A New Integrated Genetic Linkage Map of the Soybean

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2004 Mar 3

PMID 14991109

Citations 239

Authors

Q J Song

L F Marek

R C Shoemaker

K G Lark

V C Concibido

X Delannay

J E Specht

P B Cregan

Affiliations

Soon will be listed here.

Abstract

A total of 391 simple sequence repeat (SSR) markers designed from genomic DNA libraries, 24 derived from existing GenBank genes or ESTs, and five derived from bacterial artificial chromosome (BAC) end sequences were developed. In contrast to SSRs derived from EST sequences, those derived from genomic libraries were a superior source of polymorphic markers, given that the mean number of tandem repeats in the former was significantly less than that of the latter ( P<0.01). The 420 newly developed SSRs were mapped in one or more of five soybean mapping populations: "Minsoy" x "Noir 1", "Minsoy" x "Archer", "Archer" x "Noir 1", "Clark" x "Harosoy", and A81-356022 x PI468916. The JoinMap software package was used to combine the five maps into an integrated genetic map spanning 2,523.6 cM of Kosambi map distance across 20 linkage groups that contained 1,849 markers, including 1,015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, six AFLPs, ten isozymes, and 12 others. The number of new SSR markers added to each linkage group ranged from 12 to 29. In the integrated map, the ratio of SSR marker number to linkage group map distance did not differ among 18 of the 20 linkage groups; however, the SSRs were not uniformly spaced over a linkage group, clusters of SSRs with very limited recombination were frequently present. These clusters of SSRs may be indicative of gene-rich regions of soybean, as has been suggested by a number of recent studies, indicating the significant association of genes and SSRs. Development of SSR markers from map-referenced BAC clones was a very effective means of targeting markers to marker-scarce positions in the genome.

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References

Lark K, Weisemann J, Matthews B, Palmer R, Chase K, Macalma T . A genetic map of soybean (Glycine max L.) using an intraspecific cross of two cultivars: 'Minosy' and 'Noir 1'. Theor Appl Genet. 2013; 86(8):901-6. DOI: 10.1007/BF00211039. View

Zhu T, Schupp J, Oliphant A, Keim P . Hypomethylated sequences: characterization of the duplicate soybean genome. Mol Gen Genet. 1994; 244(6):638-45. DOI: 10.1007/BF00282754. View

Ramsay L, MacAulay M, Degli Ivanissevich S, MacLean K, Cardle L, Fuller J . A simple sequence repeat-based linkage map of barley. Genetics. 2000; 156(4):1997-2005. PMC: 1461369. DOI: 10.1093/genetics/156.4.1997. View

Areshchenkova T, Ganal M . Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet. 2003; 104(2-3):229-235. DOI: 10.1007/s00122-001-0775-2. View

Shoemaker R, Polzin K, Labate J, Specht J, Brummer E, Olson T . Genome duplication in soybean (Glycine subgenus soja). Genetics. 1996; 144(1):329-38. PMC: 1207505. DOI: 10.1093/genetics/144.1.329. View

Watanabe T, Bihoreau M, McCarthy L, Kiguwa S, Hishigaki H, Tsuji A . A radiation hybrid map of the rat genome containing 5,255 markers. Nat Genet. 1999; 22(1):27-36. DOI: 10.1038/8737. View

Cardle L, Ramsay L, Milbourne D, MacAulay M, Marshall D, Waugh R . Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics. 2000; 156(2):847-54. PMC: 1461288. DOI: 10.1093/genetics/156.2.847. View

Kota R, Varshney R, Thiel T, Dehmer K, Graner A . Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas. 2002; 135(2-3):145-51. DOI: 10.1111/j.1601-5223.2001.00145.x. View

Cordeiro G, Casu R, McIntyre C, Manners J, Henry R . Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci. 2001; 160(6):1115-1123. DOI: 10.1016/s0168-9452(01)00365-x. View

10.

Green E, Olson M . Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. Proc Natl Acad Sci U S A. 1990; 87(3):1213-7. PMC: 53441. DOI: 10.1073/pnas.87.3.1213. View

11.

Zhu Y, Song Q, Hyten D, Van Tassell C, Matukumalli L, Grimm D . Single-nucleotide polymorphisms in soybean. Genetics. 2003; 163(3):1123-34. PMC: 1462490. DOI: 10.1093/genetics/163.3.1123. View

12.

Areshchenkova T, Ganal M . Long tomato microsatellites are predominantly associated with centromeric regions. Genome. 1999; 42(3):536-44. View

13.

Broun P, Tanksley S . Characterization and genetic mapping of simple repeat sequences in the tomato genome. Mol Gen Genet. 1996; 250(1):39-49. DOI: 10.1007/BF02191823. View

14.

Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002; 30(2):194-200. DOI: 10.1038/ng822. View

15.

Keim P, Diers B, Olson T, Shoemaker R . RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics. 1990; 126(3):735-42. PMC: 1204227. DOI: 10.1093/genetics/126.3.735. View

16.

McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M . Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement). DNA Res. 2003; 9(6):257-79. DOI: 10.1093/dnares/9.6.257. View

17.

Thiel T, Michalek W, Varshney R, Graner A . Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003; 106(3):411-22. DOI: 10.1007/s00122-002-1031-0. View

18.

Marek L, Shoemaker R . BAC contig development by fingerprint analysis in soybean. Genome. 1997; 40(4):420-7. DOI: 10.1139/g97-056. View

19.

Eujayl I, Sorrells M, Baum M, Wolters P, Powell W . Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet. 2003; 104(2-3):399-407. DOI: 10.1007/s001220100738. View

20.

Akkaya M, Bhagwat A, Cregan P . Length polymorphisms of simple sequence repeat DNA in soybean. Genetics. 1992; 132(4):1131-9. PMC: 1205234. DOI: 10.1093/genetics/132.4.1131. View