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      Genome-wide association mapping for eyespot disease in US Pacific Northwest winter wheat

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          Abstract

          Eyespot, caused by the soil-borne necrotrophic fungi Oculimacula yallundae and O. acuformis, is a disease of major economic significance for wheat, barley and rye. Pacific Northwest (PNW) winter wheat ( Triticum aestivum L.) grown in areas of high rainfall and moderate winters is most vulnerable to infection. The objective of this research was to identify novel genomic regions associated with eyespot resistance in winter wheat adapted to the PNW. Two winter wheat panels of 469 and 399 lines were compiled for one of the first genome-wide association studies (GWAS) of eyespot resistance in US winter wheat germplasm. These panels were genotyped with the Infinium 9K and 90K iSelect SNP arrays. Both panels were phenotyped for disease resistance in a two-year field study and in replicated growth chamber trials. Growth chamber trials were used to evaluate the genetic resistance of O. acuformis and O. yallundae species separately. Best linear unbiased predictors (BLUPs) were calculated across all field and growth chamber environments. A total of 73 marker-trait associations (MTAs) were detected on nine different chromosomes (1A, 2A, 2B, 4A, 5A, 5B, 7A, 7B and 7D) that were significantly associated ( p-value <0.001) with eyespot resistance in Panel A, and 19 MTAs on nine different chromosomes (1A, 1B, 2A, 2D, 3B, 5A, 5B, 7A, and 7B) in Panel B. The most significant SNPs were associated with Pch1 and Pch2 resistance genes on the long arms of chromosome 7D and 7A. Most of the novel MTAs appeared to have a minor effect on reducing eyespot disease. Nevertheless, eyespot disease scores decreased as the number of resistance alleles increased. Seven SNP markers, significantly associated with reducing eyespot disease across environments and in the absence and presence of Pch1 were identified. These markers were located on chromosomes 2A ( IWB8331), 5A ( IWB73709), 5B ( IWB47298), 7AS ( IWB47160), 7B ( IWB45005) and two SNPs ( Ex_c44379_2509 and IAAV4340) had unknown map positions. The additive effect of the MTAs explained most of the remaining phenotypic variation not accounted for by Pch1 or Pch2. This study provides breeders with adapted germplasm and novel sources of eyespot resistance to be used in the development of superior cultivars with increased eyespot resistance.

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          Cereal breeding takes a walk on the wild side.

          Elite cultivated crop gene pools of the Triticeae tribe (wheat, barley and rye) exhibit limited genetic diversity, raising concerns about our ability to increase or simply sustain crop yield and quality in the face of dynamic environmental and biotic threats. Although exploiting their wild relatives as a source of novel alleles is challenging, it has provided notable successes in cereal improvement for >100 years. Increasingly facile gene discovery, improved enabling technologies for genetics and breeding and a better understanding of the factors limiting practical exploitation of exotic germplasm promise to transform existing, and accelerate the development of new, strategies for efficient and directed germplasm utilization.
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            GGT 2.0: versatile software for visualization and analysis of genetic data.

            Ever since its first release in 1999, the free software package for visualization of molecular marker data, graphical genotype (GGT), has been constantly adapted and improved. The GGT package was developed in a plant-breeding context and thus focuses on plant genetic data but was not intended to be limited to plants only. The current version has many options for genetic analysis of populations including diversity analyses and simple association studies. A second release of the GGT package, GGT 2.0 (available through http://www.plantbreeding.wur.nl), is therefore presented in this paper. An overview of existing and new features that are available within GGT 2.0, and a case study in which GGT 2.0 is applied to analyze an existing set of plant genetic data, are presented and discussed.
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              CerealsDB 2.0: an integrated resource for plant breeders and scientists

              Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: Resources
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                2 April 2018
                2018
                : 13
                : 4
                : e0194698
                Affiliations
                [1 ] Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United State of America
                [2 ] Department of Plant Pathology, Washington State University, Pullman, WA, United State of America
                [3 ] USDA-ARS Wheat Health, Genetics, and Quality Unit, Washington State University, Pullman, WA, United State of America
                Institute of Genetics and Developmental Biology Chinese Academy of Sciences, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤]

                Current address: School of Arts and Sciences, University of Mount Olive, Mount Olive, NC, United State of America

                Author information
                http://orcid.org/0000-0002-8019-6554
                Article
                PONE-D-17-45244
                10.1371/journal.pone.0194698
                5880388
                29608579
                2bba9ada-6a10-4180-bfe1-19173b871c48

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 29 December 2017
                : 7 March 2018
                Page count
                Figures: 4, Tables: 2, Pages: 19
                Funding
                Funded by: USDA
                Award ID: 2016-68004-24770
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007588, Washington State University;
                Award ID: 3019-0232
                Award Recipient :
                We would like to thank the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award number 2016-68004-24770 to Arron H Carter and Washington State University (3019-0232) to Arron H Carter, for providing funding to support this project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Grasses
                Wheat
                Biology and Life Sciences
                Genetics
                Molecular Genetics
                Biology and Life Sciences
                Molecular Biology
                Molecular Genetics
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Gene Mapping
                Chromosome Mapping
                Research and Analysis Methods
                Molecular Biology Techniques
                Gene Mapping
                Chromosome Mapping
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Human Genetics
                Genome-Wide Association Studies
                Biology and Life Sciences
                Agriculture
                Agronomy
                Plant Breeding
                Biology and Life Sciences
                Agriculture
                Farms
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Biology and Life Sciences
                Genetics
                Heredity
                Heterozygosity
                Custom metadata
                The data has been deposited at https://triticeaetoolbox.org/wheat/.

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