L Zhang, J Huang, Y Wang, R Xu, Z Yang, ZG Zhao, S Liu, Y Tian, X Zheng, F Li, J Wang, Y Song, J Li , Y Cui, LF Zhang, Y Cheng, J Lan , W Qiao, Q Yang

BMC Genetics 2020 Jun 11;21(1):62.

Abstract

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 rice using a set of chromosome segment substitution lines. qCL1.2 encodes a 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 increases understanding 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.

See https://pubmed.ncbi.nlm.nih.gov/32527215/

Figure 3: Fine mapping of qCL1.2 in rice. a and b Frequency distributions of plant height in segregating populations cultured in Environments 3 (a) and 5 (b), Environments information were showed in Table ​1.1. c The location of qCL1.2 was narrowed to a 131-kb interval between RM11974 and RM11982. The genetic distance (cM) between two neighbouring markers is indicated above the marker label. The number of qCL1.2 recombinants obtained is indicated under the marker labels. On the left, the number of individuals of each haplotype are shown; on the right, the average plant heights are shown. P-values were calculated using Student’s t-test