title: High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array.
abstract: 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.
authors.affiliation: Department of Plant Breeding, Justus Liebig University, Giessen, Germany.
authors.forename: Wubishet A
authors.initials: WA
authors.lastname: Bekele
authors.forename: Silke
authors.initials: S
authors.lastname: Wieckhorst
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Friedt
authors.forename: Rod J
authors.initials: RJ
authors.lastname: Snowdon
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D005828:Genetics, Population; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D017422:Sequence Analysis, DNA; D045868:Sorghum / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Illumina; Infinium; SNP chip; single-nucleotide polymorphism