With the deficiency of the synthesis for the phytochromechromophore in the maize elm1 mutant, the phytochrome activity might be reduced and the mutant plant might show characteristics of light insensitivity. In order to reveal the nucleotide polymorphisms in the maize ELM1 gene and their associations with important agronomic traits, the sequences of the maize ELM1 gene are captured in 80 inbred lines in the present study, and the associations between the sequence variations of this gene and 2 plant types (including plant height and ear height) and 7 ear traits (ear length, ear diameter, cob diameter, ear weight, kernels per row, rows per ear and kernels per ear) are determined. A total of 85 variants, including 73 SNPs and 12 indels, are detected from the full sequences of this gene in the tested inbred lines. Although in the coding regions, the indel is not included, with the SNPs of CDS sequences, the maize ELM1 gene can be classified into 7 haplotypes, which encode 6 different ELM1 proteins. There are significant differences among inbred lines for all 9 plant types and ear traits. According to the results of the association analysis, one nonsynonymous SNP is found to be associated with the ear height, while two other nonsynonymous SNPs are associated with the kernels per row.

maize  /  ELM1 gene  /  sequence variations  /  plant type and ear traits  /  association analysis