Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss's Wilt of Maize

Goss9s bacterial wilt and leaf blight is a disease of maize caused by the gram positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn). First discovered in Nebraska, Goss9s wilt has now spread to major maize growing states in the United States and three provinces in Canada. Previous studies conducted using elite maize inbred lines and their hybrids have shown that resistance to Goss9s wilt is a quantitative trait. The objective of this study was to further our understanding of the genetic basis of resistance to Goss9s wilt by using a combined approach of genome-wide association mapping and gene co-expression network analysis. Genome-wide association analysis was accomplished using a diversity panel consisting of 555 maize inbred lines and a set of 450 recombinant inbred lines (RILs) from three bi-parental mapping populations, providing the most comprehensive screening of Goss9s wilt resistance to date. Three SNPs in the diversity panel and 10 SNPs in the combined dataset, including the diversity panel and RILs, were found to be significantly associated with Goss9s wilt resistance. Each significant SNP explained 1% to 5% of the phenotypic variation for Goss9s wilt (total of 8 - 11%). To augment the results of genome-wide association mapping and help identify candidate genes, a time course RNA sequencing experiment was conducted using resistant (N551) and susceptible (B14A) maize inbred lines. Gene co-expression network analysis of this time course experiment identified one module of 141 correlated genes that showed differential regulation in response to Cmn inoculations in both resistant and susceptible lines. SNPs inside and flanking these genes explained 13.3% of the phenotypic variation. Among 1,000 random samples of genes, only 8% of samples explained more phenotypic variance for Goss9s wilt resistance than those implicated by the co-expression network analysis. While a statistically significant enrichment was not observed (P