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Background  The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 ( SD1 ) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.    Results  We identified a PH-related quantitative trait locus,  qCL1.2 ,from wild riceusing a set of chromosome segment substitution lines.  qCL1.2 encodesa novel allele of  SD1  gene. The wild allele of  SD1  is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the  SD1  gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated  japonica  and  indica  rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice  SD1  gene and provides additional evidence of this gene’s selection during rice domestication.    Conclusions  Our findings provide evidence that SD1  gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

bmc genomic data

Identification and genetic analysis of qCL1.2, a novel allele of the “green revolution” gene SD1 from wild rice (Oryza rufipogon) that enhances plant height