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      Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

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          Abstract

          We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat ( Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F 6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species.

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          Most cited references 29

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          Ascertainment biases in SNP chips affect measures of population divergence.

          Chip-based high-throughput genotyping has facilitated genome-wide studies of genetic diversity. Many studies have utilized these large data sets to make inferences about the demographic history of human populations using measures of genetic differentiation such as F(ST) or principal component analyses. However, the single nucleotide polymorphism (SNP) chip data suffer from ascertainment biases caused by the SNP discovery process in which a small number of individuals from selected populations are used as discovery panels. In this study, we investigate the effect of the ascertainment bias on inferences regarding genetic differentiation among populations in one of the common genome-wide genotyping platforms. We generate SNP genotyping data for individuals that previously have been subject to partial genome-wide Sanger sequencing and compare inferences based on genotyping data to inferences based on direct sequencing. In addition, we also analyze publicly available genome-wide data. We demonstrate that the ascertainment biases will distort measures of human diversity and possibly change conclusions drawn from these measures in some times unexpected ways. We also show that details of the genotyping calling algorithms can have a surprisingly large effect on population genetic inferences. We not only present a correction of the spectrum for the widely used Affymetrix SNP chips but also show that such corrections are difficult to generalize among studies.
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            Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves

             Weibo Jin,  Fangli Wu (2015)
            Background Botrytis cinerea Pers. Fr. is an important pathogen causing stem rot in tomatoes grown indoors for extended periods. MicroRNAs (miRNAs) have been reported as gene expression regulators related to several stress responses and B. cinerea infection in tomato. However, the function of miRNAs in the resistance to B. cinerea remains unclear. Results The miRNA expression patterns in tomato in response to B. cinerea stress were investigated by high-throughput sequencing. In total, 143 known miRNAs and seven novel miRNAs were identified and their corresponding expression was detected in mock- and B. cinerea-inoculated leaves. Among those, one novel and 57 known miRNAs were differentially expressed in B. cinerea-infected leaves, and 8 of these were further confirmed by quantitative reverse-transcription PCR (qRT-PCR). Moreover, five of these eight differentially expressed miRNAs could hit 10 coding sequences (CDSs) via CleaveLand pipeline and psRNAtarget program. In addition, qRT-PCR revealed that four targets were negatively correlated with their corresponding miRNAs (miR319, miR394, and miRn1). Conclusion Results of sRNA high-throughput sequencing revealed that the upregulation of miRNAs may be implicated in the mechanism by which tomato respond to B. cinerea stress. Analysis of the expression profiles of B. cinerea-responsive miRNAs and their targets strongly suggested that miR319, miR394, and miRn1 may be involved in the tomato leaves’ response to B. cinerea infection. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0410-4) contains supplementary material, which is available to authorized users.
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              A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

              Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                17 May 2016
                2016
                : 11
                : 5
                Affiliations
                [1 ]Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN 47907, United States of America
                [2 ]Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, United States of America
                [3 ]United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN 55108, United States of America
                [4 ]Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States of America
                [5 ]Agricultural Research Council – Small Grain Institute, Bethlehem, 9700, Free State, South Africa
                [6 ]Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, Kenya
                [7 ]International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, Nairobi, Kenya
                USDA, UNITED STATES
                Author notes

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

                Conceived and designed the experiments: JA MNR YJ PB TJT SB. Performed the experiments: PB TJT MNR GKM. Analyzed the data: PB. Contributed reagents/materials/analysis tools: JA. Wrote the paper: PB MNR TJT GKM SB YJ JA.

                Article
                PONE-D-15-37395
                10.1371/journal.pone.0155760
                4870046
                27186883

                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.

                Page count
                Figures: 5, Tables: 2, Pages: 22
                Product
                Funding
                Funding for this work was provided by the United States Department of Agriculture, Agriculture and Food Research Initiative and 2011-68002-30029 (Triticeae Coordinated Agricultural Project http://www.triticeaecap.org/), and the Borlaug Global Rust Initiative Durable Rust Resistance in Wheat Project (administered by Cornell University with a grant from the Bill & Melinda Gates Foundation), and the UK Department for International Development.
                Categories
                Research Article
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Quantitative Trait Loci
                Biology and Life Sciences
                Agriculture
                Crop Science
                Crops
                Cereal Crops
                Wheat
                Biology and Life Sciences
                Organisms
                Plants
                Grasses
                Wheat
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Gene Mapping
                Research and Analysis Methods
                Molecular Biology Techniques
                Gene Mapping
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomes
                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
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Alignment
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Sequence Analysis
                Sequence Alignment
                People and Places
                Geographical Locations
                Africa
                Kenya
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Gene Mapping
                Linkage Mapping
                Research and Analysis Methods
                Molecular Biology Techniques
                Gene Mapping
                Linkage Mapping
                Custom metadata
                Sequences for all lines as well as the parents are available on NCBI’s short read archive under study SRP057693 (experiments: SRX1010116 – SRX1010978). All other data (both phenotypic and genotypic) collected on the panel is available upon request.

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