High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives

Abstract

A lack of genetic diversity between wheat breeding lines has been recognized as a significant block to future yield increases. Wheat breeding and prebreeding strategies are increasingly using material from wheat ancestors or wild relatives to reintroduce diversity. Where molecular markers are polymorphic between the host and introgressed material, they may be used to track the size and location of the introgressed material through generations of backcrossing. To generate markers for this purpose, sequence capture targeted resequencing was carried out for a range of wheat varieties, wheat relatives, and wheat progenitors. From these sequences, putative SNPs were identified and used to generate the Axiom® Wheat HD array. A selection of varieties representing a selection of elite wheat breeding material, progenitor species, and wild relatives were used to validate the array. The procedures used are described here in detail.

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)

“…Leaf tissue was harvested 6 weeks after germination, frozen in liquid nitrogen and stored at −20 °C prior to nucleic acid extraction. Genomic DNA was prepared using a phenol–chloroform extraction method (Burridge et al ., ), treated with RNase‐A (QIAGEN Ltd., Manchester, UK) according to the manufacturer's instructions and purified using the QiaQuick PCR purification kit (QIAGEN Ltd).…”

Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach

“…This system represents a costeffective alternative to gene-based array platforms [24,44]. Previous studies demonstrated that arrays adapted for high-throughput genotyping of bread wheat offer resolutions ranging from 8 K to 550 K [29,[45][46][47][48][49][50][51].…”

High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily

“…Among molecular markers, single nucleotide polymorphisms (SNP) [14,15,16] are point mutations that result in single base-pair divergence, among DNA sequences present in both genome coding and noncoding regions. The advent of high-throughput Next Generation Sequencing (NGS) technologies enabled the large-scale identification of SNPs in plant species, and the development of efficient genotyping platforms, for association studies [17,18] and genetic characterization, also in wheat [19,20,21,22,23,24,25,26], where the tetraploid condition make the utilization of microsatellites difficult.…”