A single nuclear locus phylogeny of soybean based on DNA sequence

T. Zhu, L. Shi, J. J. Doyle, Paul S Keim

Research output: Contribution to journalArticle

28 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)991-999
Number of pages9
JournalTheoretical And Applied Genetics
Volume90
Issue number7-8
DOIs
StatePublished - Jun 1995

Fingerprint

Phylogeny
Glycine (Fabaceae)
Soybeans
Nucleotides
nucleotides
Neonotonia
soybeans
Amphicarpum
Teramnus
nucleotide sequences
loci
Glycine
phylogeny
topology
Phaseolus
Restriction Fragment Length Polymorphisms
restriction fragment length polymorphism
Neonotonia wightii
chloroplast DNA
Phaseolus vulgaris

Keywords

  • DNA sequence
  • Genomic donors
  • Glycine
  • Glycininae
  • Phaseoleae
  • Phylogeny
  • Soybean

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Plant Science
  • Horticulture
  • Agronomy and Crop Science

Cite this

A single nuclear locus phylogeny of soybean based on DNA sequence. / Zhu, T.; Shi, L.; Doyle, J. J.; Keim, Paul S.

In: Theoretical And Applied Genetics, Vol. 90, No. 7-8, 06.1995, p. 991-999.

Research output: Contribution to journalArticle

Zhu, T. ; Shi, L. ; Doyle, J. J. ; Keim, Paul S. / A single nuclear locus phylogeny of soybean based on DNA sequence. In: Theoretical And Applied Genetics. 1995 ; Vol. 90, No. 7-8. pp. 991-999.
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