Genome-wide association study (GWAS) of resistance to head smut in maize

Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a devastating global disease in maize, leading to severe quality and yield loss each year. The present study is the first to conduct a genome-wide association study (GWAS) of head smut resistance using the Illumina MaizeSNP50 array. Out of 45,868 single nucleotide polymorphisms in a panel of 144 inbred lines, 18 novel candidate genes were associated with head smut resistance in maize. These candidate genes were classified into three groups, namely, resistance genes, disease response genes, and other genes with possible plant disease resistance functions. The data suggested a complicated molecular mechanism of maize resistance against S. reiliana. This study also suggested that GWAS is a useful approach for identifying causal genetic factors for head smut resistance in maize.

► We firstly perform a genome-wide association study in resistance to head smut using the Illumina MaizeSNP50 array.
► We assessed the level of linkage disequilibrium (LD) decay for each chromosome.
► The Q + K model performed better than other five models when performing genome-wide association study.
► We obtained three groups of candidate genes.
► We proved that one of these candidate genes was indeed associated with resistance to head smut.