Fine Mapping of Rice Specific MR1, a Gene Determines Palea Identity

Abstract

The hull (palea and lemma) is the specific organ of grass florets. Although many genes related to the hull development have been cloned, the genetic mechanisms behind the development are still unclear, and the evolutionary relationship has different explanations and heated arguments between the palea and lemma. In this study, we found a specific mr1 mutant with a reduced palea, showing an enlarged mrp and degraded bop. Phenotype observations and molecular evidences showed that the bop was converted to the mrp-like organ. Our findings first reveal that the bop and mrp are homologous structures, and the palea and lemma are the same whorl floral organs. MR1 may prevent the transformation of the bop into mrp by regulating the expressions of hull identity genes. Meantime, the mr1 mutant showed altered grain size and grain quality, with defective physical and chemical contents. MR1 was controlled by a single recessive gene and was finally located on chromosome 1, with a physical distance of 70 kb. More work will be needed for confirming the target gene of MR1, which would contribute to our understanding of grain formation and the origin between the lemma, bop, and mrp.

Keywords: grain size and quality; mr1 mutant; organ origin; palea; rice (Oryza sativa L.).

FIGURE 1

Phenotypes of wild-type and mr1 florets. (A) Wild-type floret. (B) Wild-type floret without lemma. (C) Wild-type floret without lemma and palea. (D) mr1 floret. (E) mr1 floret without lemma. (F) mr1 floret without lemma and palea. (G) Lemma width. (H) Bop width. (I) mrp width. le, lemma; pa, palea; sl, sterile lemma; lo, lodicule; st, stamen; pi, pistil. Asterisk indicates the stamen. Bars, 2 mm in (A–F). **Significant difference at p < 0.01 compared with the wild-type by Student’s t-test. Error bars indicate SD.

FIGURE 2

Histological analysis of hull in the wild-type and the mr1 mutant. (A) Epiderm of the wild-type lemma. (B) Epiderm of the wild-type palea. (C) Enlarged palea in the wild-type. (D) Transverse section of wild-type floret. (E) Interlocked structure of wild-type hull. (F) Epiderm of the mr1 lemma. (G) Epiderm of the mr1 palea. (H) Enlarged palea in the mr1 mutant. (I) Transverse section of mr1 floret. (J) Interlocked structure of mr1 hull. (K) Diagram of wild-type spikelet. (L) Diagram of mr1 spikelet. le, lemma; pa, palea; lo, lodicule; st, stamen; pi, pistil; bop, body of palea; mrp, marginal region of palea; sl, sterile lemma; vb, vascular bundle. Black asterisks indicate the vascular bundles. Red lines indicate the mrp. Bars, 100 μm in (A,E,F,J); 1 mm in (B,G); 200 μm in (C,D,H,I).

FIGURE 3

Florets at early developmental stages in the wild-type and the mr1 mutant. (A–D) Wild-type floret. (A) Sp4. (B) Sp5-6. (C) Sp7. (D) Sp8. (E–H) mr1 floret. (E) Sp4. (F) Sp5-6. (G) Sp7. (H) Sp8. fm, floral meristem; sl, sterile lemma; le, lemma; pa, palea; pi, pistil. Asterisk indicates the stamen. Bars, 50 μm.

FIGURE 4

Expression of floral organ genes in the wild-type and the mr1 mutant. (A) Relative expression f genes in the wild-type and the mr1 floral organs. (B) Relative expression f genes in the bop and mrp of wild-type and the mr1 mutant. (C,D) DL expression in the wild-type floret. (E,F) OsMADS6 expression in the wild-type floret. (G,H) DL expression in the mr1 floret. (I,J) OsMADS6 expression in the mr1 floret. le, lemma; pa, palea; mrp, marginal region of palea; bop, body of palea. Bars, 50 μm.

FIGURE 5

Fine mapping of the MR1 gene. (A) Genetic linkage map for the primary location of the MR1 gene using 94 F₂ recessive plants. (B) Fine physical map of the MR1 gene using 558 F₂ recessive plants. (C) ORFs in the target region. ORFs indicate open reading frames.

FIGURE 6

Expression analysis of palea identity-associated genes by qRT-PCR. **Significant difference at p < 0.01 compared with the wild-type by Student’s t-test. Error bars indicate SD.

FIGURE 7

Grains of the wild-type and the mr1 mutant. (A) Grains of the wild-type and mr1 mutant. (B) Brown rice of the wild-type and mr1 mutant. (C–D) Grains of the wild-type and mr1 mutant. (E–J) Length, width, and weight of grains and brown rice in the wild-type and mr1 mutant. Scale bar, 2 mm in (A,B); 5 mm in (C,D). **Significant difference at p < 0.01 compared with the wild-type by Student’s t-test. Error bars indicate SD.

FIGURE 8

Characteristics of grain and starch in the wild-type and mr1 mutant. (A–F) SEM analysis of transverse sections of brown rice in the wild-type and mr1 mutant. (A–C) Brown rice of the wild-type. (D–F) Brown rice of the mr1 mutant. (G–J) Total starch, amylose, soluble sugar, and protein content in the wild-type and mr1 mutant. (K) Gelatinization characteristics of starch in urea solutions (1–9 M). Asterisks indicate the starch of mr1 endosperm is more difficult to gelatinize in 3–9 M urea solution than that of WT. The most significant difference was observed for 3 M urea (right). Bars, 500 μm in (A,D); 100 μm in (B,E); 20 μm in (C,F). *Significant difference at p < 0.05 compared with the wild-type by Student’s t-test. **Significant difference at p < 0.01 compared with the wild-type by Student’s t-test. Error bars indicate SD.