Os03g0818800

The rice gene Os03g0818800 was reported as Oryza sativa INDETERMINATE SPIKELET 1 (OsIDS1) in 2012.

Annotated Information

Function

• SNB and OsIDS1 function semi-dominantly and synergistically contribute to floral meristem fate in a dose- and photoperiod-dependent manner.

• SNB and OsIDS1 control the duration of inflorescence and branch meristems,
• SNB and OsIDS1 positively regulate panicle branching by repressing spikelet meristem identity

Mutation

• Spikelets of osids1 were occasionally abnormal as compared with wild-type (WT) spikelets that consisted of one floret subtending two pairs of glumes – rudimentary glume and empty glume (Figure 1a; Arber, 1934). A normal floret comprises the flower proper (one pistil, six stamens, and two lodicules) plus a pair of bract-like organs (palea and lemma) (Figure 1e; Bommert et al., 2005). In the researchers' osids1 spikelets, one of the empty glumes was occasionally replaced by a rudimentary glume (Figure 1b), and 3.2% of those lodicules were elongated (Figure 1f, Table 1). An extra lodicule also was often found in mutant spikelets (Figure 1f, Table 1).

• To examine the functioning of OsIDS1 further, the researchers generated double mutants between osids1 and snb. Those had more bracts, including rudimentary glumes, lemma, and palea, than did single mutants (Figure 1b–d, Table 1). For example, osids1 and snb plants averaged 4.00 and 4.07 glumes, respectively, versus 4.67 in snb osids1. The number of lemma/palea was also increased, to 3.29 in the double mutant from 2.02 and 2.10 in the single mutants. The double mutants rarely developed empty glumes, but elongated bracts were occasionally found in the boundary between a rudimentary glume and lemma. However, their epidermis was similar to that of the lemma/palea (Figures 1d and S2b). Furthermore, ectopic structures were formed between their layers of lemma and palea, sometimes in a reiterated pattern (Figure 1i,j). Scanning electron microscopy (SEM) analyses revealed that these structures contained multiple rudimentary glumes, lemma/palea organs, and rachis (Figure S2c,d), suggesting that they were underdeveloped spikelets. These observations suggested that OsIDS1 functions together with SNB in spikelet development.

• The snb osids1 mutants also exhibited abnormal floral organs. Their most conspicuous feature was a change in the size and shape of the lodicules, with approximately 50% being elongated (Figure 1h, Table 1). Moreover, the surface of those elongated lodicules was transformed into those of the lemma and palea (Figure S2c,d). Ectopic lodicules were additionally formed at the side of the palea (Figure 1h), creating a concentric whorl with the original lodicules on the lemma side. These double mutants also had fewer stamens than the WT (Figure 1f–h, Table 1).

Figure 1. Spikelet phenotypes of snb, osids1, and snb osids1. (a) Wild-type (WT) spikelet. EG, empty glume; L, lemma; P, palea; RG, rudimentary glume. (b) osids1 spikelet. (c) snb spikelet. Arrows represent bract-like structure. L/P, lemma/palea-like structure. (d) snb osids1 spikelet. Red arrowhead indicates intermediate structure between lemma and glume. (e–h) Upper side of lemma and palea was removed to observe inner floral organs: (e) wild-type spikelet with two lodicules (Lo), six stamens (St), and one carpel (Ca); (f) osids1 spikelet with three elongated lodicules (Elo); (g) snb spikelet with two elongated lodicules, two normal lodicules, four stamens (St), and one carpel (Ca); (h) snb osids1 spikelet with four elongated lodicules. (i–k) Spikelets of snb osids1 double mutants showing ectopic spikelets (arrowheads). Ectopic spikelets were formed between layers of lemma/palea (i, j). Underdeveloped spikelets were formed reiteratively on flank of rachilla. Ectopic spikelet was formed on flank of carpel (k). .

Table 1 Phenotypic characterizations from different combinations of snb and osids1 alleles .

• To study the functional roles for AP2 family genes at the molecular level, the researchers examined their expression in the spikelets and florets. They first tested the expression of AP1/FUL1 clade genes – OsMADS14, OsMADS15, and OsMADS18 – which are mainly expressed in early spikelet meristems and sterile organs. Quantitative RT-PCR analyses showed that their transcript levels were unchanged in snb osids1 plants (Figure 2a–c). They also examined B-function genes, which specify the second and third whorls. Rice has three such genes: OsMADS2, OsMADS4, and OsMADS16(Figure 2d–f). Transcript levels of the C-function gene OsMADS3 were also lower in snb osids1 (Figure 2g). Lastly, expression of E-function genes (OsMADS1, OsMADS5, OsMADS7, and OsMADS8) was examined. Similar to B- and C-function genes, expression of OsMADS1 and OsMADS7 in snb osids1 was lower than in the WT at the earlier stage (Figure 2h,i).

Figure 2. Expression analyses of floral identity genes in wild-type (WT), osids1, snb, and snb osids1 mutants. .

• In addition to their defects in floral meristem transition, panicles of snb osids1 produced fewer primary branches and spikelets than the WT (Figure 4a). The snb and osids1 single mutants had fewer branches and spikelets than the WT (Fig 4b,c).

Figure 4. Inflorescence architecture. (a) Comparison of inflorescence between wild type (WT) and snb osids1. (b) Average number of primary branches per panicle. (c) Average number of spikelets per panicle. At least 10 panicles from main culms were used for analysis. Asterisks indicate significant differences from wild type at *P < 0.05; **P < 0.01; or ***P < 0.001. .

Expression

• Quantitative RT-PCR analyses showed that SNB transcripts were highly abundant in seedlings and developing panicles, whereas those of OsIDS1 were much less abundant at all developmental stages except for seedling shoots, during which time both genes were almost equally expressed (Figure 6a). RNA in situ hybridization revealed that OsIDS1 was detected in developing branch and spikelet meristems at very early stages of inflorescence formation (Figure 6b,c). Expression of OsIDS1 was maintained uniformly in the spikelet meristems until floral organs were initiated (Figure 6d,f,g). Afterward, transcripts were evenly detected in floral organ primordia (Figure 6h).

Figure 6. Quantitative RT-PCR and RNA in situ hybridization analyses of SNB and OsIDS1. (a) Quantitative RT-PCR analysis in various organs. Each bar represents relative values between transcripts levels of regulatory genes and Ubi1. Error bars indicate standard deviation. DAG, days after germination; DAP, days after pollination. (b–d) RNA in situ hybridization of OsIDS1 in wild-type developing panicles at an early stage of branch meristem initiation (b), late stage of branch meristem initiation (c), and spikelet meristem transition stage (d). (e) OsIDS1 sense control. (f–h) OsIDS1 expression pattern in spikelet meristem. (i–k) SNB expression pattern in spikelet meristem. BM, branch meristem; SBM, secondary branch meristem; SM, spikelet meristem; FM, floret meristem; RG, rudimentary glume; EG, empty glume; Le, lemma; Pa, palea; St, stamen. Scale bar = 100 lm. .

Evolution

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Labs working on this gene

• Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea