Genome-wide association study Identified multiple Genetic Loci on Chilling Resistance During Germination in Maize

Maize (Zea mays, L.) cultivation has expanded greatly from tropical to temperate zones; however, its sensitivity to chilling often results in decreased germination rates, weak seedlings with reduced survival rates, and eventually lower yields. We conducted germination tests on the maize-282-diverse-panel (282 inbred lines) under normal (25 °C) and chilling (8 °C) conditions. Three raw measurements of germination were recorded under each condition: 1) germination rate, 2) days to 50% germination, and 3) germination index. Three relative traits were derived as indicators of cold-tolerance. By using the 2,271,584 single nucleotide polymorphisms (SNPs) on the panel from previous studies, and genome-wide association studies by using FarmCPU R package to identify 17 genetic loci associated with cold tolerance. Seven associated SNPs hit directly on candidate genes; four SNPs were in high linkage disequilibrium with candidate genes within 366 kb. In total, 18 candidate genes were identified, including 10 candidate genes supported by previous QTL studies and five genes supported by previous gene cloning studies in maize, rice, and Arabidopsis. Three new candidate genes revealed by two associated SNPs were supported by both QTL analyses and gene cloning studies. These candidate genes and associated SNPs provide valuable resources for future studies to develop cold-tolerant maize varieties.