Next Generation Sequencing Enabled Genetics in Hexaploid Wheat

Abstract

Next Generation Sequencing (NGS) is providing new methodologies to improve and complement traditional genetic approaches. These strategies, collectively termed NGS-enabled genetics, consist of identifying variation in bulks of plants that have been assembled based on a specifi c phenotype of interest. We examined NGS-enabled genetics in hexaploid wheat by using near isogenic lines (NIL) differing across a specifi c disease resistance locus. RNA-Seq of NILs allowed the identifi cation of SNPs across this locus and helped distinguish allelic SNPs from homoeologous variants. F 2 bulks were assembled based on opposing disease resistance phenotypes and the frequency of the informative allelic SNPs was examined across bulks using RNA-Seq. Variants enriched in the corresponding bulks are expected to be most closely linked to the phenotype of interest and were prioritized for validation. Recent advances in cereal genomics in the form of wheat gene models, sequenced diploid progenitors, and the advances in the Chromosome-based Survey Sequencing Project enabled us to develop a pipeline to automatically design SNP-based markers. These high-throughput assays were used to genotype the original individuals used to assemble the bulks and to generate a genetic map across the target locus. Linked markers are now being incorporated into marker assisted selection programs by breeders.

Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat

“…GWAS and linkage mapping of drought tolerance QTLs have been enabled by the availability of a high-quality reference genome for common wheat along with next-generation sequencing (NGS) technologies (Kilian and Graner, 2012;Ray and Satya, 2014;Ramirez-Gonzalez et al, 2015;IWGSC, 2018). Genotype by sequencing (GBS), a DNA sequencing method that follows the NGS protocol, does not require prior genome sequence information and has enormous potential to genotype complex genomes such as in wheat (Poland et al, 2012;Mwadzingeni et al, 2016a;Chung et al, 2017).…”