High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array

Plant Biotechnol J. 2013 Dec;11(9):1112-25. doi: 10.1111/pbi.12106. Epub 2013 Aug 7.


With its small, diploid and completely sequenced genome, sorghum (Sorghum bicolor L. Moench) is highly amenable to genomics-based breeding approaches. Here, we describe the development and testing of a robust single-nucleotide polymorphism (SNP) array platform that enables polymorphism screening for genome-wide and trait-linked polymorphisms in genetically diverse S. bicolor populations. Whole-genome sequences with 6× to 12× coverage from five genetically diverse S. bicolor genotypes, including three sweet sorghums and two grain sorghums, were aligned to the sorghum reference genome. From over 1 million high-quality SNPs, we selected 2124 Infinium Type II SNPs that were informative in all six source genomes, gave an optimal Assay Design Tool (ADT) score, had allele frequencies of 50% in the six genotypes and were evenly spaced throughout the S. bicolor genome. Furthermore, by phenotype-based pool sequencing, we selected an additional 876 SNPs with a phenotypic association to early-stage chilling tolerance, a key trait for European sorghum breeding. The 3000 attempted bead types were used to populate half of a dual-species Illumina iSelect SNP array. The array was tested using 564 Sorghum spp. genotypes, including offspring from four unrelated recombinant inbred line (RIL) and F2 populations and a genetic diversity collection. A high call rate of over 80% enabled validation of 2620 robust and polymorphic sorghum SNPs, underlining the efficiency of the array development scheme for whole-genome SNP selection and screening, with diverse applications including genetic mapping, genome-wide association studies and genomic selection.

Keywords: Illumina; Infinium; SNP chip; single-nucleotide polymorphism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breeding
  • Chromosome Mapping
  • Gene Expression Profiling
  • Genetic Linkage
  • Genetic Markers / genetics
  • Genetics, Population
  • Genome, Plant / genetics*
  • Genome-Wide Association Study
  • Genomics*
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Linkage Disequilibrium
  • Oligonucleotide Array Sequence Analysis
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics*
  • Quantitative Trait Loci / genetics
  • Sequence Analysis, DNA
  • Sorghum / genetics*


  • Genetic Markers