Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane (Saccharum spp.) clonal F1 population

Abstract The ratoon stunting disease (RSD) of sugarcane, caused by the bacterium Leifsonia xyli subsp. xyli, is one of the major concerns to sugarcane production and breeding programs worldwide. Due to no obvious external symptoms, RSD cannot be easily detected by the growers, hence has reduced the world’s sugarcane production significantly. This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection. A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay. Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population, linkage map construction and QTL analysis were conducted based on clonal F1 and F2 mapping population types with GACD V.1.2 and IciMapping V.3.3, respectively. A total of 23 QTL associated with RSD resistance were identified, which explained 6% to 13% of the phenotypic variation with the two types of software. A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes), sugarcane R570 genome (20 genes), and S. spontaneum genome (18 genes), respectively. Compared with IciMapping V.3.3, GACD V.1.2 identified more major (6 vs. 3) and stable QTL (2 vs. 0), and more disease resistance genes (51 vs. 31), indicating GACD V.1.2 (clonal F1 mapping type) is most likely to be more efficient than IciMapping (F2 mapping type) for QTL analysis of a sefling population or clonal F1 population in clonal species. The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease.