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      Genome-Wide Association Studies for Pasmo Resistance in Flax ( Linum usitatissimum L.)

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          Abstract

          Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3–23%), were stable across all datasets and explained 32–64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR ( R 2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype ( R 2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.

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          Most cited references 57

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Principal components analysis corrects for stratification in genome-wide association studies.

            Population stratification--allele frequency differences between cases and controls due to systematic ancestry differences-can cause spurious associations in disease studies. We describe a method that enables explicit detection and correction of population stratification on a genome-wide scale. Our method uses principal components analysis to explicitly model ancestry differences between cases and controls. The resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers.
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              A haplotype map of the human genome.

                (2005)
              Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                14 January 2019
                2018
                : 9
                Affiliations
                1Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, ON, Canada
                2Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP , Nanjing, China
                3Morden Research and Development Centre, Agriculture and Agri-Food Canada , Morden, MB, Canada
                4Crop Development Centre, University of Saskatchewan , Saskatoon, SK, Canada
                Author notes

                Edited by: Yuan-Ming Zhang, Huazhong Agricultural University, China

                Reviewed by: Hailong Ning, Northeast Agricultural University, China; Dan Zhang, Henan Agricultural University, China

                *Correspondence: Sylvie Cloutier sylvie.j.cloutier@ 123456canada.ca

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2018.01982
                6339956
                Copyright © 2019 He, Xiao, Rashid, Yao, Li, Jia, Wang, Cloutier and You.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 7, Tables: 8, Equations: 1, References: 57, Pages: 15, Words: 9473
                Categories
                Plant Science
                Original Research

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