Identifying Phenotypic Traits Critical for Breeding Winter Malting Barley Adapted to Ohio and the Genomic Regions Affecting Those Traits PDF Download

Author: Benjamin Matthew Eggers
Publisher:
ISBN:
Category : Barley
Languages : en
Pages : 186

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Book Description
A goal of The Ohio State University Hordeum vulgare L. breeding program is to develop winter-hardy, two-row varieties suitable for malting. Winter-hardiness and malting quality are complex traits, having multiple independent contributing components. It is critical that the program identify genotypes possessing the best agronomic and malting quality traits to guarantee Ohio barley farmers are profitable. To make better informed decisions regarding variety selection for cultivation under Ohio conditions and guide parental choice for crossing, I conducted a genome wide association study (GWAS). GWAS analyzes phenotypic data and genotypic data to test for associations between the markers and desirable traits. The GWAS was conducted using 350 barley genotypes that encompassed key germplasm contributing to the breeding program. The germplasm set was genotyped and phenotyped for agronomic and malting quality traits. Genotyping was performed using multiplexed sequencing using markers based off the barley 9k chip in collaboration with the USDA Western Regional Small Grains Genotyping Lab. Phenotypic data was collected during the 2019-2020 growing season at Wooster, North Central, and Western research branches. I identified at least one QTL associated with 27 of the 31 traits measured and identified 78 QTLs in total. Identified QTLs were all novel to Ohio malting barley and some match genomic regions previously recorded in other environments. The significant markers can be used in marker assisted selection in future breeding efforts. The phenotypic correlations found will allow for more accurate characterization of new genetic material.

Author: Daniel William Sweeney
Publisher:
ISBN:
Category :
Languages : en
Pages : 0

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Book Description
Barley (Hordeum vulgare L.) has been the primary ingredient in brewing for millennia. Recent increases in demand for local malting barley production outside of western North America for craft brewing and distilling have created a need for new varieties adapted to humid continental climates. Malting quality can be negatively affected by several seed pathogens and preharvest sprouting (PHS) in regions with wet conditions during the growing season. Genomics-assisted breeding methods, including genomic prediction and genome-wide association, have the potential to improve selection accuracy and reduce breeding cycle time to increase rates of genetic gain. My goals were to apply genomics-assisted breeding methods to address malting barley production challenges in the northeastern United States. Specific objectives included 1) examining the genetic architecture and environmental stability of the seed dormancy 2 (SD2) locus to determine if tight linkage or pleiotropy is responsible for negative correlations between PHS and malting quality, 2) studying the genetic relationships between PHS, seed dormancy, and seed germination rate to identify germplasm with PHS resistance and good malting quality, 3) exploring strategies to enhance genomic prediction accuracy in a newly established spring barley breeding program, 4) evaluating the merits of a genomic selection approach using a selection index in a newly established breeding program, and 5) releasing a two-row spring malting barley variety with disease resistance, PHS resistance, and good malting quality for local growers. The key findings of this research are 1) three functional alleles of HvMKK3 are the primary determinants of PHS resistance and seed dormancy at SD2 and HvGA20ox1 does not have an effect on these traits, 2) HvMKK3 and HvAlaAT1 are sensitive to environmental conditions and together explain a substantial portion of annual PHS variation, 3) a connected half-sib training population increases within and across family prediction accuracy and is highly powered for genome-wide association studies, 4) genomic selection using a selection index resulted in significant gain for highly weighted traits but retained genetic variance for lightly weighted traits, and 5) a new two-row spring barley variety, 'Excelsior Gold', was released as a result of these combined efforts.

Author: William Duke Pauli
Publisher:
ISBN:
Category : Barley
Languages : en
Pages : 292

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Book Description
The use of genome-wide association studies (GWAS) to detect quantitative trait loci (QTL) controlling complex traits has become a popular approach for studying key traits in crop plants. The goal of this research was to identify regions of the barley (Hordeum vulgare L.) genome that impact both agronomic and malting quality traits. By identifying these regions of the genome and their associated diagnostic markers, we gain an understanding of the genetic architecture of the traits as well as develop informative markers that can be utilized for marker-assisted selection. We used the data generated by the Barley Coordinated Agricultural Program to identify marker-trait associations impacting agronomic performance using a Q+K mixed linear model accounting for population structure and relatedness among lines. This data was also used to develop a genotyping platform specific to the Montana State University (MSU) Barley Breeding Program. This genotyping platform was used to genotype 650 advance generation lines from eleven bi-parental families to investigate the genetic basis of malting quality traits and the regions of the barley genome impacting them. We detected 41 significant marker-trait associations for the agronomic traits we studied with 31 of those being previously detected in bi-parental mapping studies. We detected 54 significant marker-trait associations for the malting quality traits with 24 of those being previously reported. The combined results from both studies indicate that major genes impacting key traits in barley are still segregating in US germplasm as well as in the MSU germplasm. This demonstrates that there is useful standing genetic variation that can be utilized for superior barley cultivar development and further genetic gain. Furthermore, by identifying the beneficial alleles, and their associated markers, we can form a "catalog" of major genes and QTL impacting agronomic and malting quality traits which can be used for marker-assisted selection. This work also demonstrates the feasibility and utility of conducting GWAS in narrow germplasm arrays like those found in regional breeding programs and serves as a paradigm for other cereal breeding programs. Together, these studies show how genomic data can be leveraged for varietal improvement in regional plant breeding programs.

Author: Adeline M. Oziel
Publisher:
ISBN:
Category : Barley
Languages : en
Pages : 82

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Book Description
Making quality and winterhardiness in barley are "ultimate" phenotypes composed of component, quantitatively inherited traits. A 69-point genome map of the seven chromosomes of barley was used, in conjunction with multi-environment phenotypes for grain yield and malting quality, to determine the chromosome locations of quantitative trait loci (QTLs). A combined analysis of the two environments identified QTLs that were both common and unique to each environment. Dispersed QTLs with positive relationships provide ready targets for marker-assisted selection. Overlapping QTLs for agronomic and making quality QTLs with favorable alleles contributed by alternate parents will require further, higher resolution mapping to determine if negative relationships are due to linkage or pleiotropy. There is preliminary evidence for orthologous agronomic trait and malting QTLs in barley. This QTL analysis will hopefully assist in the rapid development of winter making varieties that will maximize the profitability of Oregon barley production.

Author: Araby Ruth Belcher
Publisher:
ISBN:
Category : Barley
Languages : en
Pages : 202

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Book Description
This dissertation consists of a general introduction, three research manuscripts, and general conclusions regarding the mapping of quantitative trait loci (QTLs) for sustainability traits in the Triticeae Coordinated Agricultural Project (TCAP) facultative/winter 6-rowed elite malting barley genome-wide association studies (GWAS) mapping panel, the TCAP FAC-WIN6. The first research manuscript, a germplasm release, describes the general qualities of the FAC-WIN6, regarding its usefulness for mapping QTLs via GWAS and the open access of seed and data for all the lines. The other two research manuscripts concern the identification of QTLs for barley stripe rust (incited by Puccinia striiformis f. sp. hordei) resistance (14 QTLs) and malt quality (21 QTLs). For each QTL, a designation is provided as to that QTL's relative immediate usefulness in applied barley plant breeding programs, along with the information needed to use the QTL for that purpose.

Author: Amber L. Hoffstetter
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Book Description
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.

Author: Glen Patrick Fox
Publisher:
ISBN:
Category : Barley
Languages : en
Pages : 247

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Author: Jeffrey B. Endelman
Publisher:
ISBN: 9781267198815
Category :
Languages : en
Pages :

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Book Description
As part of the USDA Barley Coordinated Agricultural Project, 899 two-row spring barley lines were genotyped at 3072 SNP markers and phenotyped for four food quality traits: kernel hardness, polyphenol oxidase (PPO) activity, total phenolics, and amylose content. Analysis of the existing consensus map for this marker set revealed significant distortion in the fine structure of the Hardness locus on chromosome 5H. To create a revised barley consensus map with improved fine structure, new algorithms for the simplification and linearization of consensus graphs were developed and implemented in the R package DAGGER. DAGGER uses quadratic programming to generate a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. The root-mean-squared error between the barley linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Association mapping of the barley food quality traits identified significant features corresponding to the PPO locus on chromosome 2H and the Wax locus on 7H, but the majority of the genetic variation was unaccounted for. While the polygenic nature of the food quality traits makes traditional marker-assisted selection difficult, genomic selection is well suited for this complexity because all markers are included in the prediction model. A key method for the genomic prediction of breeding values is ridge regression (RR), which is equivalent to BLUP when the genetic covariance between lines is proportional to their similarity in genotype space. This additive model can be broadened to include epistatic effects by using other kernels, such as the Gaussian, which represent inner products in a complex feature space. To facilitate the use of RR and non-additive kernels in plant breeding, a new software package for R called rrBLUP was developed. When applied to the barley food quality traits, the cross-validation accuracy between phenotype and predicted breeding value ranged from 0.31 for total phenolics to 0.56 for kernel hardness. Although further research is needed, these results suggest genomic selection of barley food quality may be viable in the near future.

Author: Surinder Singh
Publisher:
ISBN:
Category :
Languages : en
Pages :

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"Barley is a significant industrial crop with growing role in feed, food, and bio-products especially as malt for brewing and distilling industry. Consistency in quality of malt is one of the major components in beer production. Malting quality in barley is a multifarious phenotype that combines a large number of interrelated components, each of which has a complex inheritance thus hinder genetic improvement in this important trait. Genetic mapping studies identified more than 250 QTL's (Qualitative trait loci) associated with 19 malting traits. However, limited studies have been conducted to identify genes associated with these QTLs. Map-based cloning and transposons tagging are the main approaches successfully used for gene identification and characterization. Map based cloning is tedious in barley, due to repetitive (>80%) genes and large genome size. Recent successful introduction of Ac/Ds (Activator/Dissociation) transposons in barley offers an alternative and promising approach for gene identification. One major QTL complex, QTL2 mapped on the short arm of chromosome 4H, shows large effects on malting quality parameters thus warranted its detailed characterization. Plants with single Ds insertions (TNPs), mapping near genes of interest or QTLs, become important vehicles for gene cloning through re-activation of Ds. From a publically available barley Ds insertion lines, two lines, TNP-29, and TNP-79, map to chromosome 4H, in the vicinity of QTLs for malting quality traits. Reactivation of Ds transposon using conventional and tissue culture approaches from these TNP lines lead to the identification of genes harboring in this 4H-QTL regions. Tissue-culture activation approach enabled a threefold faster development of transposon mutants for the genomic dissection of malting QTLs. Identification of unique flanking sequences, using high-efficiency thermal asymmetric interlaced PCR and inverse PCR confirmed Ds insertion in genes potentially associated with malting quality such as [beta]-GAL1 and [beta]-amylase-like genes. Alternatively, we also employed a comparative barley-rice synteny approach that detected 24 candidate genes; one of them (HvTLP8) which mapped in the QTL2 region shows differential gene expression using Real Time qPCR, among malting and non-malting barley varieties. Biochemical analyses like protein-carbohydrate binding assay, glycosylation and ELISA further confirm the association of HvTLP8 with QTL2 and malting quality. Integrated effort of saturation mutagenesis with Ds transposons and synteny- based approach will lead to a better understanding of malting quality traits and candidate genes that display quantitative variation." --

Author: C. Neal Stewart, Jr.
Publisher: John Wiley & Sons
ISBN: 1118589483
Category : Science
Languages : en
Pages : 554

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Book Description
Designed to inform and inspire the next generation of plant biotechnologists Plant Biotechnology and Genetics explores contemporary techniques and applications of plant biotechnology, illustrating the tremendous potential this technology has to change our world by improving the food supply. As an introductory text, its focus is on basic science and processes. It guides students from plant biology and genetics to breeding to principles and applications of plant biotechnology. Next, the text examines the critical issues of patents and intellectual property and then tackles the many controversies and consumer concerns over transgenic plants. The final chapter of the book provides an expert forecast of the future of plant biotechnology. Each chapter has been written by one or more leading practitioners in the field and then carefully edited to ensure thoroughness and consistency. The chapters are organized so that each one progressively builds upon the previous chapters. Questions set forth in each chapter help students deepen their understanding and facilitate classroom discussions. Inspirational autobiographical essays, written by pioneers and eminent scientists in the field today, are interspersed throughout the text. Authors explain how they became involved in the field and offer a personal perspective on their contributions and the future of the field. The text's accompanying CD-ROM offers full-color figures that can be used in classroom presentations with other teaching aids available online. This text is recommended for junior- and senior-level courses in plant biotechnology or plant genetics and for courses devoted to special topics at both the undergraduate and graduate levels. It is also an ideal reference for practitioners.