DEGENERATED LEMMA (DEL) regulates lemma development and affects rice grain yield

Abstract

In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-023-01297-6.

Keywords: Lemma; Map-based cloning; Rice; Spikelet; Yield.

Fig. 1

Phenotype of spikelets of the wild type and the del mutant. A Complete spikelet of the wild type. B The spikelet shown in A with the lemma and palea removed. C Surface of wild-type spikelet. D Surface features of the lemma. E Surface features of the palea. F Transverse sections of a wild-type spikelet. G High-magnification image of the area in the red box in F. H A del mutant spikelet with a slightly degenerated lemma. I The spikelet shown in H with the lemma and palea removed. J Surface of the slightly degenerated lemma with the inner floral organs exposed. K Surface features of the slightly degenerated lemma. L Surface features of the palea. M Transverse sections of a del mutant spikelet. N High-magnification image of the area in the red box in M. O A del mutant spikelet with a rod-like lemma. P The spikelet shown in O with the lemma and palea removed. Q, The surface of the rod-like lemma with the inner floral organs exposed. R Surface features of the rod-like lemma. S, Surface features of the palea. T Transverse sections of a del mutant spikelet. U High-magnification image of the area in the red box in T. Black stars indicate the joining of the lemma and palea. le, lemma; pa, palea; sl, sterile lemma; rg, rudimentary glume; st, stamen; pi, pistil; lo, lodicule; sdle, slightly degenerated lemma organ; rlle, rod-like lemma organ; bop, body of the palea; mrp, margin of the palea. Bars = 1 cm in A–C, H–J, and O–Q; 2 mm in D, E, G, K, L, N, R, S, and U; 500 μm in F, M, and T

Fig. 2

Investigation of yield-related agronomic traits in the wild type and del mutant. A Plant type of the wild type (left) and del mutant (right). B Main panicle of the wild type (left) and del mutant (right). C Mature grains of the wild type (upper), slightly degenerated del mutant (middle) and rod-like del mutant (lower). D Brown rice of the wild type (upper) and slightly degenerated del mutant (lower). E–I Plant height (E), panicle length (F), number of primary branches (G), number of secondary branches (H), and seed setting rate (I). J–L, length (J), width (K), and 1000-grain weight (L) of mature grains in the wild type and del mutant. M–O, length (M), width (N), and 1000-grain weight (O) of brown rice in the wild type and del mutant. Values are mean ± SD (n = 10). P value is determined using a t-test compared with 1B. * represents P < 0.05, ** represents P < 0.01, and ns represents no significance. Error bars indicate standard deviation. Bar = 5 cm in A and B, 4 mm in C and D

Fig. 3

Spikelet phenotypes of the wild type and the del mutant. A–D Spikelet of the wild type. E–H the slightly degenerated spikelet of the del. I–L the spikelet phenotypes of the rod-like lemma of the del. A, E, and I, Sp4; B, F, and J, Sp5-Sp6; C, G, and K, Sp7; D, H and L, Sp8. le, lemma; pa, palea; fm, floral meristem; st, stamen; rg, rudimentary glume; sl, sterile lemma; lo, lodicule; sdle, slightly degenerated lemma organ; rlle, rod-like lemma organ. Bars = 1 mm

Fig. 4

Localization of DEL and candidate gene analysis. A and B Primary mapping of DEL on chromosome 1 based on 358 individuals. C DEL was fine-mapped to an interval of 140 kb using 358 individuals. D Fifteen genes were annotated in the 140 kb region. E A single-nucleotide substitution from T to A was detected in Os01g0527600.Mutation site of Os01g0527600 was between the del mutant and the wild type ‘Xinong 1B’. F Schematic structure of the complementation vector pCAMBIA1301-DEL-GFP. G The spikelets of WT, del, and the complementary transgenic line. H RT-qPCR of tasiR-ARF in spikelets of the wild type and del. U6 was used as an internal control. Data are Mean ± SD (n = 3 biological replicates). Bars = 2 mm

Fig. 5

Spatiotemporal expression pattern of the DEL gene. A and B RT-qPCR of DEL. Young panicles < 0.5 cm, 0.5–1.0 cm, 1.0–2.0 cm, vegetative organ, and floral organ of the wild type were used. C–F Expression pattern of DEL in spikelets of the wild type. In situ hybridization in the spikelets of the wild type during stages Sp4 (C), Sp5-6 (D), Sp7-8 (E), and glume (F). G RT-qPCR of DEL/OsRDR6 in spikelets of wild type and del. ACTIN (LOC_Os03g50885) was used as an internal control. Data are Mean ± SD (n = 3 biological replicates). fm, floral meristem; le, lemma; pa, palea; st, stamen; pi, pistil; rg, rudimentary glume; sl, sterile lemma. The black arrows indicate the vascular bundles. Bars = 100 μm

Fig. 6

Relative expression levels of floral organ identity genes in floral organs of the wild type and del mutant. le, lemma; pa, palea; sdle, slightly degenerated lemma organ; rlle, rod-like lemma organ; st, stamen; pi, pistil. ACTIN (LOC_Os03g50885) was used as an internal control. Data are Mean ± SD (n = 3 biological replicates)