![]() This gene diversity spans important processes of high relevance for breeding, for example sugar and starch metabolism, lignin biosynthesis and stress responses. ( 2011) not only detected over 1 million genomic SNPs, but also demonstrated that over 1500 genes differentiate between sweet and grain sorghum. By whole-genome resequencing of two sweet sorghum accessions and one grain sorghum, Zheng et al. ( 2011) used reduced-representation sequencing of restriction-site-associated DNA (RAD see Baird et al., 2008) to discover genome-wide SNPs in a panel of 8 genetically diverse grain sorghum genotypes. Such techniques have the potential to considerably accelerate selection gain and improve the effectiveness of breeding. In particular, the dramatically falling costs of genome-wide screening for single-nucleotide polymorphisms (SNPs), using high-density SNP array technologies (see Batley and Edwards, 2007) or genotyping-by-sequencing (Chia and Ware, 2011 Davey et al., 2011 Elshire et al., 2011 Morris et al., 2013) on next-generation sequencing platforms (Metzker, 2010), has opened the way for genomic selection (Jannink et al., 2010) or predictive breeding strategies (Riedelsheimer et al., 2012). The small diploid genome of sorghum, the availability of a completed reference genome sequence (Paterson et al., 2009) and the consequent ability to develop cost-effective, high-throughput tools for whole-genome screening make sorghum a strikingly amenable crop for the application of genomics-based breeding methods. The ability to intercross cultivated sorghum races with related subspecies for expansion of genetic diversity and improvement in key traits is a unique aspect of this crop (Washburn et al., 2013). In comparison with more established crops like maize, wheat and barley, breeding of sorghum for bio-energy and livestock feeding is a relatively young enterprise, and an enormous genetic potential for improvement in the crop has yet to be tapped by breeders. high dry-matter biomass or grain yields), whereas in subsistent arid and semi-arid farming systems, grain yield and seed quality are the most vital traits. Breeding sorghum for temperate regions necessitates the combination of chilling tolerance from appropriate germplasm resources with photoperiod adaptation and other appropriate agronomic characters (e.g. In Australia and the US Southern Plains, grain sorghum represents a drought-tolerant alternative to maize production for livestock feeding, while in Europe, China and North America, interest is also growing rapidly in the use of sweet and/or grain sorghum forms as a potentially drought-tolerant and nutrient-efficient alternative to maize for bio-energy production (Rooney et al., 2007). Sorghum is widely grown as a staple cereal crop, particularly in Africa and parts of Asia but also for various uses in other parts of the world. 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. genotypes, including offspring from four unrelated recombinant inbred line (RIL) and F 2 populations and a genetic diversity collection. The array was tested using 564 Sorghum spp. The 3000 attempted bead types were used to populate half of a dual-species Illumina iSelect SNP array. 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. 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. 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. ![]() 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. Moench) is highly amenable to genomics-based breeding approaches. With its small, diploid and completely sequenced genome, sorghum ( Sorghum bicolor L.
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