Identification and characterization of SHORTENED UPPERMOST INTERNODE 1, a gene negatively regulating uppermost internode elongation in rice

Abstract

In rice, the elongated internodes are derived from the vegetative shoot apical meristem (SAM), and the transition of the SAM from the vegetative to the reproductive stage induces internode elongation. In this study, we characterize two shortened uppermost internode mutants (sui1-1 and sui1-2). During the seedling and tillering stages, sui1 plants are morphologically similar to wild-type plants. However, at the heading stage, the sui1-1 mutant exhibits a shortened uppermost internode and a partly sheathed panicle, and the sui1-2 mutant shows an extremely shortened uppermost internode and a fully sheathed panicle. Gibberellin treatment results in elongation of every internode, but the shortened uppermost internode phenotype remains unaltered. Microscopic analysis indicates that cell length of sui1-1 uppermost internode exhibits decreased. Map-based cloning revealed that SUI1 is located on Chromosome 1, and encodes a putative phosphatidyl serine synthase (PSS) family protein. Searches for matches in protein databases showed that OsSUI1 contains the InterPro domain IPR004277, which is conserved in both animal and plant kingdoms. Introduction of a wild-type SUI1 gene fully rescued the mutant phenotype of sui1-1 and sui1-2, confirming the identity of the cloned gene. Consistent with these results, the SUI1-RNAi transgenic plants displayed decreased elongation of the uppermost internode. Our results suggest that SUI1 plays an important role in regulating uppermost internode length by decreasing longitudinal cell length in rice.

Markers Associated with Culm Length and Elongated Internode Length in Japonica Rice

“…Among the colocalized loci, 19 known functional genes were D2 (Hong et al, 2003), SUI3 (Yin et al, 2013), and OsBRI1 (Yamamuro et al, 2000) on chromosome 1; LRK1 and GID2 (Sasaki et al, 2003) on chromosome 2; D14 (Arite et al, 2009), SSD1 (Asano et al, 2010), OsSIN (Han et al, 2005), and OsPIL1 (Todaka et al, 2012) Eight known functional genes were not colocated with the QTLs in this study. They were SUI1 (Zhu et al, 2011), OsGA3ox2 (D18) (Itoh et al, 2001), OsCCD8 (D10) (Arite et al, 2007), and OsGA20ox2 (sd1) (Maeda et al, 1997) on chromosome 1; OsGLU1 (Zhou et al, 2006) on chromosome 3; D11 (Tanabe et al, 2005) on chromosome 4; and D1 (Ashikari et al, 1999) and EUI1 (Luo et al, 2006) on chromosome 5. The 128 QTLs tagged by 70 SSR markers associated with different traits in this study (18 in 3 yr, 24 in 2 yr, and 86 in 1 yr) were not located within the same interval of the known QTLs and characterized gene, as shown in previous studies (Table 2, Supplemental Files 8 and 9).…”

“…For example, elongation was suppressed in all internodes in d3 , d10 , d14 , d17 , d27 , sinox‐6 , OsGLU1 , htd1, SSD1 , and dsg1 mutants (Zou et al, 2005; Han et al, 2005; Zhou et al, 2006; Arite et al, 2007; Asano et al, 2010; Liu et al, 2015). The elongation of uppermost internode length was most strongly inhibited in d35 , SUI1 , and SUI4 mutants (Itoh et al, 2004; Zhu et al, 2011; Ji et al, 2014). Insertion of Tos17 into the SUI2 resulted in a severe dwarf phenotype, in which all internodes of the mutant were greatly reduced; the transgenic plants with SUI3 RNA interference showed dwarf phenotypes in which upper internodes were shortened compared with wild‐type plants (Yin et al, 2013).…”

Analysis of QTLs for panicle exsertion and its relationship with yield and yield-related traits in rice (Oryza sativa L.)

“…Recently, enzymes associated with tissue development were reported to regulate the elongation of PE. The shortened uppermost internode 1 (sui1) mutant was characterized as having symptoms of a sheathed panicle, and the gene responsible was found to encode a putative phosphatidyl serine synthase (Zhu et al, 2011). Three SUI family genes (SUI1, SUI2, and SUI3) in rice, which encode base-exchange-types of phosphatidyl serine synthases, were shown to regulate the development of the intercalary meristem for culm or internode elongation (Yin et al, 2013).…”

ES5 is involved in the regulation of phosphatidylserine synthesis and impacts on early senescence in rice (Oryza sativa L.)

“…Through mapping-based cloning we have proved that these changes occurred in the mutant due to one base substitution and creation of a premature stop codon of the ES5 gene located on the long arm of chromosome 5. In rice, ES5 was reported as SUI2 which has two more homologous genes reported as SUI1 (LOC_Os01g49024) and SUI3 (LOC_Os01g02890) (Yin et al 2013;Zhu et al 2011). All these genes are reported for shortened uppermost internode phenotype.…”