Next Generation Sequencing Enabled Genetics in Hexaploid Wheat [chapter]

Ricardo H. Ramirez-Gonzalez, Vanesa Segovia, Nicholas Bird, Mario Caccamo, Cristobal Uauy
2015 Advances in Wheat Genetics: From Genome to Field  
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
more » ... oss 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.
doi:10.1007/978-4-431-55675-6_22 fatcat:zdxv2snefrfcvjskwiwss5eqf4