An Integrated High-density Linkage Map of Soybean with RFLP, SSR, STS, and AFLP Markers Using A Single F2 Population

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.

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

“…Simple-sequence-repeat marker information was retrieved from SoyBase (http://www.soybase.org) and elsewhere (74,75). Amplified fragment length polymorphism markers were generated following a standard protocol (75).…”

“…Amplified fragment length polymorphism markers were generated following a standard protocol (75). All markers (Table S4) used for fine-scale mapping of the E1 locus were developed by targeting polymorphisms between the contigs (Fig.…”

Genetic analysis of variation in sugar chain composition at the C-22 position of group A saponins in soybean, Glycine max (L.) Merrill

“…PCR amplification and detection of SSR markers were performed as described previously (Hwang et al 2009). Genotyping was carried out with SSR markers developed by USDA-ARS (Cregan et al 1999) and DuPont Corporation (Song et al 2004), SSR and sequence-tagged site (STS) markers developed by Chiba University (Xia et al 2007), and EST-derived SSR primer pairs developed by Kazusa DNA Research Institute (Hisano et al 2007). MAPMAKER/EXP v. 3.0 software was used to analyze linkage between the markers.…”

Stability Verification of the Effects of Stem Determination and Earliness of Flowering on Green Stem Disorder of Soybean against Genetic Background and Environment

“…Briefly, polymerase chain reaction (PCR) was performed using a GeneAmp PCR System 9700 thermal cycler (Applied Biosystems, USA) in a reaction mixture containing multiple simple sequence repeat (SSR) primers labeled with different florescent dyes (6-FAM, VIC, NED and PET), and the SSR fragment length in the product were measured using a DNA analyzer (3730 DNA Analyzer, Applied Biosystems, USA) instead of general gel electrophoresis. The SSR markers used here were developed by USDA-ARS (United States Department of Agriculture, Agriculture Research Service), Chiba University and Kazusa DNA Research Institute (Cregan et al, 1999;Song et al, 2004;Hisano et al, 2007;Xia et al, 2007). Genetic linkage maps with 20 linkage groups were constructed with Kosambi's map function (Kosambi, 1943) using MAPMAKER/EXP VER.…”