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Hasegawa Y, Ueno S, Matsumoto A, Ujino-Ihara T, Uchiyama K, Totsuka S, Iwai J, Hakamata T, Moriguchi Y. Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don). PLoS One 2018; 13:e0206695. [PMID: 30439978 PMCID: PMC6237302 DOI: 10.1371/journal.pone.0206695] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/17/2018] [Indexed: 11/08/2022] Open
Abstract
Pollinosis caused by Japanese cedar (Cryptomeria japonica) is a widespread social problem in Japan. To date, 23 male-sterile C. japonica trees have been selected in Japan to address pollinosis, from which four male-sterility loci (MS1, MS2, MS3, and MS4) have been identified from test crossing results. For efficient breeding of male-sterile C. japonica trees, more male-sterile individuals and individuals heterozygous for male-sterile genes are required. Therefore, we aimed to develop DNA markers for marker-assisted selection of four types of male-sterile genes from populations without a family structure. First, for four families exhibiting segregation of each male-sterile locus (MS1, MS2, MS3, and MS4), genome-wide single-nucleotide polymorphism and insertion/deletion (indel) genotyping was performed using the Axiom myDesign Targeted Genotyping Array method. Four high-density linkage maps for mapping the MS1, MS2, MS3, and MS4 families were constructed, which included 4923, 1722, 1896, and 2247 markers, respectively. In these maps, 15, 4, 2, and 2 markers were located 0.0, 3.3, 1.1, and 0.0 cM from the MS1, MS2, MS3, and MS4 loci, respectively. Second, for the markers located 0.0 cM from a male-sterile locus (i.e., MS1 and MS4), to clarify the most tightly linked markers, we calculated the prediction rate of male-sterile gene genotypes from marker genotypes for 78 trees. The markers with the highest prediction rates were AX-174127446 (0.95) for MS1 and AX-174121522 (1.00) for MS4. The AX-174121522 marker was considered to be suitable for selecting trees homozygous or heterozygous for the MS4 gene from plus-trees without a pollination test, which requires a large amount of time and effort. The nearest markers to the male-sterile loci found in this study may facilitate the isolation of male-sterile genes in C. japonica via combination with the draft genomic sequence that is currently being collated.
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Affiliation(s)
- Yoichi Hasegawa
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Asako Matsumoto
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Satoko Totsuka
- Niigata Prefectural Forest Research Institute, Murakami, Niigata, Japan
| | - Junji Iwai
- Niigata Prefectural Forest Research Institute, Murakami, Niigata, Japan
| | - Tetsuji Hakamata
- Forestry and Forest Products Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, Hamamatsu, Shizuoka, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, Japan
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Mishima K, Hirao T, Tsubomura M, Tamura M, Kurita M, Nose M, Hanaoka S, Takahashi M, Watanabe A. Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don). BMC Genomics 2018; 19:277. [PMID: 29685102 PMCID: PMC5914023 DOI: 10.1186/s12864-018-4581-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding. Results This study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS. Conclusions More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Manabu Kurita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Mine Nose
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - So Hanaoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Atsushi Watanabe
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan.
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura N, Sakurai T, Shinohara K, Tsumura Y. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics 2012; 13:136. [PMID: 22507374 PMCID: PMC3424129 DOI: 10.1186/1471-2164-13-136] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 04/16/2012] [Indexed: 12/16/2022] Open
Abstract
Background Microsatellites or simple sequence repeats (SSRs) in expressed sequence tags (ESTs) are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica). Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54%) contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%). The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3%) di-SSRs, followed by the AAG motif, found in 342 (25.9%) tri-SSRs. Most (72.8%) tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO) annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size and number of SSR repeats, respectively. EST-SSR markers exhibited less polymorphism than genomic SSRs. Conclusions We have created a new open pipeline for developing EST-SSR markers and applied it in a comprehensive analysis of EST-SSRs and EST-SSR markers in C. japonica. The results will be useful in genomic analyses of conifers and other non-model species.
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Affiliation(s)
- Saneyoshi Ueno
- Department of Forest Genetics, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
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Moriguchi Y, Ujino-Ihara T, Uchiyama K, Futamura N, Saito M, Ueno S, Matsumoto A, Tani N, Taira H, Shinohara K, Tsumura Y. The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don. BMC Genomics 2012; 13:95. [PMID: 22424262 PMCID: PMC3386010 DOI: 10.1186/1471-2164-13-95] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 03/16/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems. RESULTS We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM. CONCLUSIONS Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity.
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Affiliation(s)
- Yoshinari Moriguchi
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Norihiro Futamura
- Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Maki Saito
- Toyama Prefectural Agricultural Forestry and Fishieries Research Center, Forestry Research Institute, Yoshimine 3, Tateyama-cho, Nakashinkawagun, Toyama 930-1362, Japan
| | - Saneyoshi Ueno
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Asako Matsumoto
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences, Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Hideaki Taira
- Graduate School of Science and Technology, Niigata University, Igarashi 2-nocho, Niigata 950-2101, Japan
| | - Kenji Shinohara
- Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
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