title: Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens).
abstract: Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper. Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F2, BC1and F2:3populations derived from a cross between two inbred lines 'PBC688' (CMV-resistant) and 'G29' (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F2population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F2population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F1were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Guangjun
authors.initials: G
authors.lastname: Guo
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China. Wangsbpep@163.com.
authors.forename: Shubin
authors.initials: S
authors.lastname: Wang
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Jinbing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Baogui
authors.initials: B
authors.lastname: Pan
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Weiping
authors.initials: W
authors.lastname: Diao
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ge
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
authors.forename: Changzhou
authors.initials: C
authors.lastname: Gao
authors.affiliation: Department of Horticulture, University of Kentucky, Lexington, KY, 40546-0091, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Snyder
mesh_terms: D002212:Capsicum / Q000235:genetics* / Q000821:virology; D002874:Chromosome Mapping; D017799:Cucumovirus; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D005819:Genetic Markers; D005838:Genotype; D054643:INDEL Mutation; D040582:Inheritance Patterns; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers