Os07g0261200

Ghd7 is a gene controlling rice grain number per panicle,plant height,heading stage,and the main effect of QTL.

Grain Number, Plant Height, and Heading Date7（Ghd7） Is a Central Regulator of Growth, Development, and Stress Response in rice

Function

In long sunshine condition, the enhanced expression of Ghd7 could delay the earing, increase the plant height and grain number per panicle, and the natural mutant with weaken function can grow to temperate and even colder regions. Ghd7, therefore, has a very important role for an potential increase and adaptability in global rice yield . PhyA alone or phyB and phyC work together can induce Ghd7 mRNA accumulation, and phyB alone can reduce the Ghd7 mRNA level to some degree. In addition phyB and phyA can influence the actiity of the Ghd7 and Hd1 respectively. Hd2 and Hd16, Hd2 and genetic interactions between Ghd7. Hd2 and its genetic interactions has a very important role for heading stage by controlling the condition of long sunshine.

Grain number, plant height, and heading date7 (Ghd7) has been regarded as an important regulator of heading date and yield potential in rice;As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of Ghd7 on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. Ghd7 regulates yield traits through modulating panicle branching independent of heading date. Ghd7 also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway;so,Ghd7 functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant.

Grain number, plant height, andheading date7 (Ghd7) encoding a CCT (CONSTANS,CONSTANS-LIKE, and TIMING OF CHLOROPHYLL A/B BINDING1) domain protein is considered to be a key regulator of the rice-specific flowering pathway and also contributes to rice yield potential;Ghd7 controls the critical daylength response of Early heading date1 (Ehd1) and florigen expression through circadian gating and phytochrome action.Ghd7 showed pleiotropic effects on heading date,plant height, and yield traits, and its expression was regulated by light signal and photoperiod.

Figure 1. The effect of Ghd7 on tillering in different density conditions.A, Tillers of NIL(zs7) and NIL(mh7) under low- and high-density conditions under natural long-day conditions in Wuhan. Bar = 10 cm. B, Tiller number of NIL(zs7) and NIL(mh7) at 68 days after germination (DAG; the heading date of NIL(zs7)) and 91 DAG (the heading date of NIL(mh7); three different plantings with 30 plants each). Error bars indicate SE.)

The effect of Ghd7 on tillering in different density conditions: Researchers designated NIL(zs7) and NIL(mh7), with almost all of the genetic background of Zhenshan 97 except the introgressed segment, which contained the Ghd7; NIL(mh7) plants had significantly more tillers than NIL(zs7) plants at low-density conditions (Fig. 1), demonstrating that Ghd7 regulates tiller number in a density-dependent manner. Interestingly, there was also a significant increase in secondary branches of the panicles in NIL(mh7) relative to NIL(zs7) at low density, leading to an increased grain number without compromising the number of primary branches;These results suggest that Ghd7 regulates the plasticity of branch development of the plant to adapt to the neighborhood environment.

Ghd7 has pleiotropic effects on three agronomic traits---plant height(PH), Heading date (HD) and spikelets per panicle(SPP). Ghd7 delays HD, increases PH and panicle size, and results in enhanced gene expression of Ehd1 and Hd3a under long-day conditions. Expression pattern analysis suggested that Ghd7 may function upstream of Ehd1 and Hd3a in the rice flowering pathway. Association analysis of 19 rice cultivars identified five allelic variants of Ghd7. The Ghd7 alleles with strong genetic effects were shown to increase grain yield by adapting to the long growing season of tropical regions and the Ghd7 alleles with no or reduced effect found in temperate regions shortened the rice life cycle to ensure seed setting.

Localization

Ghd7 is located in rice chromosome 7 between markers R1440 and C1023; Further,percisely it is located between RM5436 and RM2256 range ,the length of which is 79 KB

Expression

Ghd7 cDNA of Minghui 63 is 1013 bp, encoding a nucleoprotein composed of 257 amino acid , the product is protein structure,ie,a CCT (CO, CO - LIKE the and TIMING OF CAB1) , and the CCTS OF arabidopsis CO protein domain has a lot OF similarities, but differently. it has no obvious zinc finger protein structure, and these two protein homologous relationship is not too big.

Stresses that regulate the expression of Ghd7:

Drought, abscisic acid, jasmonic acid, and high-temperature stress strongly repressed Ghd7 expression, whereas low temperature enhanced Ghd7 expression. Overexpression of Ghd7 increased drought sensitivity, whereas knock-down of Ghd7 enhanced drought tolerance. Gene chip analysis of expression profiles revealed that Ghd7 was involved in the regulation of multiple processes, including flowering time, hormone metabolism, and biotic and abiotic stresses.

Genes regulate the expression of Ghd7 are as follows:

Two orthologs of EARLY FLOWERING3 genes, which mediate the circadian and photoperiodic regulation, act as negative regulators of Ghd7 ;Rice Indeterminate1 acts as a master switch for the transition from vegetative to reproductive phase and regulates the expression of Ghd7 independent of the photoperiod;Ehd3, which contains two plant homeodomain finger motifs and is possibly involved in chromatin state modulation, negatively regulates the transcription of Ghd7;Heading date16 (Hd16), a flowering time quantitative trait locus gene, was recently shown to encode a casein kinase I protein that mediates the phosphorylation of GHD7 and enhances the photoperiod response.

Figure 2. Newly proposed model of daylength measurement in rice.Red and blue lines indicate red- and blue-light mediated responses,respectively. In addition to the two gate mechanisms, there are two phytochrome-dependent controls for time-keeping mechanisms in rice: LD-prominent promotion of Ghd7 repressor activity by phyB and LDprominent inhibition of Ehd1 activity by phyA((from reference)

By using single and double phytochrome mutant lines of rice, results show that either phyA alone or a genetic combination of phyB and phyC can induce Ghd7 mRNA, whereas phyB alone causes some reduction in levels of Ghd7 mRNA. Moreover, phyB and phyA can affect Ghd7 activity and Early heading date1 (a floral inducer) activity in the network, respectively. Therefore, each phytochrome gene of rice has distinct roles, and all of the phytochrome actions coordinately control the critical daylength response of florigen expression in rice;some time-keeping molecular mechanisms exist beside the phytochrome signaling in rice, possibly independent of the circadian clock (Fig. 1). The possible action of phyB to enhance Ghd7 activity and thus to control Ehd1 expression, and the possible action of phyA to reduce Ehd1 activity and thus control Hd3a/RFT1 expression, are likely to be both daylength sensitive. In addition to elucidating how light conditions contribute to the formation of the Ghd7 and Ehd1 gates, these results raise new questions as to the molecular mechanisms by which rice phytochromes measure daylength.

Ghd7 and Protein diversity of Ghd7:

Ghd7 is encoded by Ghd7 .

Figure 3. Protein diversity of Ghd7. The two exons (indicated in black rectangle) and the 59 and 39 UTRs (indicated in white rectangle) of Ghd7 are shown in graphics on the top. The first row indicates the position of the SNPs, the last row reveals the amino acid change. Gray indicates synonymous SNP. Eight types of Ghd7 protein were identified. Ghd7-0 was a permutation type. Hap indicates the haplotypes that share the same protein type. The numbers in the right column are the numbers of cultivars (cvs) represented in every protein type. doi:10.1371/journal.pone.0034021.g003((from reference)

Considering that the nucleotide diversity in the coding regioncannot exactly represent the protein diversity owing to synonymous

SNPs in exons, Ghd7 protein diversity was analyzed in the present study.Ghd7 has a partial-dominant effecton flowering time, plant height, and yield traits;The phenotypic effect of Ghd7 is quantitatively related to the abundance of its transcript, and the enhanced transcript level of Ghd7 caused delayed flowering, increased plant height, and yield traits.

Evolution

Ghd7 is a pleiotropic gene that controls the traits of Plant height, heading date, and yield.In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise p and h in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.

Labs working on this gene

1.National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

2.Graduate School of Frontier Sciences, University of Tokyo,and Functional Plant Research Unit, National Institute of Agrobiological Sciences

3.QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

4.Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, 305-8518, Japan

References

<references>

1. Xiaoyu Weng;Lei Wang;Jia Wang;Yong Hu;Hao Du;Caiguo Xu;Yongzhong Xing;Xianghua Li;Jinghua Xiao;Qifa Zhang

 Grain Number, Plant Height, and Heading Date7 Is a Central Regulator of Growth, Development, and Stress Response
 Plant Physiology, 2014, 164(2): 735-747

2. Li Lu;Wenhao Yan;Weiya Xue;Di Shao;Yongzhong Xing

 Evolution and Association Analysis of Ghd7 in Rice
 PLoS ONE, 2012, 7(5): e34021

3. Asami Osugi;Hironori Itoh;Kyoko Ikeda-Kawakatsu;Makoto Takano;Takeshi Izawa

 Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice
 Plant Physiology, 2011, 157(3): 1128-1137

4. Taeko Shibaya;Yasunori Nonoue;Nozomi Ono;Utako Yamanouchi;Kiyosumi Hori;Masahiro Yano

 Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions
 Theoretical and Applied Genetics, 2011, 123(7): 1133-1143

5. Weiya Xue;Yongzhong Xing;Xiaoyu Weng;Yu Zhao;Weijiang Tang;Lei Wang;Hongju Zhou;Sibin Yu;Caiguo Xu;Xianghua Li & Qifa Zhang

 Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice
 Nature Genetics, 2008, 40(6): 761-767