Comprehensive panicle phenotyping reveals that qSrn7/FZP influences higher-order branching

Abstract

Rice grain number directly affects crop yield. Identifying alleles that improve panicle architecture would greatly aid the development of high-yield varieties. Here, we show that the quantitative trait locus qSrn7 contains rice FRIZZY PANICLE (FZP), a previously reported gene encoding an ERF transcription factor that promotes floral transition. Reduced expression of FZP in the reproductive stage increases the extent of higher order branching of the panicle, resulting in increased grain number. Genotype analysis of this gene in cultivars from the publicly available National Institute of Agrobiological Sciences (NIAS) Core Collection demonstrated that the extent of higher order branching, especially in the upper panicle, was increased in those cultivars carrying the FZP allele associated with qSrn7. Furthermore, chromosome segment substitution lines resulting from a cross between Koshihikari and Kasalath, the latter of which carries qSrn7/FZP, also showed that upper panicle higher order branching and grain yield were increased by qSrn7/FZP. Our findings indicate that qSrn7/FZP influences panicle branching pattern and is thus useful in the breeding of high-yield rice varieties.

Figure 1

Panicle branching pattern of Koshihikari and ST-5. (a) Schematic of a rice inflorescence. (b) Panicle morphologies of Koshihikari and ST-5. Scale bar: 10 cm. Red circles indicate secondary rachis branches (SBs). (c–g) Comparison of panicle attributes between Koshihikari and ST-5. (c) Number of grains per main panicle. (d) Number of primary rachis branches (PBs) per main panicle. (e) Number of SBs per main panicle. (f) Number of tertiary branches per main panicle. (g) Comparison of number of SBs per PBs between Koshihikari and ST-5. (h) Panicle branching pattern of Koshihikari and ST-5. Red circles: SBs. Blue circles: Secondary rachillae (SRs). **Significant at 1% level (Student’s t-test).

Figure 2

Aanalysis of FZP expression and FZP antisense transgenic phenotype. (a–d) Fine mapping of qSrn7. (a) The qSrn7 locus was detected between RM22060 and RM22156 on Chromosome 7. (b) Numbers on the map indicate the number of recombinants. (c) The candidate region of qSrn7 was located to the 35.3-kb region between RM22114 and RM22118 by fine mapping. (d) The FZP locus. Nucleotide insertions present in ST-5 are indicated. (e) FZP expression analysis in inflorescence tissue at various developmental stages and in leaf tissue by quantitative real-time PCR. PBI: Primary rachis branch initiation stage, SBI: Secondary branch initiation stage, SI: Spikelet initiation stage of inflorescence development. LB: Leaf blade, LS: Leaf sheath of leaf. (f) Comparison of number of SBs per main panicle between vector control and FZP antisense transgenic plants. (g) In situ hybridization of FZP transcript during panicle development in Koshihikari (A,C) and ST-5 (B,D). (A–D) Developing inflorescence at the stage of primary (A,B) and secondary (C,D) branch differentiation. (Insets) Close-up view of the apical region of a developing primary branch that is initiating a secondary rachis branch meristem. Arrowheads indicate incidence region of expression. Scale bars: 100 μm. **Significant at 1% level. *Significant at 5% level (Student’s t-test).

Figure 3

Panicle branching pattern. (a) Dot plots of total SB number per panicle against the genotype determined at RM22114 and RM22115. (b) Dot plots of SB number per upper three PBs of the panicle against the genotype determined at RM22114 and RM22115. (c) Panicle branching patterns in lines carrying ST-5 (top panels) and Koshihikari (bottom panels) genotypes determined at RM22114 and RM22115. (d) Panicle branching pattern of Koshihikari, Kasalath, and two CSSLs (KKSL_221 and KKSL_222). PB: primary rachis branch. Red circles: secondary rachis branches (SBs). Blue circles: secondary rachillae (SRs). (e) Comparison of panicle branching patterns of Koshihikari, Kasalath, and CSSLs. Tln: Total number of lateral branches on the PB (SBs + SRs). Solid lines denote the loess smoothing curves and shadows represent the estimated SE. (f) Relative expression of FZP in Koshihikari and CSSLs in developing inflorescences at the secondary branch initiation stage.

Figure 4

Grain yield performance of CSSLs compared with Koshihikari. (a) Plant morphology of Koshihikari, Kasalath, and CSSLs at the grain ripening stage. Scale bar: 20 cm. (b) The panicle morphologies of Kasalath, Koshihikari, and the CSSL KKSL_222. Scale bar: 5 cm. (c–g) Comparison of main panicle traits between Koshihikari, Kasalath, and two CSSLs. (c) Grain number per panicle. (d) Number of primary rachis branches (PBs) per panicle. (e) Number of secondary rachis branches (SBs) per panicle. (f) Total number of lateral branches (secondary rachillae (SRs) + SBs) per panicle. (g) The 1000-grain weight. (h–j) Comparison of yield factors between Koshihikari, Kasalath, and two CSSLs. (h) Culm length. (i) Panicle number per plant. (j) Grain yield per plant. Blue bars: parental lines of CSSLs. Red bars: CSSLs. **P < 0.01; *P < 0.05 versus Koshihikari (Dunnett’s multiple comparison test).