Identification and Fine Mapping of Heading Date Related Mutant in Rice

Abstract

Abstract: A rice heading-date-related mutant was isolated from a 60Co-γ-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD(t) (heading date tentatively). To isolate the HD(t) gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd(t) mutant (japonica) × Zhenshan 97 (indica). Finally, the HD(t) gene was mapped to an approximate 53 kb region between the InDel markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD(t) gene based on this fine mapping results.

Key words: 60Co-γ-ray-induced, late heading date, flowering, SSR, InDel marker, fine mapping

SHANG Hai-xuan1, 2, #, YE Sheng-hai2, #, DENG Xiao-mei2, 3, ZHOU Ya1, 2, XIU Fen-lian1, 2, JI Xian-jun2, 3, LIU Ji-yun1, 2, CHEN Ping-ping1, 2, JIN Qing-sheng2, ZHANG Xiao-ming2. Identification and Fine Mapping of Heading Date Related Mutant in Rice[J]. RICE SCIENCE, 2012, 19(4): 269-276.

References

Chen X, Temnykh S, Xu Y, Cho Y G, McCouch S R. 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet, 95: 553–567.
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Atsushi Y. 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, 18: 926–936.
Dong C L, Sun Y Y, Deng X J. 2005. Progress in heading date genes of rice. Chin Agric Sci Bull, 21(6): 75–78, 128. (in Chinese with English abstract)
Fan S S, Zou D T. 2011. The photoperiod regulation of rice heading period. Heilongjiang Agric Sci, (2): 12–15. (in Chinese with English abstract)
Garner W W, Allard H A. 1920. Effect of the relative length of day and night and other factors of the environment on growth and reproduction in plants. J Agric Res, 18: 553–606.
Gong X P, Yang Z L, Zhao F M, Zhong B Q, Ling Y H, He G H. 2007. Genetic analysis and molecular mapping of a dominant heading period gene Hd(t). Acta Agron Sin, 33: 1906–1909. (in Chinese with English abstract)
Gu X Y, Foley M E. 2007. Epistatic interactions of three loci regulate flowering time under short and long day lengths in a backcross population of rice. Theor Appl Genet, 114: 745–754.
Hayama R, Izawa T, Shimamoto K. 2002. Isolation of rice genes possibly involved in the photoperiodic control of flowering by a differential display method. Plant Cell Physiol, 43: 494–504.
Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K. 2003. Adaptation of photoperiodic control of pathways produces short-day flowering in rice. Nature, 422: 719–722.
Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar H E. 2003. Identification of QTL for growth and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet, 107: 679–690.
Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T, Zhang Z W, Li M, Fan D L, Guo Y L, Wang A H, Wang L, Deng L W, Li WJ, Lu Y Q, Weng Q J, Liu K Y, Huang T, Zhou T Y, Jing Y F, Li W, Lin Z, Buckler E S, Qian Q, Zhang Q F, Li J Y, Han B. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 42: 961–967.
Khush G S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol, 35: 25–34.
Kim S L, Lee S, Kim H J, Nam H G, An G. 2007. OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a. Plant Physiol, 145: 1484–1494.
Kobayashi Y, Weigel D. 2007. Move on up, it’s time for change-mobile signals controlling photoperiod-dependent flowering. Genes Dev, 21: 2371–2384.
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, 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.
Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K. 2008. Hd3a and RFT1 are essential for flowering in rice. Development, 135: 767–774.
Komiya R, Yokoi S, Shimamoto K. 2009. A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development, 136: 3443–3450.
Lee S, Kim J, Han J J, Han M J, An G. 2004. Functional analyses of the flowering time gene OsMADS50, the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20 (SOCI/AGL20) ortholog in rice. Plant J, 38: 754–764.
Lin H X, Ashikari M, Yamanouchi U, Sasaki T, Yano M. 2002. Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breeding Sci, 52: 35–41.
Lin H X, Liang Z W, Sasaki T, Yano M. 2003. Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breeding Sci, 53: 51–59.
Maas L F, McClung A, McCouch S R. 2010. Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theor Appl Genet, 120: 875–908.
Matsubara K, Yamanouchi U, Wang Z X, Minobe Y, Izawa T, Yano M. 2008. Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating Ehd1. Plant Physiol, 148: 1425–1435.
Michelmore R W, Paran I, Kesseli R V. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA, 88: 9828–9832.
Monna L, Lin H, Kojima S, Sasaki T, Yano M. 2002. Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice. Theor Appl Genet, 104: 772–778.
Nonoue Y, Fujino K, Hirayama Y, Yamanouchi U, Lin S Y. 2008. Detection of quantitative trait loci controlling extremely early heading in rice. Theor Appl Genet, 116: 715–722.
Park S J, Kim S L, Lee S, Je B I, Piao H L, Park S H, Kim C M, Ryu C H, Park S H, Xuan Y H. 2008. Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod. Plant J, 56: 1018–1029.
Panaud O, Chen X, McCouch S R. 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 252: 597–607.
Putterill J, Robbson F, Lee K, Simon R, Coupland G. 1995. The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell, 80: 847–857.
Shao D, Li Q P, Wu B, Xing Y Z. 2009. Mapping of a major QTL for heading date in rice using chromosome segment substitution lines. J Hunan Agric Univ: Nat Sci, 35: 344–347. (in Chinese with English abstract)
Takahashi Y, Shomura A, Sasaki T, Yano M. 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. Proc Nat Acad Sci USA, 98: 7922–7927.
Tsuji H, Tamaki S, Komiya R, Shimamoto K. 2008. Florigen and the photoperiodic control of flowering in rice. Rice, 1: 25–35.
Turck F, Fornara F, Coupland G. 2008. Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol, 59: 573–594.
Uga Y, Nonoue Y, Liang Z W, Lin H X, Yamamoto S. 2007. Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar Nona Bokra. Theor Appl Genet, 114: 1457–1466.
Wu C Y, You C J, Li C H, Long T, Chen G X, Byrne M E, Zhang Q F. 2008. RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci USA, 105: 12915–12920.
Xue W Y, Xing Y Z, Weng X Y, Zhao Y, Tang W J, Wang L, Zhou H J, Yu S B, Xu C G, Li X H, Zhang Q F. 2008. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet, 40: 761–767.
Yamamoto Y, Kuboki Y, Lin S Y, Sasaki T, Yano M. 1998. Fine mapping of quantitative trait loci Hd1, Hd2, and Hd3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet, 97: 37–44.
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T. 2000. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell, 12: 2473–2483.
Yano M, Kojima S, Takahashi Y, Lin H X, Sasaki T. 2001. Genetic control of flowering time in rice, a short-day plant. Plant Physiol, 127: 1425–1429.

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