Genome-wide association study on super sweet maize seed germination rate and key gene identification under low temperature stress

【Objective】To reveal the genetic characteristics of germination traits in super sweet maize seeds under low temperature stress, identify significant single nucleotide polymorphism sites（SNP） associated with these traits and screen key genes, which could provide reference for exploring the genetic mechanisms of seed germination in super sweet maize and breeding high-germination-rate super sweet maize varieties. 【Method】Using 100 samples of super sweet maize inbred lines as the research materials, the phenotypic traits of seed germination rate under low temperature stress were analyzed. A maize 56K SNP chip was employed to conduct a genome-wide association study（GWAS） on the low-temperature germination rate of super sweet maize seeds, identifying major SNP loci associated with germination rate regulation under low temperature stress. Based on the MaizeGDB database, candidate genes within 200 kb upstream and downstream regions were extracted. GO functional annotation and KEGG signaling pathway enrichment analysis were performed on these candidate genes. Additionally, key genes were screened from the candidate genes by analyzing their average expression levels in sweet maize seed tissues under low-temperature stress. 【Result】Under low temperature stress, the germination rate of super sweet maize seeds ranged from 8% to 52%, with an average germination rate of 20%, a standard deviation of 0.073, a skewness of 1.967, a kurtosis of 7.032, and a coefficient of variation of 35.7%. A total of 6 SNPs were significantly associated with the low-temperature germination rate of super sweet maize seeds under low temperature stress, with a contribution rate of 22.9% to 28.0%. Among them, the SNP locus with the highest contribution rate was Affx-90570229. Among the SNP loci, Affx-90621601 and Affx-91200146 were in a highly linked state with adjacent loci, and the 3 superior allelic variations of T/T, C/C and A/A all had the characteristic of improving the low-temperature germination rate of seeds.Based on the significant SNP loci and combined with databases such as MaizeGDB, a total of 103 candidate genes related to seed germination rate were obtained, among which 21 candidate genes were successfully annotated, accounting for 20.4%, and were enriched in 24 GO functional terms. The 21 candidate genes were enriched in 12 signaling pathways. Gene expression difference analysis screened out 5 key genes regulating the germination rate of seeds under low temperature stress: vacuolar sorting receptor（GRMZM2G303631）, tetratricopeptide repeat（TPR）-like superfamily protein（GRMZM2G071986）,HNH endonuclease domain-containing protein（GRMZM2G074804）,microRNA（GRMZM2G 122199） and tubulin folding cofactor D（GRMZM5G816015）. Among them, GRMZM2G303631 gene had the highest average expression level（165.72）. 【Conclusion】Six significant SNPs loci associated with the lowtemperature germination rate of super sweet maize seeds were identified, and five key genes related to the regulation of the low-temperature germination rate of super sweet maize seeds were screened out, mainly involved in enzyme and protein synthesis and signal transduction processes.