Skip to main content
SpringerLink
Log in

A single nuclear locus phylogeny of soybean based on DNA sequence

  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ahmad QN, Britten EJ, Byth DE (1984) The karyotype of Glycine Soja and its relationship to that of the soybean, Glycine max. Cytologia 49: 645–658

    Google Scholar 

  • Bousquet J, Strauss SH, Doerksen AH, Price RA (1992) Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc Natl Acad Sci USA 89: 7844–7848

    Google Scholar 

  • Close PS, Shoemaker RC, Keim P (1989) Distribution of restriction site polymorphism within the chloroplast genome of the genus Glycine, subgenus Soja. Theor Appl Genet 77: 768–776

    Google Scholar 

  • Doyle JJ (1988) 5S ribosomal gene variation in the soybean and its progenitor. Theor Appl Genet 75: 621–624

    Google Scholar 

  • Doyle JJ (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Syst Bot 17: 144–163

    Google Scholar 

  • Doyle JJ, Beachy RN (1985) Ribosomal gene variation in soybean and it relatives. Theor Appl Genet 70: 369–376

    Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11–15

    Google Scholar 

  • Doyle JJ, Doyle JL (1993) Chloroplast DNA phylogeny of the papilionoid legume tribe Phaseoleae. Syst Bot 18: 309–327

    Google Scholar 

  • Doyle JJ, Doyle JL, Brown AHD (1990) A chloroplast DNA phylogeny of the wild perennial relatives of soybean (Glycine subgenus Glycine): congruence with morphological and crossing groups. Evolution 44: 371–389

    Google Scholar 

  • Doyle JJ, Lavin M, Bruneau A (1992) Contribution of molecular data to Papilionoid legume systematics. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman & Hall, New York London, pp 223–251

    Google Scholar 

  • Fuchman WH (1985) Discrepancies among published amino acid sequences of soybean leghemoglobins: experimental evidence against cultivar differences as the sources of the discrepancies. Arch Biochem Biophys 243: 454–460

    Google Scholar 

  • Grant JE, Grace JP, Brown AHD, Putievsky (1984) Interspecific hybridization in Glycine Willd. subgenus Glycine (Legumeinosae) Aust J Bot 32: 655–663

    Google Scholar 

  • Hermann FJ (1962) Revision of the genus Glycine and its immediate allies. USDA Tech Bull 1268: 1–82

    Google Scholar 

  • Hymowitz T (1970) On domestication of the soybean. Econ Bot 24: 408–421

    Google Scholar 

  • Hymowitz T, Singh RJ (1987) Taxonomy and speciation. In: Wilcox JR (ed) Soybeans: improvement, production, and uses, 2nd edn. (Agron Ser 16.) ASA, CSSA, SSSA, Madison, Wis., pp 23–48

    Google Scholar 

  • Keen NT, Lyne RL, Hymowitz T (1986) Phytoalexin production as a chemosystematic parameter within the genus Glycine. Biochem System Ecol 14: 481–496

    Google Scholar 

  • Keim P, Shoemaker RC (1988) Construction of a random recombinant DNA library that is primarily single copy sequence. Soybean Genet Newsl 15: 147–148

    Google Scholar 

  • Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 15: 150–152

    Google Scholar 

  • Keim P, Shoemaker RC, Palmer RG (1989) RFLP diversity in soybean. Theor Appl Genet 77: 786–792

    Google Scholar 

  • Keim P, Diers BW, Olson T, Shoemaker RC (1990a) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126: 735–742

    Google Scholar 

  • Keim P, Biers BW, Shoemaker RC (1990b) Genetic analysis of soybean hard seededness with molecular markers. Theor Appl Genet 79: 465–469

    Google Scholar 

  • Kenworthy WJ (1989) Potential genetic contributions of wild relatives to soybean improvement. In: Pascale AJ (ed) Proc World Soybean Res Conf IV. Assoc Argentina de La Soja, Buenos Aires, pp 883–888

    Google Scholar 

  • Kumar PS, Hymowitz T (1989) Where are the diploid (2n=2x=20) genome donors of Glycine Willd. (Leguminosae, Papilionoideae)? Euphytica 40: 221–226

    Google Scholar 

  • Lackey JA (1977) Neonotonia, a new generic name to include Glycine wightii (Arnott) Verdcourt (Leguminosae, Papilionoideae). Phytologia 37: 209–212

    Google Scholar 

  • Lackey JA (1980) Chromosome numbers in the Phaseoleae (Fabaceae: Faboideae) and their relation to taxonomy. Am J Bot 67: 595–602

    Google Scholar 

  • Lackey JA (1981) Phaseoleae. In: Polhill RN, Raven PH (eds) Advances in legume systematics, part 1. Royal Botanical Gardens, Kew, England, pp 301–328

    Google Scholar 

  • Miyamoto MM, Cracraft J (1991) Phylogenetic inference, DNA sequence analysis, and the future of molecular systematics. In: Miyamoto MM, Cracraft J (eds) Phylogenetic analysis of DNA sequences. Oxford University Press, New York Oxford, pp 3–17

    Google Scholar 

  • Newell CA, Hymowitz T (1980) Taxonomic revision in the genus Glycine subgenus Glycine (Leguminosae). Brittonia 32: 63–69

    Google Scholar 

  • Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5: 568–583

    Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467

    Google Scholar 

  • Shoemaker RC, Hatfield PM, Palmer RG, Atherly AG (1986) Chloroplast DNA variation in the genus Glycine subgenus Soja. J Hered 77: 26–30

    Google Scholar 

  • Shoemaker RC, Guffy RD, Lorenzen LL, Specht JE (1992) Molecular genetic mapping of soybean: map utilization. Crop Sci 32: 1091–1098

    Google Scholar 

  • Singh RJ, Hymowitz T (1985) The genomic relationships among six wild perennial species of the genus Glycine subgenus Glycine Willd. Theor Appl Genet 71: 221–230

    Google Scholar 

  • Singh RJ, Hymowitz T (1988) The genomic relationship between Glycine max (L.) Merr. and G. soja Sieb, and Zucc. as revealed by pachytene chromosome analysis. Theor Appl Genet 76: 705–711

    Google Scholar 

  • Singh RJ, Kollipara KP, Hymowitz T (1988) Further data on the genomic relationships among wild perennial species (2n=40) of the genus Glycine Willd. Genome 30: 166–176

    Google Scholar 

  • Singh RJ, Kollipara KP, Hymowitz T (1992) Genomic relationships among diploid wild perennial species of the genus Glycine Willd. subgenus Glycine revealed by meiotic chromosome pairing and seed protein electrophoresis. Theor Appl Genet 85: 276–282

    Google Scholar 

  • Singh RJ, Kollipara KP, Hymowitz T (1993) Backcross (BC2-BC4)derived fertile plants from Glycine max (L.) Merr. and G. tomentella Hyata intersubgeneric hybrids. Crop Sci 33: 1002–1007

    Google Scholar 

  • Sission VA, Brim CA, Levings CS III (1978) Characterization of cytoplasmic diversity in soybeans by restriction endonuclease analysis. Crop Sci 18: 991–996

    Google Scholar 

  • Song K, Osborn TC, Williams PH (1990) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs). 3. Genome relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris). Theor Appl Genet 79: 497–506

    Google Scholar 

  • Swofford DL (1990) PAUP: Phylogenetic analysis using parsimony, version 3.0. Illinois Natural History Survey, Champaigne, Ill.

    Google Scholar 

  • Tindale MD (1984) Two new eastern Australian species of Glycine Willd. (Fabaceae). Brunonia 7: 207–213

    Google Scholar 

  • Tindale MD (1986a) A new North Queensland species of Glycine Willd. (Fabaceae). Brunonia 9: 99–103

    Google Scholar 

  • Tindale MD (1986b) Taxonomic notes on three Australian and Norfolk Island species of Glycine Willd. (Fabaceae: Phaseoleae) including the choice of a neotype for G. clandestina Wend. Brunonia 9: 179–191

    Google Scholar 

  • Tindale MD, Craven LA (1988) Three new species of Glycine (Fabaceae: Phaseoleae) from north-western Australia, with notes on amphicarpy in the genus. Aust Syst Bot 1: 399–410

    Google Scholar 

  • Viviani T, Conte L, Cristofolini G, Speranza M (1991) Sero-systematic and taximetric studies on the Phaseoleae (Fabaceae) and related tribes. Bot J Linn Soc 105: 113–136

    Google Scholar 

  • Wendel JF (1989) New world tetraploid cotton contain old world cytoplasm. Proc Natl Acad Sci USA 86: 4132–4136

    Google Scholar 

  • Zaknarova ES, Epishin SM, Vinetski YuP (1989) An attempt to elucidate the origin of cultivated soybean via comparison of nucleotide sequences encoding glycinin B4 polypeptide of cultivated soybean, Glycine max, and its presumed wild progenitor, Glycine soja. Theor Appl Genet 78: 852–856

    Google Scholar 

  • Zhu T, Schupp JM, Oliphant A, Keim P (1994) Hypomethylated sequences: characterization of the duplicate soybean genome. Mol Gen Genet 244: 638–645

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Northern Arizona University, Box 5640, 86011, Flagstaff, AZ, USA

    T. Zhu, L. Shi & P. Keim

  2. L.H. Bailey Hortorium, 462 Mann Library Building, Cornell University, 14853, Ithaca, NY, USA

    J. J. Doyle

Authors
  1. T. Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. L. Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. J. Doyle
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. P. Keim
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Communicated by A. L. Kohler

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhu, T., Shi, L., Doyle, J.J. et al. A single nuclear locus phylogeny of soybean based on DNA sequence. Theoret. Appl. Genetics 90, 991–999 (1995). https://doi.org/10.1007/BF00222912

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00222912

Key words

Search

Navigation