DNA methylation and AFLP marker distribution in the soybean genome

W. P. Young, J. M. Schupp, Paul S Keim

Research output: Contribution to journalArticle

118 Citations (Scopus)

Abstract

Amplified fragment length polymorphisms (AFLPs) have become important markers for genetic mapping because of their ability to reliably detect variation at a large number of loci. We report here the dissimilar distribution of two types of AFLP markers generated using restriction enzymes with varying sensitivities to cytosine methylation in the soybean genome. Initially, AFLP markers were placed on a scaffold map of 165 RFLP markers mapped in 42 recombinant inbred (F(6:7)) lines. These markers were selected from a map of over 500 RFLPs analyzed in 300 recombinant inbred (F(6:7)) lines generated by crossing BSR101xPI437.654. The randomness of AFLP marker map position was tested using a Poisson-model distribution. We found that AFLP markers generated using EcoRI/MseI deviated significantly from a random distribution, with 34% of the markers displaying dense clustering. In contrast to the EcoRI/MseI AFLP markers, PstI/MseI-generated AFLP markers did not cluster and were under represented in the EcoRI/MseI marker clusters. The restriction enzyme PstI is notably sensitive to cytosine methylation, and these results suggest that this sensitivity affected the distribution of the AFLP markers generated using this enzyme in the soybean genome. The common presence of one EcoRI/MseI AFLP cluster per linkage group and the infrequent presence of markers sensitive to methylation in these clusters are consistent with the low recombination frequency and the high level of cytosine methylation observed in the heterochromatic regions surrounding centromeres. Thus, the dense EcoRI/MseI AFLP marker clusters may be revealing structural features of the soybean genome, including the genetic locations of centromeres.

Original languageEnglish (US)
Pages (from-to)785-792
Number of pages8
JournalTheoretical And Applied Genetics
Volume99
Issue number5
DOIs
StatePublished - 1999

Fingerprint

DNA methylation
DNA Methylation
Soybeans
Methylation
amplified fragment length polymorphism
Cytosine
Genome
soybeans
genome
Centromere
Restriction Fragment Length Polymorphisms
methylation
Poisson Distribution
cytosine
Enzymes
Genetic Markers
Genetic Recombination
Cluster Analysis
centromeres
restriction fragment length polymorphism

Keywords

  • AFLP
  • Centromeres
  • Genetic mapping
  • Glycine max
  • Methylation
  • Soybean

ASJC Scopus subject areas

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

Cite this

DNA methylation and AFLP marker distribution in the soybean genome. / Young, W. P.; Schupp, J. M.; Keim, Paul S.

In: Theoretical And Applied Genetics, Vol. 99, No. 5, 1999, p. 785-792.

Research output: Contribution to journalArticle

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