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

Summary With its small, diploid and completely sequenced genome, sorghum ( S orghum bicolor L. M oench) 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 SNP s, we selected 2124 Infinium Type II SNP s 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 SNP s with a phenotypic association to early‐stage chilling tolerance, a key trait for E uropean sorghum breeding. The 3000 attempted bead types were used to populate half of a dual‐species Illumina iS elect SNP array. The array was tested using 564 S orghum spp. genotypes, including offspring from four unrelated recombinant inbred line ( RIL ) and F 2 populations and a genetic diversity collection. A high call rate of over 80% enabled validation of 2620 robust and polymorphic sorghum SNP s, 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.