QTL analysis of low-temperature tolerance in maize germination by SLAF-seq and BSA technique

Background: Cold damage of maize during germination is a global problem; it occurs frequently in northeast China, and leads to a large-scale reduction in yield. Low temperature tolerance of maize in germination is a complex quantitative trait controlled by multigenes, and no major QTLs or key genes have been identified. Results: An F2 isolation population with S319 and R144 as parents was constructed. The bulked segregant analysis (BSA) and specific-locus amplified fragment-sequencing (SLAF-seq) methods were applied to locate the chromosomal association regions related to low-temperature tolerance of maize during germination. Sequencing obtained 221.72 Gbp clean data, with an average sequencing depth of 25.96X. Four candidate regions associated with low-temperature tolerance trait of maize in germination were obtained, with a total length of 25.71 Mb and 1513 annotated genes, including 456 nonsynonymous mutant genes and 111 frameshift mutant genes. Conclusions: This study aimed to lay the foundation for the mining of candidate genes of low-temperature tolerance in maize during germination, and accelerate the process of targeted improvement of maize low-temperature tolerance molecular marker-assisted breeding.How to cite: Yu T, Zhang J, Cao J, et al. QTL analysis of low temperature tolerance in maize germination by SLAF-seq and BSA technique. Electron J Biotechnol 2024;70. https://doi.org/10.1016/j.ejbt.2024.04.003.