title: A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis.
abstract: Brassica rapa show a wide range of morphological variations. In particular, the leaf morphologies of the Japanese traditional leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey) are distinctly different, even though they are closely related cultivars that are easy to cross. In addition to the differences in the gross morphology of leaves, some cultivars of Mibuna (Kyo-nishiki) have many trichomes on its leaves, whereas Mizuna (Kyo-mizore) does not. To identify the genes responsible for the different number of trichomes, we performed a quantitative trait loci (QTL) analysis of Mizuna and Mibuna. To construct linkage maps for these cultivars, we used RNA-seq data to develop cleaved amplified polymorphic sequence (CAPS) markers. We also performed a restriction site-associated DNA sequencing (RAD-seq) analysis to detect single-nucleotide polymorphisms (SNPs). Two QTL analyses were performed in different years, and both analyses indicated that the largest effect was found on LG A9. Expression analyses showed that a gene homologous to GLABRA1 (GL1), a transcription factor implicated in trichome development in Arabidopsis thaliana, and the sequences 3'-flanking (downstream) of BrGL1, differed considerably between Mizuna (Kyo-mizore) and Mibuna (Kyo-nishiki). These results indicate that BrGL1 on LG A9 is one of the candidate genes responsible for the difference in trichome number between Mizuna and Mibuna. Detecting genes that are responsible for morphological variations allows us to better understand the breeding history of Mizuna and Mibuna.
authors.affiliation: Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
authors.forename: Yaichi
authors.initials: Y
authors.lastname: Kawakatsu
authors.affiliation: Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
authors.forename: Hokuto
authors.initials: H
authors.lastname: Nakayama
authors.affiliation: Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Kaminoyama
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Igarashi
authors.affiliation: National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Yasugi
authors.affiliation: Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kudoh
authors.affiliation: Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan.|Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.|JST PRESTO, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan.
authors.forename: Atsushi J
authors.initials: AJ
authors.lastname: Nagano
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
authors.affiliation: Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan.
authors.forename: Nakao
authors.initials: N
authors.lastname: Kubo
authors.affiliation: Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan. seisuke@cc.kyoto-su.ac.jp.|Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan. seisuke@cc.kyoto-su.ac.jp.
authors.forename: Seisuke
authors.identifier: http://orcid.org/0000-0002-6796-3675
authors.initials: S
authors.lastname: Kimura
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D029741:Brassica rapa / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics*; D001947:Breeding; D002874:Chromosome Mapping; D004268:DNA-Binding Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D060005:Genotyping Techniques; D007564:Japan; D010641:Phenotype; D010802:Phylogeny; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors; D064201:Trichomes / Q000235:genetics*; D014675:Vegetables / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D005819:Genetic Markers; D014157:Transcription Factors; C071556:GL1 protein, Arabidopsis
keywords: Brassica rapa; QTL analysis; RAD-seq; Trichomes