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Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP. Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 2011; 18:305-20. [PMID: 21768136 PMCID: PMC3190952 DOI: 10.1093/dnares/dsr017] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species.
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Affiliation(s)
- Nirala Ramchiary
- Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea
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Hwang TY, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S, Kono I, Hoshi M, Hanawa M, Yano C, Xia Z, Harada K, Kitamura K, Ishimoto M. High-density integrated linkage map based on SSR markers in soybean. DNA Res 2009; 16:213-25. [PMID: 19531560 PMCID: PMC2725787 DOI: 10.1093/dnares/dsp010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 05/25/2009] [Indexed: 11/17/2022] Open
Abstract
A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar 'Jack' x the Japanese cultivar 'Fukuyutaka', the Chinese cultivar 'Peking' x the Japanese cultivar 'Akita', and the Japanese cultivar 'Misuzudaizu' x the Chinese breeding line 'Moshidou Gong 503') and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70-114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding.
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Affiliation(s)
- Tae-Young Hwang
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita, Sapporo, Hokkaido 060-8589, Japan
| | - Takashi Sayama
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Masakazu Takahashi
- National Agricultural Research Center for Kyushu Okinawa Region, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Yoshitake Takada
- National Agricultural Research Center for Tohoku Region, 297 Uenodai, Kariwano, Daisen, Akita 019-2112, Japan
| | - Yumi Nakamoto
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hideyuki Funatsuki
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hiroshi Hisano
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shigemi Sasamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Izumi Kono
- Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Masako Hoshi
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Masayoshi Hanawa
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Chizuru Yano
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Zhengjun Xia
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Keisuke Kitamura
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita, Sapporo, Hokkaido 060-8589, Japan
| | - Masao Ishimoto
- National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
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Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S. Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 2007; 14:271-81. [PMID: 18192281 PMCID: PMC2779906 DOI: 10.1093/dnares/dsm025] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 11/30/2007] [Indexed: 11/14/2022] Open
Abstract
We generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9%) were designed to amplify simple sequence repeats (SSRs) from 63,676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar 'Misuzudaizu' and the Chinese line 'Moshidou Gong 503', were examined using 10% polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.
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Affiliation(s)
- Hiroshi Hisano
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shigemi Sasamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tsuyuko Wada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ai Matsuno
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tsunakazu Fujishiro
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Manabu Yamada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinobu Nakayama
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yasukazu Nakamura
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Watanabe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
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Xia Z, Tsubokura Y, Hoshi M, Hanawa M, Yano C, Okamura K, Ahmed TA, Anai T, Watanabe S, Hayashi M, Kawai T, Hossain KG, Masaki H, Asai K, Yamanaka N, Kubo N, Kadowaki KI, Nagamura Y, Yano M, Sasaki T, Harada, K. An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using A single F2 population. DNA Res 2007; 14:257-69. [PMID: 18192280 PMCID: PMC2779910 DOI: 10.1093/dnares/dsm027] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 11/29/2007] [Indexed: 11/22/2022] Open
Abstract
Soybean [Glycine max (L.) Merrill] is the most important leguminous crop in the world due to its high contents of high-quality protein and oil for human and animal consumption as well as for industrial uses. An accurate and saturated genetic linkage map of soybean is an essential tool for studies on modern soybean genomics. In order to update the linkage map of a F2 population derived from a cross between Misuzudaizu and Moshidou Gong 503 and to make it more informative and useful to the soybean genome research community, a total of 318 AFLP, 121 SSR, 108 RFLP, and 126 STS markers were newly developed and integrated into the framework of the previously described linkage map. The updated genetic map is composed of 509 RFLP, 318 SSR, 318 AFLP, 97 AFLP-derived STS, 29 BAC-end or EST-derived STS, 1 RAPD, and five morphological markers, covering a map distance of 3080 cM (Kosambi function) in 20 linkage groups (LGs). To our knowledge, this is presently the densest linkage map developed from a single F2 population in soybean. The average intermarker distance was reduced to 2.41 from 5.78 cM in the earlier version of the linkage map. Most SSR and RFLP markers were relatively evenly distributed among different LGs in contrast to the moderately clustered AFLP markers. The number of gaps of more than 25 cM was reduced to 6 from 19 in the earlier version of the linkage map. The coverage of the linkage map was extended since 17 markers were mapped beyond the distal ends of the previous linkage map. In particular, 17 markers were tagged in a 5.7 cM interval between CE47M5a and Satt100 on LG C2, where several important QTLs were clustered. This newly updated soybean linkage map will enable to streamline positional cloning of agronomically important trait locus genes, and promote the development of physical maps, genome sequencing, and other genomic research activities.
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Affiliation(s)
- Zhengjun Xia
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasutaka Tsubokura
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masako Hoshi
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Masayoshi Hanawa
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Chizuru Yano
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Kayo Okamura
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Talaat A. Ahmed
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Faculty of Agriculture, Agronomy Department, Assiut University, Assiut 71515, Egypt
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Honjo-machi 1, Saga 840-8502, Japan
| | - Satoshi Watanabe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Masaki Hayashi
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Kawai
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Khwaja G. Hossain
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Division of Science and Mathematics, Mayville State University, 330 3rd Street NE, Mayville, ND 58257, USA
| | - Hirokazu Masaki
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Kazumi Asai
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Nakao Kubo
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Koh-ichi Kadowaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yoshiaki Nagamura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takuji Sasaki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kyuya Harada,
- Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Yamanaka N, Sato H, Yang Z, Xu DH, Catelli LL, Binneck E, Arias CAA, Abdelnoor RV, Nepomuceno AL. Genetic relationships between Chinese, Japanese, and Brazilian soybean gene pools revealed by simple sequence repeat (SSR) markers. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences, Japan; EMBRAPA-Soja, Brazil
| | - Hiroyuki Sato
- Japan International Research Center for Agricultural Sciences, Japan; Chiba University, Japan
| | - Zhenyu Yang
- Jilin Academy of Agricultural Sciences, China
| | - Dong He Xu
- Japan International Research Center for Agricultural Sciences, Japan
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Yamanaka N, Watanabe S, Toda K, Hayashi M, Fuchigami H, Takahashi R, Harada K. Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:634-9. [PMID: 15657740 DOI: 10.1007/s00122-004-1886-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 11/17/2004] [Indexed: 05/06/2023]
Abstract
Fine-mapping of loci related to complex quantitative traits is essential for map-based cloning. A residual heterozygous line (RHL) of soybean (Glycine max) derived from a recombinant inbred line (RIL) was used for fine-mapping FT1, which is a major quantitative trait locus (QTL) responsible for soybean flowering time. The residual heterozygous line RHL1-156 was selected from the RILs that were derived from two distantly related varieties, Misuzudaizu and Moshidou Gong 503. The genome of RHL1-156 contains a heterozygous segment (approximately 17 cM) surrounding the FT1 locus but is homozygous in other regions, including three other loci affecting flowering time. A large segregating population of 1,006 individuals derived by selfing of RHL1-156 included two homozygous genotypes for the nearest marker of FT1 whose flowering time differed by 26 days. No continuous range of phenotypes was observed, in contrast to the F2 population, suggesting that a single FT1 locus affected the flowering time in the RHL1-156 line. Linkage analysis revealed that the FT1 locus mapped as a single Mendelian factor between two tightly linked DNA markers, Satt365 and GM169, at distances of approximately 0.1 cM and 0.4 cM, respectively. Our results show that a RHL derived from RILs can be used to fine-map a QTL and that RHLs can be an efficient tool for a systematic fine-mapping of QTLs.
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Affiliation(s)
- Naoki Yamanaka
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, 271-8510, Japan
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Watanabe S, Tajuddin T, Yamanaka N, Hayashi M, Harada K. Analysis of QTLs for Reproductive Development and Seed Quality Traits in Soybean using Recombinant Inbred Lines. BREEDING SCIENCE 2004. [PMID: 0 DOI: 10.1270/jsbbs.54.399] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
| | - Teuku Tajuddin
- Graduate School of Science and Technology, Chiba University
- Present address: Center for the Assessment and Application of Biotechnology
| | - Naoki Yamanaka
- Graduate School of Science and Technology, Chiba University
- Present address: Biological Resources Division, Japan International Research Center for Agricultural Sciences
| | - Masaki Hayashi
- Graduate School of Science and Technology, Chiba University
| | - Kyuya Harada
- Graduate School of Science and Technology, Chiba University
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