Chin Bull Bot ›› 2016, Vol. 51 ›› Issue (4): 488-495.doi: 10.11983/CBB15136

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Functional Genes of Panicle Development in Response to Nitrogen Fertilizer in Rice

Chengqiang Ding, Shaohua Wang, Yanfeng Ding*   

  1. College of Agronomy, Nanjing Agricultural University, Nanjing 210095, China
  • Received:2015-08-03 Accepted:2015-11-05 Online:2016-08-05 Published:2016-07-01
  • Contact: Ding Yanfeng E-mail:dingyf@njau.edu.cn
  • About author:

    # Co-first authors

Abstract:

Deep-sequencing technologies provide quantitative measures of transcript abundance. We studied the effect of nitrogen fertilizer on genes by deep-sequencing. Many genes were differentially expressed under different levels of nitrogen. The differentially expressed genes were classified into several functional categories including transcriptional regulation, hormone metabolism and signal transduction, metabolism and transportation, stress response, signal transduction (receptor), and protein degradation. Mutant analyses and map-based cloning have revealed many genes controlling the number of spikelets per panicle. Several genes were regulated by nitrogen fertilizer. Some genes regulate panicle development and also plant height, heading date, tiller number, and seed setting rate. Researching the function of these differentially expressed genes will help reveal the molecular mechanisms of nitrogen fertilizer in regulating panicle development in rice.

Table 1

Statistical analysis of differentially expressed genes"

Up-regulation Down-regulation Total
LN vs. LC 1547 1933 3480
PN vs. PC 271 468 739

Table 2

The expression of genes in leaves and young panicle of rice"

Gene Phenotype LC
(TPM)
LN
(TPM)
log2 Ratio
(LN/LC)
PC
(TPM)
PN
(TPM)
log2 Ratio
(PN/PC)
References
D3 Tiller number 15.31 8.43 -0.86 18.01 10.96 -0.72 Zhao et al., 2014
DEP1 Spikelet number per panicle, panicle type 0.01 0.01 0 0.17 0.01 -4.09 Huang et al., 2009; Sun et al., 2014
DEP2/EP2 Panicle type, grain size 1.96 1.08 -0.86 55.17 63.91 0.21 Li et al., 2010a; Zhu et al., 2010
DEP3 Spikelet number per panicle, panicle type 0.01 0.01 0 0.52 0.35 -0.57 Qiao et al., 2011
DLT, D62 Tiller number 0.36 0.01 -5.17 34.72 46.6 0.42 Li et al., 2010c
Ehd2/RID1 Heading time, photoperiod sensitivity 1.42 0.54 -1.39 0.01 0.26 4.7 Matsubara et al., 2008
EUI1 Panicle length, plant height 0.71 0.01 -6.15 - - - Luo et al., 2006
FC1/OsCAD7 Heading time, plant height, grain size 0.01 0.01 0 4.52 6.17 0.45 Li et al., 2009c
FZP/BFL1 Panicle branching 0.01 0.01 0 1.39 0.78 -0.83 Komatsu et al., 2003b
Ghd8/DTH8 Heading time, spikelet num- ber per panicle, plant height 3.92 3.23 -0.28 0.01 0.01 0 Yan et al., 2011
Hd1 Heading time, photoperiod sensitivity 1.78 0.36 -2.31 0.7 0.7 0 Takahashi et al., 2009
Hd17/Ef7 Heading time 17.27 34.44 1 20.01 16 -0.32 Yang et al., 2013
Hd6/CK2α Heading time, photoperiod sensitivity 33.29 47.17 0.5 69 67.38 -0.03 Takahashi et al., 2001
HGW Heading time, grain size 26.35 27.08 0.04 35.85 47.04 0.39 Li et al., 2012
LAX1 Panicle branching, plant height, fertility 0.01 0.01 0 16.1 14.95 -0.11 Komatsu et al., 2003a
LAX2 Panicle branching, tiller number 0.01 0.01 0 0.17 0.01 -4.09 Tabuchi et al., 2011
LP Panicle length, panicle type 1.25 1.97 0.66 29.93 17.48 -0.78 Li et al., 2011b
MIP1 Dwarf/semi-dwarf, tiller number 59.81 67.26 0.17 247.03 115.12 -1.1 Sun et al., 2010
OGR1 Dwarf/semi-dwarf, tiller number, fertility 2.67 4.3 0.69 4.44 3.04 -0.55 Kim et al., 2009
OsAPC6 Panicle length, fertility, grain size, plant height 0.89 1.61 0.86 15.84 19.56 0.3 Awasthi et al., 2012
OsCD1 Spikelet number per panicle, leaf shape, plant height 0.01 0.54 5.75 79.18 115.2 0.54 Luan et al., 2011
OsCKX2/Gn1a Spikelet number per panicle 0.01 0.36 5.17 0.52 1.04 1 Ashikari et al., 2005
OsDof12 Heading time 100.04 56.14 -0.83 17.66 11.22 -0.65 Li et al., 2009a
OsEF3 Heading time, grain size 2.49 0.01 -7.96 2 0.52 -1.94 Fu et al., 2009
OsGRF1 Heading time, plant height 0.01 0.01 0 17.66 8.87 -0.99 Luo et al., 2005
OsGS1;1 Heading time, grain filling, plant height 0.01 0.72 6.17 0.44 0.35 -0.33 Kusano et al., 2011
OsGS2, OsGLN2 Tiller number 482.23 722.61 0.58 28.54 19.65 -0.54 Ishiyama et al., 2004
OsHDT1 Heading time 43.61 10.58 -2.04 393.73 291.71 -0.43 Li et al., 2011a
OsJAG Tiller number, fertility 0.01 0.01 0 4.18 5.56 0.41 Duan et al., 2010
OsLFL1 Heading time 0.01 0.01 0 19.93 11.48 -0.8 Peng et al., 2008
OsMADS15/ DEP Panicle development, fertility 0.01 0.01 0 0.17 0.96 2.5 Wang et al., 2010a
OsMADS50 Heading time 0.71 1.61 1.18 5.74 6.61 0.2 Ryu et al., 2009
Gene Phenotype LC
(TPM)
LN
(TPM)
log2 Ratio
(LN/LC)
PC
(TPM)
PN
(TPM)
log2 Ratio
(PN/PC)
References
OsMADS51 Heading time 42.72 50.94 0.25 201.96 254.06 0.33 Kim et al., 2007
OsMADS56 Heading time 2.49 0.36 -2.79 0.35 0.17 -1.04 Ryu et al., 2009
OsPH1 Heading time, plant height, panicle length 87.76 294.32 1.75 88.58 131.55 0.57 Kovi et al., 2011
OsPht1;8 Fertility, phosphorus content 153.45 734.99 2.26 2.96 3.3 0.16 Jia et al., 2011
OsSPL14 Spikelet number per panicle, tiller number 0.01 0.01 0 376.77 296.49 -0.35 Miura et al., 2010
OsSUT2 Plant height, tiller number, grain size 0.53 0.01 -5.73 0.01 0.01 0 Eom et al., 2011
OsTB1, FC1 Tiller number 0.01 0.01 0 1.48 2.87 0.96 Takeda et al., 2003
OsTEF1 Tiller number 233.02 55.42 -2.07 14.71 8.43 -0.8 Paul et al., 2012
PPS Heading time 8.37 24.93 1.57 13.4 20.61 0.62 Tanaka et al., 2011
RFL/APO2 Heading time, panicle development 0.01 0.01 0 85.1 109.55 0.36 Ikeda-Kawakatsu et al., 2012
SG1 Panicle length, plant height, leaf color and shape, grain size 0.01 0.01 0 47.94 64.51 0.43 Nakagawa et al., 2012
SGL1 Panicle length, plant height, leaf color and shape, grain size 0.01 0.01 0 0.17 0.01 -4.09 Nakagawa et al., 2012
SP1 Panicle length 0.01 1.08 6.75 80.23 81.29 0.02 Li et al., 2009b
TAD1 Tiller number 1.96 0.01 -7.61 2.44 2.09 -0.22 Su'udi et al., 2012
WAF1 Panicle length, leaf shape 0.53 0.36 -0.56 26.36 37.13 0.49 Abe et al., 2010
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