A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1

Abstract

SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin) is an important insect pest of wheat (Triticum aestivum) in many growing regions. Sm1 is the only described OWBM resistance gene and is the foundation of managing OWBM through host genetics. Sm1 was previously mapped to wheat chromosome arm 2BS relative to simple sequence repeat (SSR) markers and the dominant, sequence characterized amplified region (SCAR) marker WM1. The objectives of this research were to saturate the Sm1 region with markers, develop improved markers for marker-assisted selection (MAS), and examine the synteny between wheat, Brachypodium distachyon, and rice (Oryza sativa) in the Sm1 region. The present study mapped Sm1 in four populations relative to single nucleotide polymorphisms (SNPs), SSRs, Diversity Array Technology (DArT) markers, single strand conformation polymorphisms (SSCPs), and the SCAR WM1. Numerous high quality SNP assays were designed that mapped near Sm1. BLAST delineated the syntenic intervals in B. distachyon and rice using gene-based SNPs as query sequences. The Sm1 region in wheat was inverted relative to B. distachyon and rice, which suggests a chromosomal rearrangement within the Triticeae lineage. Seven SNPs were tested on a collection of wheat lines known to carry Sm1 and not to carry Sm1. Sm1-flanking SNPs were identified that were useful for predicting the presence or absence of Sm1 based upon haplotype. These SNPs will be a major improvement for MAS of Sm1 in wheat breeding programs.

Multiple wheat genomes reveal global variation in modern breeding

“…3a). Sm1 is the only gene in wheat known to provide resistance to OWBM 6 . CDC Landmark, Robigus and Paragon are all resistant to the OWBM, and all three carry the same 7.3-Mb haplotype within the Sm1 locus on chromosome 2B (Fig.…”

“…Characterization of Sm1. Sm1-linked markers 6 were located in RQAs using BLAST v.2.8.0. Two high-resolution mapping populations were developed, 99B60-EJ2D/Thatcher and 99B60-EJ2G/Infinity.…”

“…Approximately 6,000 M 2 seeds were space planted in two field nurseries located in Brandon and Glenlea, Manitoba, Canada. Spikes were collected on a per-plant basis at maturity and were classified as resistant, susceptible or undamaged as done previously 6,72 . Putative Sm1-knockout mutants were re-tested for OWBM resistance in indoor cage tests 73 in the M 3 and M 4 generations.…”

“…Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.…”

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

“…Marker saturation in the vicinity of the target resistance gene is a critical step for mapped-based or positional cloning of R-genes which results in the development of diagnostic markers [20]. RGAs-based marker development strategies have been successfully applied for the development of diagnostic markers for orange wheat blossom midge and wheat stem rust resistance genes [21, 22]. This strategy involves four iterative steps: (1) identification of genome-wide RGAs, (2) identification of potential RGA candidates in the vicinity of the target resistance gene using comparative genomics analysis, (3) design of SNP markers for candidate RGAs, and (4) marker evaluation using biparental genetic populations and/or association panels.…”