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      Mapping Late Leaf Spot Resistance in Peanut ( Arachis hypogaea) Using QTL-seq Reveals Markers for Marker-Assisted Selection

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          Abstract

          Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut ( Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.

          Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

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          Most cited references 38

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          QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.

          The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps. © 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.
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            SHOREmap: simultaneous mapping and mutation identification by deep sequencing.

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              QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber.

              Next-generation sequencing enabled a fast discovery of a major QTL controlling early flowering in cucumber, corresponding to the FT gene conditioning flowering time in Arabidopsis. Next-generation sequencing technologies are making it faster and more efficient to establish the association of agronomic traits with molecular markers or candidate genes, which is the requirement for marker-assisted selection in molecular breeding. Early flowering is an important agronomic trait in cucumber (Cucumis sativus L.), but the underlying genetic mechanism is unknown. In this study, we identified a candidate gene for early flowering QTL, Ef1.1 through QTL-seq. Segregation analysis in F2 and BC1 populations derived from a cross between two inbred lines "Muromskij" (early flowering) and "9930" (late flowering) suggested quantitative nature of flowering time in cucumber. Genome-wide comparison of SNP profiles between the early and late-flowering bulks constructed from F2 plants identified a major QTL, designated Ef1.1 on cucumber chromosome 1 for early flowering in Muromskij, which was confirmed by microsatellite marker-based classical QTL mapping in the F2 population. Joint QTL-seq and traditional QTL analysis delimited Ef1.1 to an 890 kb genomic region. A cucumber gene, Csa1G651710, was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis. Quantitative RT-PCR study of the expression level of Csa1G651710 revealed significantly higher expression in early flowering genotypes. Data presented here provide support for Csa1G651710 as a possible candidate gene for early flowering in the cucumber line Muromskij.
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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
                05 February 2018
                2018
                : 9
                Affiliations
                1Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics and Genomics, University of Georgia , Athens, GA, United States
                2Department of Horticulture, Institute of Plant Breeding, Genetics and Genomics, University of Georgia , Tifton, GA, United States
                3Department of Plant Pathology, University of Georgia , Tifton, GA, United States
                4Department of Crop and Soil Sciences, North Carolina State University , Raleigh, NC, United States
                5United States Department of Agriculture-Agricultural Research Service , Tifton, GA, United States
                Author notes

                Edited by: Bunyamin Tar’an, University of Saskatchewan, Canada

                Reviewed by: Ibrokhim Abdurakhmonov, The Center of Genomics and Bioinformatics, Uzbekistan; Ksenija Gasic, Clemson University, United States

                *Correspondence: Peggy Ozias-Akins, pozias@ 123456uga.edu

                These authors have contributed equally to this work.

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

                Article
                10.3389/fpls.2018.00083
                5807350
                Copyright © 2018 Clevenger, Chu, Chavarro, Botton, Culbreath, Isleib, Holbrook and Ozias-Akins.

                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 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: 4, Tables: 3, Equations: 0, References: 45, Pages: 10, Words: 0
                Funding
                Funded by: U.S. Department of Agriculture 10.13039/100000199
                Award ID: 2012-85117-19435
                Categories
                Plant Science
                Original Research

                Plant science & Botany

                arachis, qtl-seq, late leaf spot, polyploidy, resistance

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