An Integrated Genomic Approach Towards Cloning the Stem Solidness Gene SSt1 in Wheat

Solid-stemmed wheat lines develop pith in the culm and are resistant to damage caused by the wheat stem sawfly (Cephus cinctus). Pith acts as a barrier against sawfly stem cutting, impedes larval growth and development, and mechanically crushes sawfly eggs deposited inside the stem. In addition, the expression of pith may also be associated with improved drought resistance. A single major gene, SSt1, conferring the solid stem phenotype was previously localized to chromosome 3BL in durum wheat. Our goal is to identify the conferring locus by positional cloning of  SSt1 using DH and F2 fine mapping populations derived from the durum cross Kofa x W9262-260D3 (hollow x solid),  coupled with exome sequencing of over 120 durum and common wheat lines. With this approach, the map location of SSt1 has been narrowed to a 500 kb genomic interval near the telomeric region of chromosome 3BL.  To further compare the durum interval to that of hexaploid wheat, we performed a haplotype analysis using datasets from the wheat 90K assay collected from over 500 lines. These studies suggest that both species likely carry the same gene.  Gene expression within the SSt1 interval was analyzed using RNAseq, revealing three differentially expressed genes between hollow and solid varieties.  Work is currently underway to characterize and validate candidate genes using a population of 2400 EMS derived mutant lines derived from the solid cultivar CDC Fortitude, from which several putative M2 lines that express a hollow phenotype have already been identified.