RNAseq Bulked Segregants Suppression Subtractive Method for Tagging of Stem Solidness Genes in Common Wheat

Stems of some common wheat accessions when filled with soft, spongy and compact parenchyma cells, known as pith, are a primary strategy in combatting wheat stem sawfly (Cephus cinctus) in wheat. However, stem solidness in common wheat (Triticum aestivum L.) is affected by many background inhibitors and by genotype × environment interactions. Also, little is known about the molecular mechanism and genes underlying stem solidness in common wheat. In order to dissect the genetic basis of stem solidness in common wheat, we developed two doubled haploid populations from wheat cvs. Sadash and AAC Innova, each crossed with P2711, a completely solid stem line. Both populations were subjected to extensive phenotyping for two years (2014 and 2015) using an improved and precise method and genotyping (using either wheat 15K or 90K Infinium iSelect SNP Assay) followed by QTL analysis. Two major QTLs, SSt_3B and SSt_3D, were identified on distal regions of chromosome arms 3BL and 3DL in addition to two inhibitors in Sadash (on 2A) and two in AAC Innova (on 2A, 5A). Additionally, minor QTL were identified in Innova (on 2B) and P2711 (on 5B). To identify the candidate genes underlying SSt QTLs, we coupled QTL analysis results with a new approach RNAseq bulked segregants suppression subtractive method and conducted on different bulks made from Sadash/P2711 population. This analysis enabled us to identify a single SSt_3B candidate and three SSt_3D candidate genes. Work is currently underway to characterize and validate candidate genes.