Abstract
Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.
Highlights
Extensive archaeological evidence indicates that rice was first domesticated along the middle and lower Yangtze River corridors in South China about 8000 years ago [1,2]
Population Structure 24 simple sequence repeat (SSR) markers were randomly selected from one each short and long arms of the 12 rice chromosomes, all of them were shown to be polymorphic among the 104 rice accessions
The two japonica subpopulations may correspond with a deeper population structure division
Summary
Extensive archaeological evidence indicates that rice was first domesticated along the middle and lower Yangtze River corridors in South China about 8000 years ago [1,2]. In this domestication process, two genetically distinct Oryza sativa subspecies, indica and japonica, were formed. The domestication of the two subspecies occurred independently in different ecological and geographical environments. In both subspecies human selection has maintained the introgressions containing the most agriculturally valuable alleles [5]. Besides the two subspecies (indica and japonica), a deeper population structure has been defined by previous researchers, subdividing them into five genetically distinct subpopulations: indica, aus, temperate japonica, tropical japonica and aromatic [6]
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