Akio Ohyama

Publications of Akio Ohyama

• Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets.

  Authors: Hiroyuki Fukuoka, Koji Miyatake, Tsukasa Nunome, Satomi Negoro, Kenta Shirasawa, Sachiko Isobe, Erika Asamizu, Hirotaka Yamaguchi, Akio Ohyama

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 02/2012;

  We constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F(2) populations. The linkageWe constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F(2) populations. The linkage map consisted of 12 linkage groups and encompassed 1,285.5 cM in total. We mapped 952 DNA markers, including 313 genomic SSR markers developed by random sequencing of simple sequence repeat (SSR)-enriched genomic libraries, and 623 single-nucleotide polymorphisms (SNP) and insertion/deletion polymorphisms (InDels) found in eggplant-expressed sequence tags (ESTs) and related genomic sequences [introns and untranslated regions (UTRs)]. Because of their co-dominant inheritance and their highly polymorphic and multi-allelic nature, the SSR markers may be more versatile than the SNP and InDel markers for map-based genetic analysis of any traits of interest using segregating populations derived from any intraspecific crosses of practical breeding materials. However, we found that the distribution of microsatellites in the genome was biased to some extent, and therefore a considerable part of the eggplant genome was first detected when gene-derived SNP and InDel markers were mapped. Of the 623 SNP and InDel markers mapped onto the eggplant integrated map, 469 were derived from eggplant unigenes contained within Solanum orthologous (SOL) gene sets (i.e., sets of orthologous unigenes from eggplant, tomato, and potato). Out of the 469 markers, 326 could also be mapped onto the tomato map. These common markers will be informative landmarks for the transfer of tomato's more saturated genomic information to eggplant and will also provide comparative information on the genome organization of the two solanaceous species. The data are available from the DNA marker database of vegetables, VegMarks ( http://vegmarks.nivot.affrc.go.jp ).

• Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.).

  Authors: Koji Miyatake, Takeo Saito, Satomi Negoro, Hirotaka Yamaguchi, Tsukasa Nunome, Akio Ohyama, Hiroyuki Fukuoka

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 02/2012;

  Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (SolanumParthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 × AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro × AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.

• An interspecific linkage map of SSR and intronic polymorphism markers in tomato.

  Authors: Kenta Shirasawa, Erika Asamizu, Hiroyuki Fukuoka, Akio Ohyama, Shusei Sato, Yasukazu Nakamura, Satoshi Tabata, Shigemi Sasamoto, Tsuyuko Wada, Yoshie Kishida, Hisano Tsuruoka, Tsunakazu Fujishiro, Manabu Yamada, Sachiko Isobe

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 08/2010; 121(4):731-9.

  Despite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using publicDespite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using public genome sequence data in tomato, we developed three types of DNA markers: expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers (TES markers), genome-derived SSR markers (TGS markers) and EST-derived intronic polymorphism markers (TEI markers). A total of 2,047 TES, 3,510 TGS and 674 TEI markers were established and used in the polymorphic analysis of a cultivated tomato (Solanum lycopersicum) 'LA925' and its wild relative Solanum pennellii 'LA716', parents of the Tomato-EXPEN 2000 mapping population. The polymorphic ratios between parents revealed by the TES, TGS and TEI markers were 37.3, 22.6 and 80.0%, respectively. Those showing polymorphisms were used to genotype the Tomato-EXPEN 2000 mapping population, and a high-density genetic linkage map composed of 1,433 new and 683 existing marker loci was constructed on 12 chromosomes, covering 1,503.1 cM. In the present map, 48% of the mapped TGS loci were located within heterochromatic regions, while 18 and 21% of TES and TEI loci, respectively, were located in heterochromatin. The large number of SSR and SNP markers developed in this study provide easily handling genomic tools for molecular breeding in tomato. Information on the DNA markers developed in this study is available at http://www.kazusa.or.jp/tomato/.

• Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato.

  Authors: Hiroyuki Fukuoka, Hirotaka Yamaguchi, Tsukasa Nunome, Satomi Negoro, Koji Miyatake, Akio Ohyama

  Gene. 10/2009;

  Eggplant (Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. UnlikeEggplant (Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato, Solanum crops that belong to subgenus Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus, Leptostemonum, and therefore, would be a unique member for comparative molecular biology in Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5'- and 3'-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally Solanum torvum were clustered separately from subgenus Potatoe species, and then, all Solanum species were clustered separately from the genus Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in Solanum species.

• Gene expression analysis in cadmium-stressed roots of a low cadmium-accumulating solanaceous plant, Solanum torvum.

  Authors: Hirotaka Yamaguchi, Hiroyuki Fukuoka, Tomohito Arao, Akio Ohyama, Tsukasa Nunome, Koji Miyatake, Satomi Negoro

  Journal of experimental botany. 10/2009;

  Solanum torvum Sw. cv. Torubamubiga (TB) is a low cadmium (Cd)-accumulating plant. To elucidate the molecular mechanisms of the Cd acclimation process in TB roots, transcriptional regulation wasSolanum torvum Sw. cv. Torubamubiga (TB) is a low cadmium (Cd)-accumulating plant. To elucidate the molecular mechanisms of the Cd acclimation process in TB roots, transcriptional regulation was analysed in response to mild Cd treatment: 0.1 muM CdCl(2) in hydroponic solution. A unigene set consisting of 6296 unigene sequences was constructed from 18 816 TB cDNAs. The distribution of functional categories was similar to tomato, while 330 unigenes were suggested to be TB specific. For expression profiling, the SuperSAGE method was adapted for use with Illumina sequencing technology. Expression tag libraries were constructed from Cd-treated (for 3 h, 1 d, and 3 d) and untreated roots, and 34 269 species of independent tags were collected. Moreover, 6237 tags were ascribed to the TB or eggplant (aubergine) unigene sequences. Time-course changes were examined, and 2049 up- and 2022 down-regulated tags were identified. Although no tags annotated to metal transporter genes were significantly regulated, a tag annotated to AtFRD3, a xylem-loading citrate transporter, was down-regulated. In addition to induction of heavy metal chaperone proteins, antioxidative and sulphur-assimilating enzymes were induced, confirming that oxidative stress developed even using a mild Cd concentration. Rapid repression of dehydration-related transcription factors and aquaporin isoforms suggests that dehydration stress is a potential constituent of Cd-induced biochemical impediments. These transcriptional changes were also confirmed by real-time reverse transcription-PCR. Further additions of TB unigene sequences and functional analysis of the regulated tags will reveal the molecular basis of the Cd acclimation process, including the low Cd-accumulating characteristics of TB.

• Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.).

  Authors: Tsukasa Nunome, Satomi Negoro, Izumi Kono, Hiroyuki Kanamori, Koji Miyatake, Hirotaka Yamaguchi, Akio Ohyama, Hiroyuki Fukuoka

  TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 09/2009;

  Eggplant (Solanum melongena L.), also known as aubergine or brinjal, is an important vegetable in many countries. Few useful molecular markers have been reported for eggplant. We constructed simpleEggplant (Solanum melongena L.), also known as aubergine or brinjal, is an important vegetable in many countries. Few useful molecular markers have been reported for eggplant. We constructed simple sequence repeat (SSR)-enriched genomic libraries in order to develop SSR markers, and sequenced more than 14,000 clones. From these sequences, we designed 2,265 primer pairs to flank SSR motifs. We identified 1,054 SSR markers from amplification of 1,399 randomly selected primer pairs. The markers have an average polymorphic information content of 0.27 among eight lines of S. melongena. Of the 1,054 SSR markers, 214 segregated in an intraspecific mapping population. We constructed cDNA libraries from several eggplant tissues and obtained 6,144 expressed sequence tag (EST) sequences. From these sequences, we designed 209 primer pairs, 7 of which segregated in the mapping population. On the basis of the segregation data, we constructed a linkage map, and mapped the 236 segregating markers to 14 linkage groups. The linkage map spans a total length of 959.1 cM, with an average marker distance of 4.3 cM. The markers should be a useful resource for qualitative and quantitative trait mapping and for marker-assisted selection in eggplant breeding.

• Structures and Antioxidant Activity of Anthocyanins in Many Accessions of Eggplant and Its Related Species.

  Authors: Keiko Azuma, Akio Ohyama, Katsunari Ippoushi, Takashi Ichiyanagi, Atsuko Takeuchi, Takeo Saito, Hiroyuki Fukuoka

  Journal of agricultural and food chemistry. 11/2008;

  Anthocyanins were detected in extracts from the peels of 123 accessions of eggplant ( Solanum melongena) and its related species. Their anthocyanin profiles were classified into four types, includingAnthocyanins were detected in extracts from the peels of 123 accessions of eggplant ( Solanum melongena) and its related species. Their anthocyanin profiles were classified into four types, including known Japanese eggplant type (type 1) and non-Japanese eggplant type (type 2). Although most of the eggplant accessions had one of the two known profiles, one accession had a novel profile (type 3). Two accessions of related species showed another novel profile (type 4). The major anthocyanins were identified as delphinidin 3-( p-coumaroylrutinoside)-5-glucoside (nasunin) (type 1), delphinidin 3-rutinoside (type 2), delphinidin 3-glucoside (type 3), and petunidin 3-( p-coumaroylrutinoside)-5-glucoside (petunidin 3RGc5G) (type 4). Delphinidin 3-caffeoylrutinoside-5-glucoside (delphinidin 3RGcaf5G) was isolated from the hybrid (F1) plants of a type 1 cultivar and a type 3 germplasm. Among the five purified anthocyanins, delphinidin 3RGcaf5G showed the highest radical-scavenging activities toward both 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and linoleic acid radical, followed in order by nasunin and petunidin 3RGc5G.

• CIP353 encodes an AP2/ERF-domain protein in potato (Solanum tuberosum L.) and responds slowly to cold stress.

  Authors: Toshiki Mine, Toru Hiyoshi, Keisuke Kasaoka, Akio Ohyama

  Plant & cell physiology. 01/2003; 44(1):10-5.

  We isolated the CIP353 cDNA, which encodes a novel cold-inducible protein, from cold-stored tubers of potato (Solanum tuberosum L.). The level of CIP353 transcripts began to increase in tubers 2We isolated the CIP353 cDNA, which encodes a novel cold-inducible protein, from cold-stored tubers of potato (Solanum tuberosum L.). The level of CIP353 transcripts began to increase in tubers 2 weeks after storage at 3 degrees C and continued increasing for at least 3 months during storage. This increase was not observed in tubers stored at >or=9 degrees C. The increased level of transcripts in tubers stored at 3 or 6 degrees C decreased when the tubers were shifted to 20 degrees C. These data suggest that CIP353 is a temperature-dependent and slowly responsive cold-inducible gene of potato. The middle of the deduced amino acid sequence of CIP353 cDNA showed high similarity to the AP2/ERF domain, which occurs in some plant regulatory factors. The deduced protein contained a putative basic nuclear-localization signal and potential acidic activation domains. These data suggest that CIP353 protein is a transcription factor of genes expressed in tubers under long-term storage at low temperatures.