Objectives To better understand the polymorphism of pheophorbide a oxygenase gene (ZmPAO) in maize and the functional sites related to the contents of chlorophyll components in maize ear leaves, the structural information used for the development of ZmPAO functional markers was analyzed to clarify the genetic mechanism of chlorophyll metabolism at late maturity stage of maize.
Methods A total of 141 of maize inbred lines with extensive genetic variation was used as a related population. The chlorophyll component contents in two sites from 7 time points were measured as phenotypic data. Tassel 5.0 was used to analyze the relationship between the expression profiles of pheophorbide a oxygenase gene (ZmPAO) and the changes of chlorophyll components at different periods after maturity by the mixed linear model (MLM, Mixed linear model), and the effective association sites were investigated by haplotype analysis.
Results The chlorophyll contents at the late growth stage of maize revealed greater variation, and chlorophyll a generally has lower accumulation than chlorophyll b, but the total chlorophyll (the sum of chlorophyll a and chlorophyll b) showed a downward trend. A total of 19 of effective functional sites were identified, in which 4 sites were existed in the exon region, one of them located at UTR and others settled in the intron. The phenotypic interpretation rate in the functional site for chlorophyll component content variation was ranged from 3.89% to 16.57%, the total phenotypic effect ranged from 5.24% to 41.78%. Site S3235 from the sixth intron had a phenotypic interpretation rate of 16.57% for Yang-chlb6; Site S3675 of the seventh exon represented 12.16% phenotypic interpretation rate for the phenotypic variation for Yang-chla1 and 14.14% for Yang-chlb1, respectively. The favorable trait sites with obvious haplotypes was the same as preferred variation sites in association analysis.
Conclusions The excavation of effective functional sites and haplotype analysis of traits showed that two amino acids mutated in the ZmPAO exon, and the hydrophobic amino acids were transformed into hydrophilic amino acids, indicating that the ZmPAO gene might be regulated by the protein structure variation and as well as the transcriptional level because more related sites appeared in noncoding regions, although they are not yet identified. However, the transcription level is greatly affected by environmental factors which usually lead to the inconsistency of the related sites that found in different locations of the gene at different growth stages, but the existence of effective mutation sites is universal.
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