS) to identify marker-trait associations and estimate marker effects. Where GWAS studies estimate each marker separately and use a p-value to determine significance, GS ignores significant thresholds and uses a training population (TP) with phenotypic and genotypic data to estimate all markers simultaneously. These effects are then used to predict the genomic estimated breeding values (GEBV) of other individuals. We performed a GWAS analysis using an elite population of soft red winter wheat lines and identified 14 QTL for grain yield (GY), four for Fusarium Head Blight (FHB) index, four for flour yield (FY), and five for softness equivalence (SE) Across all traits the R2 values ranged from 1.8 to 3.5%. We also determined the prediction accuracy GS for these four traits. Using all markers and lines we found the prediction accuracies ranged from 0.35 (FHB) to 0.57 (GY, Wooster, Ohio). In general using only data from TP lines with low GEI or marker subsets increased the GS accuracy. When using the TP to predict the performance of the 23 parental lines, accuracies using weighted correlations based on the parent’s contribution to the TP produced the highest prediction accuracies (r = 0.08 to 0.85). The accuracy of the TP model for predicting the phenotypes of the validation population was low (r = -0.25 to 0.22), especially for GY, but improved when using a subset of VP lines more related to the TP (r = 0.01 to 0.71). When analyzing the impact of GS on diversity and linkage disequilibrium (LD) we found that there was a loss of diversity across the two cycles of GS and that the second cycle of GS (GC1) is more inbred than the TP. LD for most marker pairs remains low across all three populations. The correlation of R2 values across the three populations ranged from 0.46 to 0.65. As LD between markers in the TP increases, a similar or higher LD is found with the F2 individuals comprising the two cycles of GS (GC0 and GC1). The frequency of the 1 allele for majority (46%) of markers associated with GY in Wooster, Ohio decreases while the remaining markers have either the 1 allele increasing or remaining unchanged. The preferred allele for these two trends is increasing for 95% and 80% of the markers respectively. The frequency of the 1 allele for individuals in the top 10% (best) and bottom 10% (worst) of the GC0 and GC1 individuals relative to the TP indicates that in the first cycle the majority (53%) of markers show signs of genetic drift while in the second cycle the majority (60%) show signs of direction selection. The results of this work show that these two breeding strategies could be useful for the SRWW program here of Ohio State. And indicates that GS impacts genetic diversity, LD, and allele frequencies.
Book Synopsis Marker Assisted Selection and QTL Mapping for Fusarium Head Blight Resistance in Durum Wheat by : Suresh Bhamidimarri
Download or read book Marker Assisted Selection and QTL Mapping for Fusarium Head Blight Resistance in Durum Wheat written by Suresh Bhamidimarri and published by . This book was released on 2007 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Advances in Wheat Genetics: From Genome to Field by : Yasunari Ogihara
Download or read book Advances in Wheat Genetics: From Genome to Field written by Yasunari Ogihara and published by Springer. This book was released on 2015-09-15 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: This proceedings is a collection of 46 selected papers that were presented at the 12th International Wheat Genetics Symposium (IWGS). Since the launch of the wheat genome sequencing project in 2005, the arrival of draft genome sequences has marked a new era in wheat genetics and genomics, catalyzing rapid advancement in the field. This book provides a comprehensive review of the forefront of wheat research, across various important topics such as germplasm and genetic diversity, cytogenetics and allopolyploid evolution, genome sequencing, structural and functional genomics, gene function and molecular biology, biotic stress, abiotic stress, grain quality, and classical and molecular breeding. Following an introduction, 9 parts of the book are dedicated to each of these topics. A final, 11th part entitled “Toward Sustainable Wheat Production” contains 7 excellent papers that were presented in the 12th IWGS Special Session supported by the OECD. With rapid population growth and radical climate changes, the world faces a global food crisis and is in need of another Green Revolution to boost yields of wheat and other widely grown staple crops. Although this book focuses on wheat, many of the newly developed techniques and results presented here can be applied to other plant species with large and complex genomes. As such, this volume is highly recommended for all students and researchers in wheat sciences and related plant sciences and for those who are interested in stable food production and food security.
Book Synopsis Development of New Tools and Germplasms for Improvement of Wheat Resistance to Fusarium Head Blight by : Yaoguang Li
Download or read book Development of New Tools and Germplasms for Improvement of Wheat Resistance to Fusarium Head Blight written by Yaoguang Li and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Wheat Fusarium head blight (FHB) is a devastating disease of wheat worldwide, which can significantly reduce grain yield and quality. Although the application of fungicides can reduce FHB damage, growing FHB resistant wheat is the most effective and eco-friendly approach to reduce the losses. To develop locally adapted FHB-resistant hard winter wheat germplasm, we transferred three major QTLs: Fhb1, Qfhs.ifa-5A, and Qfhb.rwg-5A.2 into two hard winter wheat cultivars, 'Everest' and 'Overland', using marker-assisted backcrossing and multiplex restriction amplicon sequencing (MRASeq). Ten 'Overland' background lines and nine 'Everest' background lines with better FHB resistance, recurrent parent similar agronomic traits were selected. They can be used as FHB resistant bridge parents for hard winter wheat breeding. To identify native FHB resistant sources, a population of 201 U.S. breeding lines and cultivars were genotyped using 90K wheat SNP arrays and phenotyped for the percentage of symptomatic spikelets (PSS), Fusarium damaged kernels (FDK) and deoxynivalenol (DON), a toxin produced by the pathogen. Genome-wide association studies (GWAS) identified significant trait associations with single nucleotide polymorphisms (SNPs) on chromosomes 1A, 1D, 2B, 3A, 3B, 4A, 5B and 5D. These marker-trait associations (MTAs) were significant for at least two of the three traits or a single trait in at least two experiments. To accelerate the evaluation of the FDK, we developed an algorithm that can separate FDK from healthy kernels with an accuracy of 90% based on color differences using image processing and unsupervised machine learning methods. Discovery and creation of the new FHB resistant germplasms and development of the fast FDK phenotyping algorithm will accelerate the improvement of U.S. hard winter wheat cultivars for FHB resistance.
Book Synopsis Biotechnological and genomic approaches for enhancing agronomic performance of crops by : Sreepriya Pramod
Download or read book Biotechnological and genomic approaches for enhancing agronomic performance of crops written by Sreepriya Pramod and published by Frontiers Media SA. This book was released on 2023-04-05 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Plant Breeding Reviews, Volume 45 by : Irwin Goldman
Download or read book Plant Breeding Reviews, Volume 45 written by Irwin Goldman and published by John Wiley & Sons. This book was released on 2021-10-21 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops.
Book Synopsis Improving Breeding Program Efficiency and Genetic Gain Through the Implementation of Genomic Selection in Diverse Wheat Germplasm by : Dylan Larkin
Download or read book Improving Breeding Program Efficiency and Genetic Gain Through the Implementation of Genomic Selection in Diverse Wheat Germplasm written by Dylan Larkin and published by . This book was released on 2020 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic selection (GS) is an important tool for increasing genetic gain for economically important traits in breeding programs. Genomic selection uses molecular markers across the entire genome in order to predict the performance of breeding lines for a trait of interest prior to phenotyping. A training population (TP) of elite germplasm, representative of the University of Arkansas wheat breeding program, was developed in order to predict important agronomic and Fusarium head blight (FHB) resistance traits within the University of Arkansas wheat breeding program through cross-validation and forward prediction. A genome-wide association study (GWAS) was performed on the TP to identify novel FHB resistance loci for deoxynivalenol (DON) accumulation, Fusarium damaged kernels (FDK), incidence (INC), and severity (SEV). Significantly loci were used as fixed effects in a GS model (GS+GWAS) and compared to a naïve GS (NGS) model, where the NGS models had significantly higher prediction accuracies (PA) than the GS+GWAS models for all four FHB traits. The GWAS identified novel loci for all four FHB traits, most notably on chromosomes 3BL and 4BL. Multivariate GS (MVGS) models using correlated traits as covariates were also compared to NGS models and the MVGS models significantly outperformed the NGS models for all four traits. The same TP was also evaluated for five agronomic traits, including grain yield (GY), heading date (HD), maturity date (MD), plant height (PH), and test weight (TW), where MVGS models were compared to NGS models. Again, MVGS models significantly outperformed NGS models for all five agronomic traits, especially when there were strong genetic correlations between predicted traits and covariates. Additionally, MVGS models were tested using GY data for genotypes only grown in some environments to predict said genotypes in missing environments. This method significantly improved PA for GY between 6% and 21% for four of six tested environments. The abovementioned TP was then used for forward prediction to predict GY for untested F4:6 breeding lines and DON, FDK, and SEV for F4:7 breeding lines. The MVGS models were comparable to phenotypic selection and had higher selection accuracies for two of three breeding cycles for GY, both cycles for DON, and at least one cycle for FDK and SEV. The MVGS model also had higher PAs for all four traits compared with the NGS models. These results show that GS, and MVGS, can be successfully implemented in a wheat breeding program over multiple breeding cycles and can be effective alongside phenotypic selection for economically important traits. The MVGS models are particularly effective when predicted traits share strong genetic correlations with covariate traits, and covariate traits have a higher heritability than the predicted traits.
Book Synopsis Mapping Quantitative Trait Loci for Fusarium Head Blight Resistance in the U.S. Winter Wheat by : Abdulrahman Hashimi
Download or read book Mapping Quantitative Trait Loci for Fusarium Head Blight Resistance in the U.S. Winter Wheat written by Abdulrahman Hashimi and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Fusarium head blight (FHB) is one of the devastating wheat diseases worldwide. It reduces not only yield, but also grain quality due to mycotoxins produced by the pathogen Fusarium graminearum. To identify consistent quantitative trait loci (QTLs) for FHB resistance in two US winter wheat 'CI13227' and 'Lyman', we genotyped a double haploid (DH) population from '' x 'CI13227' X 'Lakin' using Illumina wheat 90K single nucleotide polymorphism (SNP) chips and two recombinant inbred line (RIL) populations from 'Lyman'x 'Overley' and 'Lyman'x 'CI13227' using genotyping-by-sequencing (GBS) and evaluated the three populations for FHB type II resistance in greenhouse and field experiments. QTL mapping identified four QTLs on chromosomes 4BS, 5AL, 2DS and 7A in the 'CI13227' x 'Lakin' population, which explained 8-17% of the phenotypic variation in different experiments. The QTL on 4BS from CI13227 showed the largest effect among QTLs detected in the 'CI13227' x 'Lakin' population and were consistently detected in three experiments. 'CI13227' contributed the resistance alleles at QTLs on 2DS and 7A, whereas 'Lakin' contributed the resistance allele at 5AL QTL. The 7A QTL was detected in only one experiment. The QTLs on the chromosomes 4B and 2D showed a high correlation with plant height, suggesting a linked genes or pleiotropic effect of these QTLs. In the 'Lyman'/'Overley' population, six QTLs were located on the chromosomes 1A, 2A, 3A, 1B, 2B and 4B, and explained 5.5 -21% of the phenotypic variations for type II resistance. The QTL on 3A from 'Lyman' showed the largest effects and detected in two greenhouses experiments. Significant correlation was not detected between the PSS and plant height in this population. In the 'Lyman'/'CI13227' population, four QTLs were detected with two QTLs on chromosomes 1A and 7A from 'CI13227' and chromosomes 2B and 3A from 'Lyman' and QTLs on 7A from 'CI13227' and 2B and 3A from 'Lyman' confirmed the results from the previous two populations. Markers for the repeatable QTLs were converted into Kompetitive allele specific PCR (KASP) markers for marker-assisted breeding to pyramid these QTLs in U.S. winter wheat.
Book Synopsis Fungal Wheat Diseases: Etiology, Breeding, and Integrated Management by : Maria Rosa Simon
Download or read book Fungal Wheat Diseases: Etiology, Breeding, and Integrated Management written by Maria Rosa Simon and published by Frontiers Media SA. This book was released on 2021-05-31 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genome-wide Prediction of Hybrid Performance and Yield Stability Analysis in Winter Wheat by : Guozheng Liu
Download or read book Genome-wide Prediction of Hybrid Performance and Yield Stability Analysis in Winter Wheat written by Guozheng Liu and published by . This book was released on 2018* with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Hybrid wheat; Yield stability; Quality trait; Disease resistance; Genomic selection; Marker-assisted selection
