26 Li Y, Fan C, Xing Y, et al. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet, 2014, 46: 398-404
[2]
27 Peng B, Kong H, Li Y, et al. OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nat Commun, 2014, 5: 4847
[3]
28 Xue W, Xing Y, Weng X, et al. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet, 2008, 40: 761-767
[4]
29 Yan W, Liu H, Zhou X, et al. Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res, 2013, 23: 969-971
[5]
30 Luo J, Liu H, Zhou T, et al. An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell, 2013, 25: 3360-3376
[6]
31 Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency. PLoS Genet, 2011, 7: e1002196
[7]
32 Hu X, Qian Q, Xu T, et al. The U-Box E3 ubiquitin ligase TUD1 functions with a heterotrimeric G a subunit to regulate Brassinosteroid-mediated growth in rice. PLoS Genet, 2013, 9: e1003391
[8]
33 Jiao Y, Wang Y, Xue D, et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet, 2010, 42: 541-544
[9]
34 Chen J, Ding J, Ouyang Y, et al. A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proc Natl Acad Sci USA, 2008, 105: 11436-11441
[10]
35 Yang J, Zhao X, Cheng K, et al. A killer-protector system regulates both hybrid sterility and segregation distortion in rice. Science, 2012, 337: 1336-1340
[11]
36 Du H, Ouyang Y, Zhang C, et al. Complex evolution of S5, a major reproductive barrier regulator, in the cultivated rice Oryza sativa and its wild relatives. New Phytol, 2011, 191: 275-287
[12]
37 Chen C, Chen H, Lin Y, et al. A two-locus interaction causes interspecific hybrid weakness in rice. Nat Commun, 2014, 5: 3357
[13]
38 Ding J, Lu Q, Ouyang Y, et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci USA, 2012, 109: 2654-2659
[14]
39 Zhou H, Liu Q, Li J, et al. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res, 2012, 22: 649-660
[15]
40 Zhang H, Xu C, He Y, et al. Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production. Proc Natl Acad Sci USA, 2013, 110: 76-81
[16]
41 Zhou H, Zhou M, Yang Y, et al. RNase ZS1 processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice. Nat Commun, 2014, 5: 4884
[17]
42 Wang W, Liu Z, Guo Z, et al. Comparative transcriptomes profiling of photoperiod-sensitive male sterile rice nongken 58s during the male sterility transition between short-day and long-day. BMC Genomics, 2011, 12: 462-471
[18]
43 Chen X, Hu J, Zhang H, et al. DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions. Gene, 2014, 537: 143-148
[19]
44 Yuan M, Chu Z, Li X, et al. The bacterial pathogen Xanthomonas oryzae overcomes rice defenses by regulating host copper redistribution. Plant Cell, 2010, 22: 3164-3176
[20]
45 Liu Q, Yuan M, Zhou Y, et al. A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant Cell Environ, 2011, 34: 1958-1969
[21]
46 Wang C, Zhang X, Fan Y, et al. XA23 is an executor R protein and confers broad-spectrum disease resistance in rice. Mol Plant, 2015, 8: 290-302
[22]
47 Park C H, Chen S, Shirsekar G, et al. The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ligase APIP6 for suppression of PAMP-triggered immunity in rice. Plant Cell, 2012, 24: 4748-4762
[23]
48 Li W, Zhong S, Li G, et al. Rice RING protein OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell wall defence. Cell Res, 2011, 21: 835-848
[24]
49 Wang Q, Liu Y, He J, et al. STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus. Nat Commun, 2014, 5: 4768
[25]
50 Ding B, Bellizzi M R, Ning Y, et al. HDT701, a histone H4 deacetylase, negatively regulates plant innate immunity by modulating histone h4 acetylation of defense-related genes in rice. Plant Cell, 2012, 24: 3783-3794
[26]
51 Li T, Chen X, Zhong X, et al. Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice. Plant Cell, 2013, 25: 4725-4736
[27]
52 Liu B, Li J, Ao Y, et al. Lysin motif-containing proteins LYP4 and LYP6 play dual roles in peptidoglycan and chitin perception in rice innate immunity. Plant Cell, 2012, 24: 3406-3419
[28]
53 Liu J, Park C H, He F, et al. The RhoGAP SPIN6 associates with SPL11 and OsRac1 and negatively regulates programmed cell death and innate immunity in rice. PLoS Pathog, 2015, 11: e1004629
[29]
54 Cheng X, Zhu L, He G. Towards understanding of molecular interactions between rice and the brown planthopper. Mol Plant, 2013, 6: 621-634
[30]
55 Du B, Zhang W, Liu B, et al. Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci USA, 2009, 106: 22163-22168
[31]
56 Chen X, Wu Y, Guo J, et al. A rice lectin receptor-like kinase that is involved in innate immune responses also contributes to seed germination. Plant J, 2013, 76: 687-698
[32]
57 Liu Y, Wu H, Chen H, et al. A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice. Nat Biotechnol, 2015, 33: 301-305
[33]
58 Jena K, Kim S M. Current status of brown planthopper (BPH) resistance and genetics. Rice, 2010, 3: 161-171
[34]
59 Qiu Y, Guo J, Jing S, et al. Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6. Theor Appl Genet, 2011, 124: 485-494
[35]
60 Hu J, Cheng M, Gao G, et al. Pyramiding and evaluation of three dominant brown planthopper resistance genes in the elite indica rice 9311 and its hybrids. Pest Manag Sci, 2013, 69: 802-808
[36]
70 Tang Z, Fan X, Li Q, et al. Knockdown of a rice stelar nitrate transporter alters long-distance translocation but not root influx. Plant Physiol, 2012, 160: 2052-2063
[37]
71 Tsay Y, Chiu C, Tsai C, et al. Nitrate transporters and peptide transporters. FEBS Lett, 2007, 581: 2290-2300
[38]
72 Lin C, Koh S, Stacey G, et al. Cloning and functional characterization of a constitutively expressed nitrate transporter gene, OsNRT1, from rice. Plant Physiol, 2000, 122: 379-388
[39]
73 Li S, Qian Q, Fu Z, et al. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. Plant J, 2009, 58: 592-605
[40]
74 Fan X, Xie D, Chen J, et al. Over-expression of OsPTR6 in rice increased plant growth at different nitrogen supplies but decreased nitrogen use efficiency at high ammonium supply. Plant Sci, 2014, 227: 1-11
[41]
75 Fang Z, Xia K, Yang X, et al. Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnol J, 2013, 11: 446-458
[42]
76 Li B, Merrick M, Li S, et al. Molecular basis and regulation of ammonium transporter in rice. Rice Science, 2009, 16: 314-322
[43]
77 Ranathunge K, El-Kereamy A, Gidda S, et al. AMT1;1 transgenic rice plants with enhanced NH4(+) permeability show superior growth and higher yield under optimal and suboptimal NH4(+) conditions. J Exp Bot, 2014, 65: 965-979
[44]
78 Sun H, Qian Q, Wu K, et al. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice. Nat Genet, 2014, 46: 652-656
[45]
79 Zhang Y, Tan L, Zhu Z, et al. TOND1 confers tolerance to nitrogen deficiency in rice. Plant J, 2015, 81: 367-376
[46]
80 Seo H, Jung Y, Song S, et al. Increased expression of OsPT1, a high-affinity phosphate transporter, enhances phosphate acquisition in rice. Biotechnol Lett, 2008, 30: 1833-1838
[47]
81 Ai P, Sun S, Zhao J, et al. Two rice phosphate transporters, OsPht1;2 and OsPht1;6, have different functions and kinetic properties in uptake and translocation. Plant J, 2009, 57: 798-809
[48]
82 Zhang F, Sun Y, Pei W, et al. Involvement of OsPht1;4 in phosphate acquisition, and mobilization facilitates embryo development in rice. Plant J, 2015, doi: 10.1111/tpj.12804
[49]
83 Jia H, Ren H, Gu M, et al. The phosphate transporter gene OsPht1;8 is involved in phosphate homeostasis in rice. Plant Physiol, 2011, 156: 1164-1175
[50]
84 Wang X, Wang Y, Pineros M, et al. Phosphate transporters OsPHT1;9 and OsPHT1;10 are involved in phosphate uptake in rice. Plant Cell Environ, 2014, 37: 1159-1170
[51]
85 Paszkowski U, Kroken S, Roux C, et al. Rice phosphate transporters include an evolutionarily divergent gene specifically activated in arbuscular mycorrhizal symbiosis. Proc Natl Acad Sci USA, 2002, 99: 13324-13329
[52]
86 Guimil S, Chang H, Zhu T S, et al. Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization. Proc Natl Acad Sci USA, 2005, 102: 8066-8070
[53]
87 Sun S, Gu M, Cao Y, et al. A constitutive expressed phosphate transporter, OsPht1;1, modulates phosphate uptake and translocation in phosphate-replete rice. Plant Physiol, 2012, 159: 1571-1581
[54]
88 Li J, Long Y, Qi G, et al. The Os-AKT1 channel is critical for K+ uptake in rice roots and is modulated by the rice CBL1-CIPK23 complex. Plant Cell, 2014, 26: 3387-3402
[55]
89 Zhang Q. Strategies for developing Green Super Rice. Proc Natl Acad Sci USA, 2007, 104: 16402-16409
[56]
90 Yu H, Xie W, Li J, et al. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J, 2014, 12: 28-37
[57]
91 Chen H, Xie W, He H, et al. A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant, 2014, 7: 541-553
[58]
92 Zhang Q, Li J, Xue Y, et al. Rice 2020: A call for an international coordinated effort in rice functional genomics. Mol Plant, 2008, 1: 715-719
[59]
1 Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4. Nature, 2002, 420: 316-320
[60]
2 Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 2002, 296: 79-92
[61]
3 Yang Y, Li Y, Wu C. Genomic resources for functional analyses of the rice genome. Curr Opin Plant Biol, 2013, 16: 157-163
[62]
4 Chen W, Gong L, Guo Z, et al. A novel integrated method for large-scale detection, identification and quantification of widely-targeted metabolites: Application in study of rice metabolomics. Mol Plant, 2013, 6: 1769-1780
[63]
5 Gong L, Chen W, Gao Y, et al. Genetic analysis of the metabolome exemplified using a rice population. Proc Natl Acad Sci USA, 2013, 110: 20320-20325
[64]
6 Chen W, Gao Y, Xie W, et al. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet, 2014, 46: 714-721
[65]
7 Yang W, Duan L, Chen G, et al. Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies. Curr Opin Plant Biol, 2013, 16: 180-187
[66]
8 Yang W, Guo Z, Huang C, et al. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun, 2014, 5: 5087
[67]
9 Huang X, Feng Q, Qian Q, et al. High-throughput genotyping by whole-genome resequencing. Genome Res, 2009, 19: 1068-1076
[68]
10 Xie W, Feng Q, Yu H, et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA, 2010, 107: 10578-10583
[69]
11 Huang X, Wei X, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961-967
[70]
12 Huang X, Zhao Y, Wei X, et al. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet, 2012, 44: 32-39
[71]
13 Huang X, Kurata N, Wei X, et al. A map of rice genome variation reveals the origin of cultivated rice. Nature, 2012, 490: 497-501
15 Fan C, Xing Y, Mao H, et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet, 2006, 112: 1164-1171
[74]
16 Mao H, Sun S, Yao J, et al. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA, 2010, 107: 19579-19584
[75]
17 Huang X, Qian Q, Liu Z, et al. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet, 2009, 41: 494-497
[76]
18 Li Y, Fan C, Xing Y, et al. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet, 2011, 43: 1266-1269
[77]
19 Song X, Huang W, Shi M, et al. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 2007, 39: 623-630
[78]
20 Weng J, Gu S, Wan X, et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res, 2008, 18: 1199-1209
[79]
21 Wang S, Wu K, Yuan Q, et al. Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet, 2012, 44: 950-954
[80]
22 Qi P, Lin Y, Song X, et al. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Res, 2012, 22: 1666-1680
[81]
23 Zhang X, Wang J, Huang J, et al. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci USA, 2012, 109: 21534-21539
[82]
24 Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature, 2013, 504: 401-405
[83]
25 Zhou F, Lin Q, Zhu L, et al. D14-SCFD3-dependent degradation of D53 regulates strigolactone signalling. Nature, 2013, 504: 406-410
[84]
61 Du H, Wang N, Cui F, et al. Characterization of the b-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiol, 2010, 154: 1304-1318
[85]
62 Yaish M W, El-Kereamy A, Zhu T, et al. The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice. PLoS Genet, 2010, 6: e1001098
[86]
63 Sun L, Zhang Q, Wu J, et al. Two rice authentic histidine phosphotransfer proteins, OsAHP1 and OsAHP2, mediate cytokinin signaling and stress responses in rice. Plant Physiol, 2014, 165: 335-345
[87]
64 Zhang Q, Li J, Zhang W, et al. The putative auxin efflux carrier OsPIN3t is involved in the drought stress response and drought tolerance. Plant J, 2012, 72: 805-816
[88]
65 Zhu X, Xiong L. Putative megaenzyme DWA1 plays essential roles in drought resistance by regulating stress-induced wax deposition in rice. Proc Natl Acad Sci USA, 2013, 110: 17790-17795
[89]
66 Ambavaram M M, Basu S, Krishnan A, et al. A Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. Nat Commun, 2014, 5: 5302
[90]
67 Du H, Wu N, Cui F, et al. A homolog of ETHYLENE OVERPRODUCER, OsETOL1, differentially modulates drought and submergence tolerance in rice. Plant J, 2014, 78: 834-849
[91]
68 Lin C, Lee K, Chen C, et al. SnRK1A-interacting negative regulators modulate the nutrient starvation signaling sensor SnRK1 in source-sink communication in cereal seedlings under abiotic stress. Plant Cell, 2014, 26: 808-827
[92]
69 Ma Y, Dai X, Xu Y et al. COLD1 confers chilling tolerance in rice. Cell, 2015, 160: 1209-1221