High-density Integrated Linkage Map Based on SSR Markers in Soybean

DNA RESEARCH 16, 213–225, (2009) doi:10.1093/dnares/dsp010 High-density Integrated Linkage Map Based on SSR Markers in Soybean TAE-YOUNG Hwang1,2, TAKASHI Sayama1, MASAKAZU Takahashi3, YOSHITAKE Takada4,†, YUMI Nakamoto1, HIDEYUKI Funatsuki1, HIROSHI Hisano5, SHIGEMI Sasamoto5, SHUSEI Sato5, SATOSHI Tabata5, IZUMI Kono6, MASAKO Hoshi7, MASAYOSHI Hanawa7, CHIZURU Yano7, ZHENGJUN Xia8, KYUYA Harada8, KEISUKE Kitamura2, and MASAO Ishimoto1, * National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan1; Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita, Sapporo, Hokkaido 060-8589, Japan2; National Agricultural Research Center for Kyushu Okinawa Region, 2421 Suya, Koshi, Kumamoto 861-1192, Japan3; National Agricultural Research Center for Tohoku Region, 297 Uenodai, Kariwano, Daisen, Akita 019-2112, Japan4; Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan5; Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan6; Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan7 and National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan8 (Received 2 April 2009; accepted 25 May 2009; published online 16 June 2009) 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’ 3 the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ 3 the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ 3 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. Key words: EST-derived SSR marker; integrated linkage map; microsatellite marker; polymorphism information content 1. † * Edited by Masahiro yano Present address: National Agricultural Research Center for Western Region, 1-3-1 Senyuu, Zentsuuji, Kagawa 765-8508, Japan To whom correspondence should be addressed. Tel. þ81-11857-9312. Fax. þ81-11-859-2178. E-mail: # The Author 2009. Kazusa DNA Research Institute. Introduction Soybean [Glycine max (L.) Merrill] is one of the most important grain legumes because it is a staple source of high-quality vegetable protein and oil for food products and industrial material. Over the past 20 years, the global growing area of soybean has increased by a factor of 1.7, whereas the average yield has increased The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact 214 High-density SSR Integrated Linkage Map of Soybean by a factor of 2.3, reaching 2.5 tons/hectare in 2006.1 However, the rate of growth in soybean yield has declined during the last 10 years, increasing by only 8% in this period. It is therefore imperative to develop new technologies and resources that will allow the supply of soybean to meet the large growth in demand anticipated in the near future. An accurate and well-saturated genetic linkage map is fundamental to modern plant breeding because it allows both the identification of agronomic trait loci, including quantitative trait loci, and an understanding of genetic diversity and genome structure of genetic resources. Furthermore, such a linkage map is required for construction of a physical map. Since the first genetic map of soybean was constructed with phenotypic traits,2 several linkage maps have been developed either alone or in combination with various types of molecular markers such as restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers.3 – 7 Among these molecular markers, SSRs (also known as microsatellite markers) possess several favorable features: (i) they are inherited in a codominant manner at individual loci; (ii) they exhibit high levels of polymorphism and exist in multiple alleles; (iii) they are distributed evenly and randomly in the genome and (iv) they can be readily analyzed by the polymerase chain reaction (PCR) and subsequent gel electrophoresis.5,6,8,9 Multiallelic molecular markers with a high level of polymorphism are useful for the detection of allelic differences among many genetic resources.10 – 12 SSR markers are applicable to analysis of many of the segregating populations derived from the hybridization of any given genotypes. In addition, most PCR primer pairs for SSR markers yield a single amplification product for each soybean genotype,13 allowing the use of a variety of means for the detection of SSR length polymorphisms. The amplification products are usually analyzed by electrophoresis on a polyacrylamide or agarose gel, but they can also be analyzed with a genetic sequencer in combination with a labeling protocol.6,10,14 Moreover, SSR markers can be genotyped more rapidly and cost efficiently by simultaneous detection of multiple loci with the use of multiplex PCR analysis.15 Such analysis is ideal for high-throughput and repetitive genotyping applications for which common sets of SSR marker loci are advantageous. Given that SSR markers were found to map to individual loci with the same order in three different mapping populations, 606 such loci were integrated and aligned with RFLP, RAPD, AFLP and classical markers into a consensus set of 20 linkage groups (LGs) corresponding to the 20 pairs of soybean [Vol. 16, chromosomes.16 The (...truncated)