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

Bekele, W.A. and Wieckhorst, S. and Snowdon, R.J. (2013) High-throughput genomics in sorghum: From whole-genome resequencing to a SNP screening array. Plant Biotechnology Journal, 11. pp. 1112-1125.

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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.

Item Type: Article
Additional Information: . German Federal Ministry of Education. Grant Number: 0315421B . Research (BMBF) . Federal Ministry for Consumer Affairs . Nutrition and Agriculture (BMVEL). Grant Number: 23/12-13CHN12 . DAAD
Uncontrolled Keywords: Illumina, Infinium, single nucleotide polymorphism, SNP chip.
Author Affiliation: Department of Plant Breeding, Justus Liebig University, Giessen, Germany
Subjects: Crop Improvement > Genetics/Genomics
Crop Improvement > Biotechnology
Divisions: Sorghum
Depositing User: Mr Siva Shankar
Date Deposited: 08 Aug 2013 08:00
Last Modified: 23 Jul 2014 08:32
Official URL: http://dx.doi.org/10.1111/pbi.12106
URI: http://eprints.icrisat.ac.in/id/eprint/11413

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