Genome-wide association analysis of chilling-tolerant germination in a new maize association mapping panel

Maize is a crop that is highly susceptible to the negative effects of low temperature. Low temperature can delay seed germination and cause a decrease in seed vigor, which seriously affects seedling emergence and yield. In this study, 190 maize accessions (inbred lines) with strong germination potential at normal temperature (25℃) were selected from more than 500 accessions to construct a new association mapping panel to further investigate germination under chilling stress (5℃). We re-sequenced the genomes of the 190 diverse accessions and obtained 4,886,919 high quality SNPs. We then used this data to analyze population structure, perform principal components analysis, and construct a phylogenetic tree of the new maize panel. The relative germination rate (RGR) and relative germination index (RGI) are two traits that are significantly related to chilling-tolerant germination. Genome-wide association analysis showed that RGR and RGI shared a major QTL, and they also shared the top SNP. There were a total of 26 significant SNPs in common. These SNPs hit directly or indirectly within 37 candidate genes. Among these 37 gene candidates are homologs of eight genes previously reported to be related to both germination and low temperature stress, and another 12 genes related to low temperature stress or other abiotic stresses such as drought, salinity, oxidative, and high light stress. In addition, RGR and RGI had another 15 and 26 significant SNPs, respectively, which were associated with 17 and 92 candidate genes, respectively. Further qRT-PCR analysis using 26 chilling-tolerant and 22 chilling-sensitive accessions implied that Zm00001eb272370 , Zm00001eb272390 , and Zm00001eb272400 associated with the top SNP, may play different roles during cold-germination. Thus, our study not only established a new association mapping panel suitable for investigation of germination at low temperature, but also provided valuable genetic resources for future studies to improve chilling-tolerant maize varieties.