Single-nucleotide polymorphisms in soybean (original) (raw)

Abstract

Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

Full Text

The Full Text of this article is available as a PDF (114.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Cardon L. R., Bell J. I. Association study designs for complex diseases. Nat Rev Genet. 2001 Feb;2(2):91–99. doi: 10.1038/35052543. [DOI] [PubMed] [Google Scholar]
  2. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C. R., Lim E. P., Kalyanaraman N. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet. 1999 Jul;22(3):231–238. doi: 10.1038/10290. [DOI] [PubMed] [Google Scholar]
  3. Churchill G. A., Doerge R. W. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. doi: 10.1093/genetics/138.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Collins F. S., Brooks L. D., Chakravarti A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 1998 Dec;8(12):1229–1231. doi: 10.1101/gr.8.12.1229. [DOI] [PubMed] [Google Scholar]
  5. Cooper D. N., Smith B. A., Cooke H. J., Niemann S., Schmidtke J. An estimate of unique DNA sequence heterozygosity in the human genome. Hum Genet. 1985;69(3):201–205. doi: 10.1007/BF00293024. [DOI] [PubMed] [Google Scholar]
  6. Halushka M. K., Fan J. B., Bentley K., Hsie L., Shen N., Weder A., Cooper R., Lipshutz R., Chakravarti A. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet. 1999 Jul;22(3):239–247. doi: 10.1038/10297. [DOI] [PubMed] [Google Scholar]
  7. Hanfstingl U., Berry A., Kellogg E. A., Costa J. T., 3rd, Rüdiger W., Ausubel F. M. Haplotypic divergence coupled with lack of diversity at the Arabidopsis thaliana alcohol dehydrogenase locus: roles for both balancing and directional selection? Genetics. 1994 Nov;138(3):811–828. doi: 10.1093/genetics/138.3.811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kawabe A., Miyashita N. T. DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana. Genetics. 1999 Nov;153(3):1445–1453. doi: 10.1093/genetics/153.3.1445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kawabe A., Yamane K., Miyashita N. T. DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arabidopsis thaliana. Genetics. 2000 Nov;156(3):1339–1347. doi: 10.1093/genetics/156.3.1339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kuittinen H., Aguadé M. Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana. Genetics. 2000 Jun;155(2):863–872. doi: 10.1093/genetics/155.2.863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kwok P. Y., Deng Q., Zakeri H., Taylor S. L., Nickerson D. A. Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics. 1996 Jan 1;31(1):123–126. doi: 10.1006/geno.1996.0019. [DOI] [PubMed] [Google Scholar]
  12. Lindblad-Toh K., Winchester E., Daly M. J., Wang D. G., Hirschhorn J. N., Laviolette J. P., Ardlie K., Reich D. E., Robinson E., Sklar P. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet. 2000 Apr;24(4):381–386. doi: 10.1038/74215. [DOI] [PubMed] [Google Scholar]
  13. Marth G. T., Korf I., Yandell M. D., Yeh R. T., Gu Z., Zakeri H., Stitziel N. O., Hillier L., Kwok P. Y., Gish W. R. A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999 Dec;23(4):452–456. doi: 10.1038/70570. [DOI] [PubMed] [Google Scholar]
  14. Nordborg Magnus, Borevitz Justin O., Bergelson Joy, Berry Charles C., Chory Joanne, Hagenblad Jenny, Kreitman Martin, Maloof Julin N., Noyes Tina, Oefner Peter J. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2002 Jan 7;30(2):190–193. doi: 10.1038/ng813. [DOI] [PubMed] [Google Scholar]
  15. Olsen Kenneth M., Womack Andrew, Garrett Ashley R., Suddith Jane I., Purugganan Michael D. Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway. Genetics. 2002 Apr;160(4):1641–1650. doi: 10.1093/genetics/160.4.1641. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Pollak E. On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics. 1987 Oct;117(2):353–360. doi: 10.1093/genetics/117.2.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Purugganan M. D., Suddith J. I. Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana. Genetics. 1999 Feb;151(2):839–848. doi: 10.1093/genetics/151.2.839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reich D. E., Cargill M., Bolk S., Ireland J., Sabeti P. C., Richter D. J., Lavery T., Kouyoumjian R., Farhadian S. F., Ward R. Linkage disequilibrium in the human genome. Nature. 2001 May 10;411(6834):199–204. doi: 10.1038/35075590. [DOI] [PubMed] [Google Scholar]
  19. Remington D. L., Thornsberry J. M., Matsuoka Y., Wilson L. M., Whitt S. R., Doebley J., Kresovich S., Goodman M. M., Buckler E. S., 4th Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A. 2001 Sep 18;98(20):11479–11484. doi: 10.1073/pnas.201394398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rozas J., Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics. 1999 Feb;15(2):174–175. doi: 10.1093/bioinformatics/15.2.174. [DOI] [PubMed] [Google Scholar]
  21. Shoemaker R. C., Polzin K., Labate J., Specht J., Brummer E. C., Olson T., Young N., Concibido V., Wilcox J., Tamulonis J. P. Genome duplication in soybean (Glycine subgenus soja). Genetics. 1996 Sep;144(1):329–338. doi: 10.1093/genetics/144.1.329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stephens J. C., Schneider J. A., Tanguay D. A., Choi J., Acharya T., Stanley S. E., Jiang R., Messer C. J., Chew A., Han J. H. Haplotype variation and linkage disequilibrium in 313 human genes. Science. 2001 Jul 12;293(5529):489–493. doi: 10.1126/science.1059431. [DOI] [PubMed] [Google Scholar]
  23. Stone Roger T., Grosse W. Michael, Casas Eduardo, Smith Timothy P. L., Keele John W., Bennett Gary L. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mamm Genome. 2002 Apr;13(4):211–215. doi: 10.1007/s00335-001-2124-9. [DOI] [PubMed] [Google Scholar]
  24. Taillon-Miller P., Piernot E. E., Kwok P. Y. Efficient approach to unique single-nucleotide polymorphism discovery. Genome Res. 1999 May;9(5):499–505. [PMC free article] [PubMed] [Google Scholar]
  25. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tenaillon M. I., Sawkins M. C., Long A. D., Gaut R. L., Doebley J. F., Gaut B. S. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A. 2001 Jul 24;98(16):9161–9166. doi: 10.1073/pnas.151244298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wang D. G., Fan J. B., Siao C. J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998 May 15;280(5366):1077–1082. doi: 10.1126/science.280.5366.1077. [DOI] [PubMed] [Google Scholar]
  29. Xue Z. T., Xu M. L., Shen W., Zhuang N. L., Hu W. M., Shen S. C. Characterization of a Gy4 glycinin gene from soybean Glycine max cv. forrest. Plant Mol Biol. 1992 Mar;18(5):897–908. doi: 10.1007/BF00019204. [DOI] [PubMed] [Google Scholar]