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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1699-1707.doi: 10.3724/SP.J.1006.2023.22028

• RESEARCH NOTES • Previous Articles     Next Articles

Identification and gene mapping of long grain and degenerated palea (lgdp) in rice (Oryza sativa L.)

LIN Xiao-Xin(), HUANG Ming-Jiang, WEI Yi, ZHU Hong-Hui, WANG Zi-Yi, LI Zhong-Cheng, ZHUANG Hui, LI Yan-Xi, LI Yun-Feng*(), CHEN Rui*()   

  1. Rice Research Institute, Southwest University/Academy of Agricultural Sciences, Southwest University/Transgenic Plants and Safety Control, Chongqing Key Laboratory, Chongqing 400715, China
  • Received:2022-05-09 Accepted:2022-10-10 Online:2023-06-12 Published:2022-11-17
  • Contact: *E-mail: chenruin998@gmail.com;E-mail: liyf1980@swu.edu.cn
  • Supported by:
    National Natural Science Foundation of China(32172044)

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Abstract:

The grain shape, which consists of grain length and grain width, is the primary determinant of grain yield and one of the important appearance quality traits in rice. It is of great significance to identify the related genes associated with grain shape and to study molecular mechanisms for improving the yield and quality of rice. In this study, a long grain mutant named long grain and degenerated palea (lgdp) deriving from EMS (ethyl methane sulfonate) mutation groups of Xida 1B was reported. In lgdp mutant, the elongation of lemma resulted in a long grain. Further SEM analysis revealed that the main reason for lemma elongation was the extremely significant increase in the number of glume cells. Genetic analysis showed that the lgdp trait was regulated by a pair of recessive genes. Using BSA method and the F2 population crossing lgdp with ZH11, the target gene was located between the molecular markers ZLN43 and ZLN-1 on chromosome 3, with a physical distance of about 810 kb. The analysis of RNA-seq and PCR indicated the LGDP candidate gene might encode a MADS-box protein. The qPCR referred that LGDP negatively regulated the relative expression levels of several positive grain length regulatory factors, GW7/GL7, GS3, TGW6, which affected the cell proliferation of glumes and the grain length. The results of this study laid a foundation for the molecular function analysis of LGDP gene in the future.

Key words: rice (Oryza sativa L.), grain shape, cell number, gene mapping

Fig. 1

Phenotype identification of wild-type (WT) and lgdp mutant A: WT spikelet; B: the lemma and palea were removed in A; C: the transverse sections of WT spikelet; D: amplified part of Fig. 1-C; E: scanning electron microscopy (SEM) mi-croscopical structure of wild-type spikelet primordium; F, K: Type1 and Type2 spikelets of lgdp; G, L: the lemma and palea were removed in F, K; H: transverse sections of Type1 lgdp spikelet; I: amplified part of picture H; J: SEM mi-croscopical structure of Type1 lgdp spikelet primordium; M: transverse sections of Type2 lgdp spikelet; N: amplified part of picture. O: SEM mi-croscopical structure of Type1 lgdp spikelet primordium; le: lemma; sl: sterile lemma; lo: lodicule; pa: palea; pi: pistil; st: stamen. Bar: 22 mm (A); 20 mm (B); 240 μm (C); 75 μm (D); 100 μm (E, J, O); 23 mm (F, G, K, L); 300 μm (H); 78 μm (I); 300 μm (M); 80 μm (N)."

Fig. 2

Plant and grain characters of the wild-type (WT) and lgdp mutant A: plants of WT and lgdp; B: the comparison of grain width between WT and lgdp; C: the comparison of kernel width between WT and lgdp; D: the comparison of grain length between WT and lgdp; E: the comparison of kernel length between WT and lgdp; F: the statistics of plant height. G: the number of internodes; H: the statistics of panicle height; I: the number of primary branch; J: the number of secondary branch; K: the number of spikelets; L: the number of seeds per panicle; M: the statistics of grain width; N: the statistics of kernel width; O: the statistics of grain length; P: the statistics of kernel length; Q: the statistics of seed-setting rate; R: the statistics of 1000-grain weight. ** and * indicate significant difference between WT and lgdp by t-test at the 0.01 and 0.05 probability levels, respectively. Bar: 40 cm (A); 33 mm (B); 40 mm (C); 90 mm (D)."

Fig. 3

Scanning electron microscopy (SEM) analysis of glumes in wild-type (WT) and lgdp mutant A: grain glume of WT; B: grain glume of lgdp; C, D: the epidermal cells of lemma of WT and lgdp were observed by scanning electron microscope; E, F: the epidermal cells of palea of WT and lgdp were observed by scanning electron microscope; F: lemma length statistics; G: number of longitudinal epidermal cells in lemma; H: number of longitudinal epidermal cells in palea; I: number of longitudinal epidermal cells in palea; J: number of epidermal cells in lemma per unit area. K: statistics of cell size of palea epidermis. L: statistics of cell size of lemma epidermis. le: lemma; pa: palea. ** and * indicate significant difference at P < 0.01 and P < 0.05 between WT and lgdp by t-test, respectively. Bar: 5 mm (A, B); 300 μm (C-F)."

Table 1

Test of Chi-square on segregation rate of F2 population between wild-type (WT) and lgdp mutant"

名称
Name		 父本
Male parent		 母本
Female parent		 野生型
Wild type		 突变型
Mutant type		 卡方值
Chi-square value (χ20.05=3.84)
组合1 Combination 1 lgdp 56S 355 106 0.89
组合2 Combination 2 lgdp ZH11 176 44 2.67
组合3 Combination 3 lgdp NIP 70 13 3.38

Fig. 4

Map-based cloning of the LGDP A: mapping of the LGDP gene; B: RNA-sequencing analysis of LGDP candidate gene; C: PCR analysis and sequence alignment of LGDP candidate gene. N: asparagine; E: glutamic acid; A: alanine; D: aspartic acid; M: methionine; V: valine; H: histidine; TGA: the terminate codon."

Fig. 5

Expression analysis of grain shape genes Set the transcription level in the panicle of 1B to 1.0, Bars represent standard deviation (n = 3); ** indicates significant difference at P < 0.01 between 1B and lgdp by t-test."

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