A High Density Integrated Genetic Linkage Map of Soybean and the Development of a 1536 Universal Soy Linkage Panel for Quantitative Trait Locus Mapping

Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high-throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1141 SNP markers to the map. Our objectives were to add 2500 additional SNP markers to the soybean integrated map and select a set of 1536 SNPs to create a universal linkage panel for high-throughput soybean quantitative trait locus (QTL) mapping. The GoldenGate assay is one high-throughput analysis method capable of genotyping 1536 SNPs in 192 DNA samples over a 3-d period. We designed GoldenGate assays for 3456 SNPs (2956 new plus 500 previously mapped) which were used to screen three recombinant inbred line populations and diverse germplasm. A total of 3000 workable assays were obtained which added about 2500 new SNP markers to create a fourth version of the soybean integrated linkage map. To create a “Universal Soy Linkage Panel” (USLP 1.0) of 1536 SNP loci, SNPs were selected based on even distribution throughout each of the 20 consensus linkage groups and to have a broad range of allele frequencies in diverse germplasm. The 1536 USLP 1.0 will be able to quickly create a comprehensive genetic map in most QTL mapping populations and thus will serve as a useful tool for high-throughput QTL mapping. D.L. Hyten, I-Y. Choi, Q. Song, E-Y Hwang, and P.B. Cregan, USDAARS, Soybean Genomics and Improvement Lab., Beltsville, MD 20705. Q. Song and E-Y. Hwang, Dep. of Plant Science and Landscape Architecture, Univ. of Maryland, College Park, MD 20742. J.E. Specht, Dep. of Agronomy and Horticulture, Univ. of Nebraska, Lincoln, NE 68583. T.E. Carter, USDA-ARS, Soybean and Nitrogen Fixation Research, Raleigh, NC 27607. R.C. Shoemaker, USDA-ARS, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011. L.K. Matukumalli, USDA-ARS, Bovine Functional Genomics Lab., Beltsville, MD 20705. I-Y. Choi, current address: National Instrumentation Center for Environmental Management, Seoul National Univ., Seoul, 151-921, South Korea. Mention of a trade name, proprietary product, or specifi c equipment does not constitute a guarantee or warranty by the USDA and does not imply approval of a product to the exclusion of others that may be suitable. Received 30 June 2009. *Corresponding author ([email protected]). Abbreviations: BARC, Beltsville Agricultural Research Center; BSA, bulked segregant analysis; cM, centimorgan; INDEL, insertion/deletion; LG, linkage group; OPA, oligo pool all; QTL, quantitative trait locus; RIL, recombinant inbred line; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; STS, sequence tagged site; USLP 1.0, Universal Soy Linkage Panel 1.0. Published in Crop Sci. 50:960–968 (2010). doi: 10.2135/cropsci2009.06.0360 Freely available online through the author-supported open-access option. Published online 9 Mar. 2010. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.