title: QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L.
abstract: SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots.
authors: Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan.
authors: Zhongwei
authors: Z
authors: Zou
authors: Masahiko
authors: M
authors: Ishida
authors: Feng
authors: F
authors: Li
authors: Tomohiro
authors: T
authors: Kakizaki
authors: Sho
authors: S
authors: Suzuki
authors: Hiroyasu
authors: H
authors: Kitashiba
authors: Takeshi
authors: T
authors: Nishio
mesh_terms: D015079:2-Isopropylmalate Synthase / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant / Q000235:genetics*; D020224:Expressed Sequence Tags; D005961:Glucosinolates / Q000096:biosynthesis*; D059014:High-Throughput Nucleotide Sequencing; D008291:Malate Dehydrogenase / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D060885:Multiplex Polymerase Chain Reaction; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D031224:Raphanus / Q000235:genetics* / Q000378:metabolism; D026801:Synteny; D000637:Transaminases / Q000235:genetics / Q000378:metabolism
chemical_list: C507366:4-methylthio-3-butenyl glucosinolate; D018744:DNA, Plant; D005961:Glucosinolates; D010940:Plant Proteins; D008291:Malate Dehydrogenase; D015079:2-Isopropylmalate Synthase; D000637:Transaminases; C019798:branched-chain-amino-acid transaminase