Genome-wide patterns of large-size presence/absence variants in sorghum

J Integr Plant Biol. 2014 Jan;56(1):24-37. doi: 10.1111/jipb.12121.


The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.) genomes, each 12× coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode cell death and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA transposons as the major components. The frequency and distribution of these PAVs differed substantially across 96 sorghum inbred lines, and the low- and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.

Keywords: Breeding; Sorghum bicolour; genetic diversity; genomics; presence/absence variants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Plant / genetics
  • Crosses, Genetic
  • DNA Transposable Elements / genetics
  • Gene Ontology
  • Genes, Plant / genetics
  • Genetic Variation*
  • Genome Size / genetics*
  • Genome, Plant / genetics*
  • Inbreeding
  • Inheritance Patterns / genetics
  • Molecular Sequence Annotation
  • Retroelements / genetics
  • Sequence Analysis, DNA
  • Sorghum / genetics*


  • DNA Transposable Elements
  • Retroelements