Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes

PLoS One. 2013 Nov 12;8(11):e79192. doi: 10.1371/journal.pone.0079192. eCollection 2013.

Abstract

Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19(th) century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09) and dw3 (SBI-07) had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • Chromosomes, Plant
  • DNA Methylation
  • Euchromatin / genetics
  • Evolution, Molecular
  • Genome, Plant*
  • Genotype
  • Haplotypes
  • Phylogeny
  • Polymorphism, Genetic*
  • Polymorphism, Single Nucleotide
  • Recombination, Genetic
  • Selection, Genetic
  • Sequence Analysis, DNA
  • Sorghum / genetics*

Substances

  • Euchromatin

Grant support

All authors have no financial, personal, or professional interests that could be construed to have influenced the paper. Partial funding for genome sequencing was provided by Pioneer Hi-Bred International, however, the authors confirm that this does not alter our adherence to all of the PLOS ONE policies on sharing data and materials as detailed in the PLOS ONE guide to authors. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.