Abstract
To better understand the molecular mechanisms that regulate inflorescence and flower architecture, we characterized the rice panicle and spikelet degeneration (psd) mutant, which exhibited small panicles with a reduced number of primary and secondary branches. The psd mutant had few spikelets per panicle, and they were deformed and could not form seeds. The psd mutant had a unique panicle organization phenotype that was not present in other aberrant panicle organization mutants. Genetic analysis revealed that the mutation was controlled by a single recessive gene. A map-based cloning strategy was employed to isolate the PSD locus. The PSD locus was initially located between RM13046 and RM5356 on chromosome 2. Recessive individuals (n = 7307) in F2 mapping populations from two crosses between heterozygous Psdpsd plants and two indica rice varieties, IR28 and 93-11, were used to finely map the PSD locus. The PSD locus was mapped to a 14.6 kb region between two newly developed dCAPS markers, dC7 and dC8, within BAC OJ1115_D03. The candidate regions harbored two ORFs, Os02g0284500 and Os02g0284600. Sequence analysis revealed that only one single amino acid substitution mutation in the Os02g0284500 gene in the candidate region, which altered the predicted three-dimensional Os02g0284500 protein structure. A tetra-primer amplification refractory mutation system-PCR marker, TP-psd, was developed from the psd mutant mutation site. All 7307 homozygote recessive plants in the two F2 populations showed the same band pattern as that of psdpsd. This suggested that Os02g0284500 is most likely the PSD gene. Our results provide a basis for future functional PSD studies.
Similar content being viewed by others
Abbreviations
- APO1 :
-
ABERRANT PANICLE ORGANIZATION1
- APO2 :
-
ABERRANT PANICLE ORGANIZATION2
- ASP1 :
-
ABERRANT SPIKELET AND PANICLE1
- bp:
-
Base pair
- CDS:
-
Coding sequence
- FZP :
-
FRIZZY PANICLE
- LAX1 :
-
LAX PANICLE1
- LAX2 :
-
LAX PANICLE2
- LP :
-
LARGER PANICLE
- ORF:
-
Open reading frame
- psd :
-
Panicle and spikelet degeneration
- SP1 :
-
SHORT PANICLE1
- TAW1 :
-
TAWAWA1
- FRS:
-
FAR1-RELATED SEQUENCE
References
Akter MB, Piao R, Kim B, Lee Y, Koh E, Koh H-J (2014) Fine mapping and candidate gene analysis of a new mutant gene for panicle apical abortion in rice. Euphytica 197:387–398. doi:10.1007/s10681-014-1074-8
Hoen DR, Bureau TE (2012) Transposable element exaptation in plants. In: Grandbastien M, Casacuberta JM (eds) Plant transposable elements impact on genome structure and function. Springer, Berlin, Heidelberg, pp 219–251
Ikeda K, Nagasawa N, Nagato Y (2005) ABERRANT PANICLE ORGANIZATION1 temporally regulates meristem identity in rice. Dev Biol 282:349–360. doi:10.1016/j.ydbio.2005.03.016
Ikeda K, Ito M, Nagasawa N, Kyozuka J, Nagato Y (2007) Rice ABERRANT PANICLE ORGANIZATION1, encoding an F-box protein, regulates meristem fate. Plant J 51:1030–1040. doi:10.1111/j.1365-313X.2007.03200.x
Ikeda-Kawakatsu K, Yasuno N, Oikawa T, Iida S, Nagato Y, Maekawa M, Kyozuka J (2009) Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem. Plant Physiol 150:736–747. doi:10.1104/pp.109.136739
Ikeda-Kawakatsu K, Maekawa M, Izawa T, Itoh J, Nagato Y (2012) ABERRANT PANICLE ORGANIZATION2/RFL, the rice ortholog of Arabidopsis LEAFY, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1. Plant J 69:168–180. doi:10.1111/j.1365-313X.2011.04781.x
Kato T, Horibata A (2012) A novel frameshift mutant allele, fzp-10, affecting the panicle architecture of rice. Euphytica 184:65–72. doi:10.1007/s10681-011-0547-2
Kobayashi K, Yasuno N, Sato Y, Yoda M, Yamazaki R, Kimizu M, Yoshida H, Nagamura Y, Kyozuka J (2012) Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene. Plant Cell 24:1848–1859. doi:10.1105/tpc.112.097105
Komatsu K, Maekawa M, Ujiie S, Satake Y, Furutani I, Okamoto H, Shimamoto K, Kyozuka J (2003a) LAX and SPA: major regulators of shoot branching in rice. Proc Natl Acad Sci USA 100:11765–11770. doi:10.1073/pnas.1932414100
Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J (2003b) FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development 130:3841–3850. doi:10.1242/dev.00564
Kyozuka J, Konishi S, Nemoto K, Izawa T, Shimamoto K (1998) Down-regulation of RFL, the FLO/LFY homolog of rice, accompanied with panicle branch initiation. Proc Natl Acad Sci USA 95:1979–1982
Li S, Qian Q, Fu Z, Zeng D, Meng X, Kyozuka J, Maekawa M, Zhu X, Zhang J, Li J, Wang Y (2009) Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. Plant J 58:592–605. doi:10.1111/j.1365-313X.2009.03799.x
Li M, Tang D, Wang K, Wu X, Lu L, Yu H, Gu M, Yan C, Cheng Z (2011) Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnol J 9:1002–1013. doi:10.1111/j.1467-7652.2011.00610.x
Lin R, Wang H (2004) Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development. Plant Physiol 136:4010–4022. doi:10.1104/pp.104.052191
Miura K, Yamamoto E, Morinaka Y, Takashi T, Kitano H, Matsuoka M, Ashikari M (2008) The hybrid breakdown 1(t) locus induces interspecific hybrid breakdown between rice Oryza sativa cv. Koshihikari and its wild relative O. nivara. Breed Sci 58:99–105. doi:10.1270/jsbbs.58.99
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. doi:10.1002/jcc.20084
Tabuchi H, Zhang Y, Hattori S, Omae M, Shimizu-Sato S, Oikawa T, Qian Q, Nishimura M, Kitano H, Xie H, Fang X, Yoshida H, Kyozuka J, Chen F, Sato Y (2011) LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems. Plant Cell 23:3276–3287. doi:10.1105/tpc.111.088765
Ye S, Dhillon S, Ke X, Collins AR, Day IN (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29:e88–e88
Yoshida A, Ohmori Y, Kitano H, Taguchi-Shiobara F, Hirano HY (2012) Aberrant spikelet and panicle1, encoding a TOPLESS-related transcriptional co-repressor, is involved in the regulation of meristem fate in rice. Plant J 70:327–339. doi:10.1111/j.1365-313X.2011.04872.x
Yoshida A, Sasao M, Yasuno N, Takagi K, Daimon Y, Chen R, Yamazaki R, Tokunaga H, Kitaguchi Y, Sato Y, Nagamura Y, Ushijima T, Kumamaru T, Iida S, Maekawa M, Kyozuka J (2013) TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition. Proc Natl Acad Sci USA 110:767–772. doi:10.1073/pnas.1216151110
Acknowledgments
This project was supported by the National Natural Science Foundation of China (31100145, 31100168 and 31260317) and Jiangsu Agriculture Science and Technology Innovation Fund (CX(12)5019).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
S. Zhang and F. Xu have contributed equally to this work.
Rights and permissions
About this article
Cite this article
Zhang, S., Xu, F., Zhang, Y. et al. Fine mapping and candidate gene analysis of a novel PANICLE AND SPIKELET DEGENERATION gene in rice. Euphytica 206, 793–803 (2015). https://doi.org/10.1007/s10681-015-1525-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10681-015-1525-x