Diversity of Heading date 1 (Hd1) gene that conditions flowering time in traditional tropical japonica and traditional indica rice from Thailand
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Abstract
The traditional rice cultivars are genetic resources in breeding programs that possess variable of DNA sequence of genes, but variants of gene of these resources have been limited in Thailand. Therefore, DNA sequence variation of the heading date 1 (Hd1) gene was explored in these rice cultivars collected from north (tropical japonica rice) and northeastern (indica rice) regions of the country. Results from re-sequencing of the Hd1 gene identified 3 nonsynonymous SNPs in coding sequence (exon2) and there are four SNPs in noncoding sequence of the gene. For coding sequences, first nonsynonymous SNP, AGT/GGT leading to amino acid sequence changes in Hd1 protein at position 339 of 407 residues. The allele S (AGT:Serine) of Hd1 gene were dominant in tropical japonica rice in northern region. Whereas the allele G (GGT:Glycine) was mostly found in indica rice from northeastern region. In addition, two traditional cultivars from the northern, a premature stop codon at exon2 was identified. Furthermore, 2 others nonsynonymous SNPs was distributed in both populations, including allele S (AGC:Serine) was dominant in tropical japonica rice, while the allele A (AGA:Arginine) were mostly found in indica rice.
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References
Bhat F.M. and Riar C.S. 2015 Health benefits of traditional rice varieties of
temperate regions. Med. Aromat. Plants 4, 198.
doi:10.4172/2167- 0412.1000198
Chen W.B., Sato Y..I, Nakamura I. and Nakai H. 1994 Indica-Japonica differentiation in Chinese rice landraces. Euphytica 74, 195-201. https://doi.org/10.1007/BF00040401
Choi S., Prabhakar P., Chowdhury R., Iv Pendergast T.H., Urbanowicz B.R.,
Maranas C., et al. 2023 A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass. J. Exp. Bot. 47, 5532-5546.
https://doi.org/10.1093/jxb/erad255
Castillo, C. 2011 Rice in Thailand: The Archaeobotanical contribution. Rice 4,
–120. https://doi.org/10.1007/s12284-011-9070-2
Doebley J.F., Gaut B.S. and Smith B.D. 2006 The molecular genetics of crop
domestication. CellPress 12, 1309-1321.
https://doi.org/10.1016/j.cell.2006.12.006
Doi K., Izawa T., Fuse T., Yamanouchi U., Kubo T., Shimatani Z. et al. 2004
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 8, 926–936. https://doi.org/10.1101/gad.1189604
Doyle J.J. and Doyle J.L. 1987 A rapid DN A isolation procedure for small
quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15. https://webpages.charlotte.edu/~jweller2/pages/BINF8350f2011/BINF8350_Readings/Doyle_plantDNAext ractCTAB_1987.pdf
Endo-Higashi N. and Izawa T. 2011 Flowering time genes Heading date
and Early heading date 1 together control panicle development in rice. Plant Cell Physiol. 52, 1083– 1094.
https://doi.org/10.1093/pcp/pcr059
Fongfon S., Pusadee T., Prom-U-Thai C., Rerkasem B. and Jamjod S. 2021 Diversity
of purple rice (Oryza sativa L.) landraces in northern Thailand. Agronomy 11, 2029
https://doi.org/10.3390/agronomy11102029
Fujino K., Wu J., Sekiguchi H., Ito T., Izawa T. and Matsumoto T. 2010 Multiple
introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L. Mol. Genet. Genomic 284, 137–146. https://doi.org/10.1007/s00438-010-0555-2
Hayama R., Yokoi S., Tamaki S., Yano M. and Shimamoto K. 2003 Adaptation of
photoperiodic control pathways produces short-day flowering in rice. Nature 422, 719-722. https://doi.org/10.1038/nature01549
Huang C.L., Hung C.Y., Chiang Y.C., Hwang C.C., Hsu T.W., Huang C.C. et al.
Footprints of natural and artificial selection for photoperiod pathway genes in Oryza. The Plant Journal. 70, 769-782.
https://doi.org/10.1111/j.1365-313x.2012.04915.x
Itoh H., Wada K.C., Sakai H., Shibasaki K., Fukuoka S., Wu J. et al. 2018
Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area. Plant J. 94, 895–909. https://doi.org/10.1111/tpj.13906
Izawa T., Oikawa T., Sugiyama N., Tanisaka T., Yano M. and Shimamoto K. 2002 Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev. 16, 2006-20020.
https://doi:10.1101/gad.999202
Izawa T. 2007 Adaptation of flowering-time by natural and artificial selection
in Arabidopsis and rice. Exp. Bot. 58, 3091-3097. https://doi.org/10.1093/jxb/erm159
Kanno A., Watanabe N., Nakamura I. and Hirai A. 1993 Variations in chloroplast
DNA from rice (Oryza sativa): Differences between deletions mediated by short direct-repeat sequences within a single species. Theor. Appl. Genet. 86, 579-584. https://doi.org/10.1007/BF00838712
Kojima S., Takahashi Y., Kobayashi Y., Monna L., Sasaki T., Araki T. and Yano
M. 2002 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol. 43, 1096-1105. https://doi.org/10.1093/pcp/pcf156
Komiya R., Ikegami A., Tamaki S., Yokoi S. and Shimamoto K. 2008 Hd3a and
RFT1 are essential for flowering in rice. Development. 135, 767-774.
https://doi.org/10.1242/dev.008631
Mo Y., Lee C.M., Park H.M., Ha S.K., Kim M.J., Kwak J. et al. 2021 Hd1 Allele types and their associations with major agronomic traits in Korean rice cultivars. Plants (Basel) 10, 2408.
https://doi.org/10.3390/plants10112408
Nakamura I., Kameya N., Kato Y., Yamanaka S.I., Jomori H. and Sato Y. 1997
A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants. Breed. Sci. 47, 385-388. https://doi.org/10.1270/jsbbs1951.47.385
Oka H.I. and Chang W.T. 1963 A note on rice varieties of japonica type found in
northern Thailand. Bot. Bull. Acad Sinica 4, 163-168.
https://ejournal.sinica.edu.tw/bbas/content/1963/2/bot042-08.PDF
Prathepha P. 2008 Analysis of plastid subtype ID sequences in traditional
upland and lowland rice cultivars from Thailand. Asian J. Plant Sc. 7, 60-66. https://doi.org/10.3923/ajps.2008.60.66
Purwestri Y.A., Susanto F.A. and Tsuji H. 2017 Hd3a Florigen Recruits Different
Proteins to Reveal Its Function in Plant Growth and Development. In: Juric S., Plant Engineering, InTechOpen. doi:10.5772/intechopen.70263.
Robson F., Costa M..M, Hepworth S.R., Vizir I., Pineiro M., Reeves P.H. et al.
Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J. 28, 619-631.
https://doi.org/10.1046/j.1365-313x.2001.01163.x
Rozas J., Sanchez-DelBarrio J.C., Messseguer X. and Rozas R. 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 19, 2496-2497. https://doi: 10.1093/bioinformatics/btg359.
Shrestha R., Gómez-Ariza J., Brambilla V. and Fornara F. 2014 Molecular control
of seasonal flowering in rice, Arabidopsis and temperate cereals. Ann. Bot. 114, 1445–1458. https://doi.org/10.1093/aob/mcu032
Tajima F. 1983 Evolutionary relationship of DNA sequences in finite
populations. Genetics 105, 437-460. https://doi.org/10.1093/genetics/105.2.437
Tamura K., Stecher G. and Kumar S. 2021 MEGA 11: Molecular
Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 38, 3022-3027.
https://doi.org/10.1093/molbev/msab120.
Takahashi Y., Teshima K.M., Yokoi S., Innan H. and Shimamoto K. 2009 Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc. Natl. Acad. Sci. USA 106, 4555-4560.
https://doi.org/10.1073/pnas.0812092106
Tamaki S., Matsuo S., Wong H.L., Yokoi S. and Shimamoto K. 2007 Hd3a protein is a mobile flowering signal in rice. Science 316(5827), 1033–1036.
https://doi.org/10.1126/science.1141753
Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F. and Higgins D.G. 1997 The CLUSTAL_W windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882. https://doi.org/10.1093%2Fnar%2F25.24.4876
Thomson M.J., Septiningsih E.M., Suwardjo F., Santoso T.J., Jilitonga T.S. and
McCouch S.R. 2007 Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114, 559–568.
https://doi.org/10.1007/s00122-006-0457-1
Tsuji H., Taoka K.I. and Shimamoto K. 2013 Florigen in rice: complex gene
network for florigen transcription, florigen activation complex, and multiple functions. Curr. Opin. Plant Biol. 16, 228–235.
https://doi.org/10.1016/j.pbi.2013.01.005
Wright S.I. and Gaut B.S. 2005 Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22, 506-519. http://dx.doi.org/10.1093/molbev/msi035
Wu C.C., Wei F.J., Chiou W.Y., Tsai Y.C., Wu H.P., Gotarkar D. et al. 2020 Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments. PLoS ONE 15, e0239028. https://doi.org/10.1371/journal.pone.0239028
Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T. et al.
Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. The Plant Cell 12, 2473–2483.
https://doi.org/10.1105/tpc.12.12.2473
Zong W., Ren D., Huang M., Sun K., Feng J., Zhao J. et al. 2021 Strong
photoperiod sensitivity is controlled by cooperation and competition among Hd1, Ghd7 and DTH8 in rice heading. New Phytol. 229, 1635-1649.