Journalartikel

Jahr der Veröffentlichung: 2013

Seiten: 1112-1125

Zeitschrift: Plant Biotechnology Journal

Bandnummer: 11

Heftnummer: 9

ISSN: 1467-7644

Open Access Status: Hybrid

DOI Link: https://doi.org/10.1111/pbi.12106

Verlag: Wiley

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 6x to 12x 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 F-2 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.

Harvard-Zitierstil: Bekele, W., Wieckhorst, S., Friedt, W. and Snowdon, R. (2013) High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array, Plant Biotechnology Journal, 11(9), pp. 1112-1125. https://doi.org/10.1111/pbi.12106

APA-Zitierstil: Bekele, W., Wieckhorst, S., Friedt, W., & Snowdon, R. (2013). High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array. Plant Biotechnology Journal. 11(9), 1112-1125. https://doi.org/10.1111/pbi.12106