Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Homozygosity mapping through whole genome analysis identifies a COL18A1 mutation in an Indian family presenting with an autosomal recessive neurological disorder.

The use of genome wide genotyping arrays has the potential to assess entire groups of genetic disorders in one application and has begun to emerge as an aid to diagnosis in clinical practice. Recessive families may suffer from diseases because of homozygosity of recessive alleles; homozygosity tracks can be easily identified by using these high throughput SNPs arrays, allowing the rapid mapping of autozygous segments that may be associated with the disease. According to this, we performed homozygosity mapping using genome wide SNP arrays in a North Indian family with an autosomal recessive disorder of ataxia, epilepsy, cognitive decline and visual problems. In this kindred, a large number of homozygous regions were identified. In silico analysis was also carried out. The COL18A1 gene found in one of the homozygous tracks has genetic defects previously reported with a similar phenotype as our family. Hence, it was the most likely candidate gene and at large the first to be analyzed. A homozygous COL18A1 two base pair deletio segregating with the disease was identified; expanding the spectrum of disease seen in COL18A1 and proving that the genetic lesion underlying recessive disorders can rapidly identify by employing genotyping arrays along with detailed candidate gene analysis.