Abstract
Rice yield potentiality has been enhanced much after incorporating semi-dwarf trait in rice, which has led to the Green Revolution worldwide, but afterward, yield potentiality has increased marginally. To keep pace with increasing food grain demand due to increasing population, rice production needs to be enhanced even though available land, water, and other natural resources are limited. Thus, the only option is to improve intrinsic yield potentiality. Generally, rice yield is determined by different direct and indirect source and sink size-related components such as grain number per panicle, weight of grains, number of tillers, panicle architecture, heading date, etc. During the last two decades, QTL mapping and map-based cloning have identified several QTLs and genes controlling intrinsic and extrinsic factors of yield, followed by proper validation for their yield-enhancing ability in diverse rice backgrounds of indica and japonica subspecies. Because of the character's complexity, identifying favorable alleles of these genes, followed by gene pyramiding is the main strategy for high-yielding variety development. Any update regarding the molecular mechanism, gene functions and gene-to-gene interaction will assist a breeder to move a step ahead toward yield improvement. This review summarizes the recent progress of these genes and their contributions to yield and this information will further advance and facilitate rice breeding with more precision and efficiency.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Akabane T, Suzuki N, Tsuchiya W, Yoshizawa T, Matsumura H, Hirotsu N, Katoh E (2022) Expression, purification and crystallization of TGW6, which limits grain weight in rice. Protein Expr Purif 188:105975. https://doi.org/10.1016/j.pep.2021.105975
Ali J, Xu JL, Gao Y, Fontanilla M, Li Z (2012) Enhanced productivity across different rice ecologies through green super Rice (GSR) breeding strategy. Int Dialog Desig Rice Future, ICRISAT, Hyderabad. https://doi.org/10.1371/journal.pone.0164456
Aloni R (2010) The induction of vascular tissues by auxin. In: Davies, Peter J (eds) Plant hormones: biosynthesis, signal transduction, Action! Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 485–518. https://doi.org/10.1007/978-1-4020-2686-7_22
Arite T, Iwata H, Ohshima K, Maekawa M, Nakajima M, Kojima M, Sakakibara H, Kyozuka J (2007) DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice. Plant J 51(6):1019–1029. https://doi.org/10.1111/j.1365-313X.2007.03210.x
Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J (2009) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol 50(8):1416–1424. https://doi.org/10.1093/pcp/pcp091
Arunkumar M, Geetha S, Amudha K, Suresh R, Ravichandran V, Geetha K (2022) Genetic diversity and QTL-marker association analysis of rice germplasm for grain number per panicle and its contributing traits. Electron J Plant Breed 13(2):558–566. https://doi.org/10.37992/2022.1302.068
Ashikari M, Wu J, Yano M, Sasaki T, Yoshimura A (1999) Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes theα-subunit of GTP-binding protein. Proc Natl Acad Sci 96(18):10284–10289. https://doi.org/10.1073/pnas.96.18.10284
Ashikari M, Sakakibara H, Lin SY, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741–745. https://doi.org/10.1126/science.1113373
Becraft PW, Li K, Dey N, Asuncion-Crabb Y (2002) The maize dek1 gene functions in embryonic pattern formation and cell fate specification. J Dev 129:5217–5225. https://doi.org/10.1242/dev.129.22.5217
Beveridge CA, Kyozuka J (2010) New genes in the strigolactone-related shoot branching pathway. Curr Opin Plant Biol 13:34–39. https://doi.org/10.1016/j.pbi.2009.10.003
Botella JR (2012) Canheterotrimeric Gproteins help to feed the world? Trends Plant Sci 17:563–568. https://doi.org/10.1016/j.tplants.2012.06.002
Businessline, The Hindu (2023) https://www.thehindubusinessline.com/economy/agri-business/indian-wheat-rice-production-estimated-at-record-high/article66508474.ece
Chakravorty D, Trusov Y, Zhang W, Acharya BR, Sheahan MB, McCurdy DW, Assman SM, Botella JR (2011) An atypical heterotrimeric G-proteinγ-subunit is involved in guard cell K+-channel regulation and morphological development in Arabidopsis thaliana. Plant J 67:840–851. https://doi.org/10.1111/j.1365-313X.2011.04638.x
Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P (2012) Fine mapping of a major QTL for flag leaf width in rice qFLW4 which might be caused by alternative splicing of NAL1. Plant Cell Rep 31:863–872. https://doi.org/10.1007/s00299-011-1207-7
Chen L, Zhao Y, Xu S, Zhang Z, Xu Y, Zhang J, Chong K (2018) OsMADS57 together with OsTB1 coordinates transcription of its target OsWRKY94 and D14 to switch its organogenesis to defense for cold adaptation in rice. New Phytol 218(1):219–231. https://doi.org/10.1111/nph.14977
Chen F, Zhang H, Li H, Lian L, Wei Y, Lin Y, Wang L, He W, Cai Q, Xie H, Zhang H, Zhang J (2023) IPA1 improves drought tolerance by activating SNAC1 in rice. BMC Plant Biol 23(1):1–12. https://doi.org/10.1186/s12870-023-04062-9
Cho SH, Yoo SC, Zhang H, Pandeya D, Koh HJ, Hwang JY, Kim GT, Paek NC (2013) The rice narrow leaf2 and narrow leaf3 loci encode WUSCHEL-related homeobox 3A (OsWOX3A) and function in leaf, spikelet, tiller and lateral root development. New Phytol 198:1071–1084. https://doi.org/10.1111/nph.12231
Choi MS, Woo MO, Koh EB, Lee J, Ham TH, Seo HS, Koh HJ (2012) Teosinte Branched 1 modulates tillering in rice plants. Plant Cell Rep 31:57–65. https://doi.org/10.1007/s00299-011-1139-2
Cubas P, Lauter N, Doebley J, Coen E (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J 18:215–222. https://doi.org/10.1046/j.1365-313x.1999.00444.x
Cui Y, Hu X, Liang G, Feng A, Wang F, Ruan S, Dong G, Shen L, Zhang B, Chen D, Zhu L, Hu J, Lin Y, Longbiao Guo L, Matsuoka M, Qian Q (2020) Production of novel beneficial alleles of a rice yield-related QTL by CRISPR/Cas9. Plant Biotechnol J 18(10):1987–1989. https://doi.org/10.1111/pbi.13370
Deng X, Wang J, Liu X, Yang J, Zhou M, Kong W, Jiang Y, Ke S, Sun T, Li Y (2022) QTL Analysis and heterosis loci of effective tiller using three genetic populations derived from indica-japonica crosses in rice. Agronomy 12(9):2171. https://doi.org/10.3390/agronomy12092171
Din MSu, Wang X, Alamery S, Fiaz S, Rasheed H, Khan MA et al (2022) Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice. PLoS ONE 17(3):e0264478. https://doi.org/10.1371/journal.pone.0264478
Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386:485–488. https://doi.org/10.1038/386485a0
Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G, Huang K, Huang L, Xu R, Ge S, Qian Q, Li Y (2017) Natural variation in the promoter of GSE5 contributes to grain size diversity in rice. Mol Plant 10(5):685–694. https://doi.org/10.1016/j.molp.2017.03.009
Duan E, Wang Y, Li X, Lin Q, Zhang T, Wang Y, Zhou C, Zhang H, Jiang L, Wang J, Lei C, Zhang X, Guo X, Wang H, Wan J (2019) OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 in Rice. Plant Cell 31(5):1026–1042. https://doi.org/10.1105/tpc.19.00023
Eragam A, Shukla V, Kola VS, Latha P, Akkareddy S, Kommana ML, Ramireddy E, Vemireddy LR (2022) Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes. Mol Biol Rep 49(8):7649–7663. https://doi.org/10.1007/s11033-022-07581-0
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) 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 112:1164–1171. https://doi.org/10.1007/s00122-006-0218-1
Fan CC, Yu SB, Wang CR, Xing YZ (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118:465–472. https://doi.org/10.1007/s00122-008-0913-1
Fei C, Geng X, Xu Z, Xu Q (2019) Multiple areas investigation reveals the genes related to vascular bundles in rice. Rice 12:17. https://doi.org/10.1186/s12284-019-0278-x
Feng Y, Xue Q (2006) The serine carboxypeptidase like gene family of rice (Oryza sativa L. ssp. japonica). Funct Integr Genomics 6:14–24. https://doi.org/10.1007/s10142-005-0131-8
Feng X, Wang C, Nan J, Zhang X, Wang R, Jiang G, Yuan Q, Lin S (2017) Updating the elite rice variety Kongyu 131 by improving the Gn1a locus. Rice 10:35. https://doi.org/10.1186/s12284-017-0174-1
Ferrero-Serrano Á, Cantos C, Assmann SM (2019) The role of dwarfing traits in historical and modern agriculture with a focus on rice. Cold Spring Harb Perspect Biol 11(11):a034645. https://doi.org/10.1101/cshperspect.a034645
Finlayson SA (2007) Arabidopsis Teosinte Branched1-like 1 regulates axillary bud out growth and is homologous to monocot Teosinte Branched1. Plant Cell Physiol 48(5):667–677. https://doi.org/10.1093/pcp/pcm044
Fraser CM, Rider LW, Chapple C (2005) An expression and bioinformatics analysis of the Arabidopsis serine carboxypeptidase-like gene family. Plant Physiol 138:1136–1148. https://doi.org/10.1104/pp.104.057950
Fujii S, Toriyama K (2009) Suppressed expression of retrograde-regulated male sterility restores pollen fertility in cytoplasmic male sterile rice plants. Proc Natl Acad Sci 106(23):9513–9518. https://doi.org/10.1073/pnas.0901860106
Fujita D, Ebron LA, Araki E, Kato H, Khush GS, Sheehy JE, Lafarge T, Fukuta Y, Kobayashi N (2010) Fine mapping of a gene for low tiller number, Ltn, in rice (Oryza sativa L.) variety Aikawa 1. Theor Appl Genet 120:1233–1240. https://doi.org/10.1007/s00122-009-1251-7
Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihar S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N (2013) NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci 110(51):20431–20436. https://doi.org/10.1073/pnas.1310790110
Fukuda H (2004) Signals that control plant vascular cell differentiation. Nat Rev Mol Cell Biol 5:379–391. https://doi.org/10.1038/nrm1364
Fukushima A, Ohta H, Yokogami N, Tsuda N, Yoshida A, Kyozuka J, Maekawa M (2017) Effects of genes increasing the number of spikelets per panicle, TAW1 and APO1, on yield and yield- relatedtraitsinrice. PlantProdSci 20(4):485–489. https://doi.org/10.1080/1343943X.2017.1365614
Gao H, Jin M, Zheng XM, Chen J, Yuan D, Xin Y, Wang M, Huang D, Zhang Z, Zhou K, Sheng P, Ma J, Ma W, Deng H, Jiang L, Liu S, Wang H, Wu C, Yuan L, Wan J (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. Proc Natl Acad Sci 111(46):16337–16342. https://doi.org/10.1073/pnas.1418204111
Gao X, Zhang X, Lan H, Huang J, Wang J, Zhang H (2015) The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons. BMC Plant Biol 15(1):1–13. https://doi.org/10.1186/s12870-015-0515-4
Gomez-Roldan V, Fermas S, Brewer PB, Puech-Pages V, Dun EA, Pillot JP, Letisse F, Matusova R, Danoun S, Portais JC, Bouwmeester H, Bécard G, Beveridge CA, Rameau C, Rochange SF (2008) Strigolactone inhibition of shoot branching. Nature 455:189–194. https://doi.org/10.1038/nature07271
Goto Y, Tanabe M, Ishibashi T, Tsutsumi N, Yoshimura A, Nemoto K (2005) Tillering behavior of the rice fineculm1 mutant. Plant Prod Sci 8(1):68–70. https://doi.org/10.1626/pps.8.68
Gouda G, Gupta MK, Donde R, Kumar J, Parida M, Mohapatra T, Dash SK, Pradhan SK, Behera L (2020) Characterization of haplotypes and single nucleotide polymorphisms associated with Gn1a for high grain number formation in rice plant. Genomics 112(3):2647–2657. https://doi.org/10.1016/j.ygeno.2020.02.016
Gunasekaran A, Seshadri G, Ramasamy S, Muthurajan R, Karuppasamy KS (2023) Identification of newer stable genetic sources for high grain number per panicle and understanding the gene action for important panicle traits in rice. Plants 12(2):250. https://doi.org/10.3390/plants12020250
Guo S, Xu Y, Liu H, Mao Z, Zhang C, Ma Y, Zhang Q, Meng Z, Chong K (2013) The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun 4:1566. https://doi.org/10.1038/ncomms2542
Han Y, Luo D, Usman B, Nawaz G, Zhao N, Liu F, Li R (2018) Development of high yielding glutinous cytoplasmic male sterile rice (Oryza sativa L) lines through CRISPR/Cas9 based mutagenesis of Wx and TGW6 and proteomic analysis of anther. Agronomy 8(12):290. https://doi.org/10.3390/agronomy8120290
Haritha G, Vishnukiran T, Yugandhar P, Sarla N, Subrahmanyam D (2017) Introgressions from Oryza rufipogon increase photosynthetic efficiency of KMR3 rice lines. Rice Sci 24(2):85–96. https://doi.org/10.1016/j.rsci.2016.07.006
He Y, Zhu M, Li Z, Jiang S, He Z, Xu S, Chen X, Hu Z, Zhang Z (2021) IPA1 negatively regulates early rice seedling development by interfering with starch metabolism via the GA and WRKY pathways. Int J Mol Sci 22(12):6605. https://doi.org/10.3390/ijms22126605
Heang D, Sassa H (2012a) An atypical bHLH protein encoded by positive regulator of grain length 2 is involved in controlling grain length and weight of rice through interaction with a typical bHLH protein APG. Breed Sci 62(2):133–141. https://doi.org/10.1270/jsbbs.62.133
Heang D, Sassa H (2012b) Antagonistic Actions of HLH/bHLH proteins are involved in grain length and weight in rice. PLoS ONE 7(2):e31325. https://doi.org/10.1371/journal.pone.0031325
Hibara K, Obara M, Hayashida E, Abe M, Ishimaru T, Satoh H, Itoh J, Nagato Y (2009) The ADAXIALIZEDLEAF1 gene functions in leaf and embryonic pattern formation in rice. Dev Biol 334:345–354. https://doi.org/10.1016/j.ydbio.2009.07.042
Hirotsu N, Ujiie K, Perera I, Iri A, Kashiwagi T, Ishimaru K (2017) Partial loss-of-function of NAL1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice. Sci Rep 7:15958. https://doi.org/10.1038/s41598-017-15886-5
Hu WJ, Zhang SH, Zhao Z, Sun CR, Zhao YJ, Luo D (2003) The analysis of the structure and expression of OsTB1 gene in rice. Physiol Mol Biol Plants 29(6):507–514
Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41(4):494–497. https://doi.org/10.1038/ng.352
Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226. https://doi.org/10.1016/j.tplants.2012.11.001
Huang L, Zhang R, Huanga G, Lic Y, Melakua G, Zhanga S, Chen H, Zhaoa Y, Zhanga J, Zhang Y, Hua F (2018) Developing superior alleles of yield genes in rice by artificial mutagenesis using the CRISPR/Cas9 system. Crop J 6(5):475–481. https://doi.org/10.1016/j.cj.2018.05.005
Huang L, Hua K, Xu R, Zeng D, Wang R, Dong G, Zhang G, Lu X, Fang N, Wang D, Duan P, Zhang B, Liu Z, Li N, Luo Y, Qian Q, Yao S, Li Y (2021a) The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice. Plant Cell 33(4):1212–1228. https://doi.org/10.1093/plcell/koab041
Huang LY, Li XX, Zhang Y, Fahad S, Wang F (2021b) dep1 improves rice grain yield and nitrogen use efficiency simultaneously by enhancing nitrogen and dry matter translocation. J Integr Agric 21(11):2021. https://doi.org/10.1016/S2095-3119(21)63795-4
Huang J, Gao L, Luo S et al (2022) The genetic editing of GS3 via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality. Mol Breeding 42:22. https://doi.org/10.1007/s11032-022-01290-z
Huo X, Wu S, Zhu Z, Liu F, Fu Y, Cai H, Sun X, Gu P, Xie D, Tan L, Sun C (2017) NOG1 increases grain production in rice. Nat Commun 8:1497. https://doi.org/10.1038/s41467-017-01501-8
Ikeda K, Nagasawa N, Nagato Y (2005) ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice. Dev Biol 282:349–360. https://doi.org/10.1016/j.ydbio.2005.03.016
Ikeda K, Ito M, Nagasawa N, Kyozuka J, Nagato Y (2007) Rice aberrant panicle organization 1, encoding an F-box protein, regulates meristem fate. Plant J 51:1030–1040. https://doi.org/10.1111/j.1365-313X.2007.03200.x
Ikeda KK, Yasuno N, Oikawa T, Iida S, Nagato Y, Maekawa M, Kyozuka J (2009) Expression level of aberrant panicle organization1 determines rice inflorescence form through control of cell proliferation in the meristem. Plant Physiol 150:736–747. https://doi.org/10.1104/pp.109.136739
Ikeda-KK MM, Izawa T, Itoh JI, Yasuo Nagato Y (2012) Aberrant panicle organization 2/RFL, the rice ortholog of Arabidopsis Leafy, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1. Plant J 69:168–180. https://doi.org/10.1111/j.1365-313X.2011.04781.x
Imai I, Kimball JA, Conway B, Yeater KM, McCouch SR, McClung A (2013) Validation of yield-enhancing quantitative trait loci from a low-yielding wild ancestor of rice. Mol Breed 32:101–120. https://doi.org/10.1007/s11032-013-9855-7
Ishimaru K (2003) Identification of a locus increasing rice yield and physiological analysis of its function. Plant Physiol 133:1083–1090. https://doi.org/10.1104/pp.103.027607
Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45(6):707–711. https://doi.org/10.1038/ng.2612
Ishizaki T, Ueda Y, Takai T, Maruyama K, Tsujimoto Y (2023) In-frame mutation in rice teosinte branched1 (OsTB1) improves productivity under phosphorus deficiency. Plant Sci 330:111627. https://doi.org/10.1016/j.plantsci.2023.111627
Jeong DH, Park S, Zhai J, Gurazada SGR, De Paoli E, Meyers BC, Green PJ (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage. Plant Cell 23(12):4185–4207. https://doi.org/10.1105/tpc.111.089045
Jia M, Luo N, Meng X, Song X, Jing Y, Kou L, Liu G, Huang X, Wang Y, Li J, Wang B, Yu H (2022) OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice. J Genet Genomics 49(8):766–775. https://doi.org/10.1016/j.jgg.2022.06.009
Jiang D, Fang JJ, Lou L, Zhao J, Yuan S, Yin S, Sun W, Peng L, Guo B, Li X (2015) Characterization of a null allelic mutant of the rice NAL1 gene reveals its role in regulating cell division. PLoS ONE 10(2):e0118169. https://doi.org/10.1371/journal.pone.0118169
Jiang S, Wang D, Yan S, Liu S, Liu B, Kang H, Wang GL (2019) Dissection of the genetic architecture of rice tillering using a genome-wide association study. Rice 12:1–11. https://doi.org/10.1186/s12284-019-0302-1
Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB (2020) CRISPR based assessment of genomic structure in the conserved SQUAMOSA promoter binding like gene clusters in rice. Plant J 104(5):1301–1314. https://doi.org/10.1111/tpj.15001
Jiao YQ, Wang YH, Xue DW, Wang J, Yan MX, Liu GF, Dong GJ, Zeng DL, Lu ZF, Zhu XD, Qian Q, Li JY (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544. https://doi.org/10.1038/ng.591
Jun W, Jie Y, Xiang X, Jinyan Z, Fangjun F, Wenqi L, Fangquan W, Wei-gong Z (2014) Development and application of a functional marker for grain weight gene TGW6 in rice. Chin J Rice Sci 28:473–478
Kaladhar K, Swamy BPM, Babu AP, Reddy CS, Sarla N (2008) Mapping quantitative trait loci for yield traits in BC2F2 population derived from Swarna x O. nivara cross. Rice Genet Newslett 24:34–36. https://doi.org/10.1093/jhered/esr145
Khush GS (2000) New plant type of rice for increasing the genetic yield potential. In: Nanda JS (ed) Rice breeding and genetics. Science Publishers, New Hampshire, USA, pp 99–108
Khush GS (2001) Green revolution: the way forward. Nat Rev Genet 2(10):815–822. https://doi.org/10.1038/35093585
Kikuta M, Menge DM, Gichuhi EW, Samejima H, Tomita R, Kimani JM, Musila RN, Doi K, Ashikari M, Angeles-Shim R, Jena KK, Makihara D (2023) Contribution of genes related to grain number (Gn1a and WFP) introgressed into NERICA 1 to grain yield under tropical highland conditions in central Kenya. Plant Prod Sci 26(3):309–319. https://doi.org/10.1080/1343943X.2023.2245127
Kim SR, Ramos J, Ashikari M, Virk PS, Torres EA, Nissila E, Hechanova SL, Mauleon R, Jena KK (2016) Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice. Oryza Sativa l Rice 9:12. https://doi.org/10.1186/s12284-016-0084-7
Kim SR, Ramos JM, Hizon RJM, Ashikari M, Virk PS, Torres EA, Nissila E, Jena KK (2018) Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield. Sci Rep 8:3833. https://doi.org/10.1038/s41598-018-21355-4
Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I, Yano M, Kitano H, Iwasaki Y (2010) A novel kinesin 13 protein regulating rice seed length. Plant Cell Physiol 51(8):1315–1329. https://doi.org/10.1093/pcp/pcq092
Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J (2003) FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. J Dev 130(16):3841–3850. https://doi.org/10.1242/dev.00564
Kong F, Wang JY, Zou JC, Shi LX, Jin MD, Xu ZJ, Wang B (2007) Molecular tagging and mapping of the erect panicle gene in rice. Mol Breed 19:297–304. https://doi.org/10.1007/s11032-006-9062
Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang Z, Li J, Li Z, Paek NC (2013) Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. Mol Plant 6:1877–1888. https://doi.org/10.1093/mp/sst088
Kosugi S, Ohashi Y (1997) PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 9:1607–1619. https://doi.org/10.1105/tpc.9.9.1607
Kunihiro S, Saito T, Matsuda T, Inoue M, Kuramata M, Taguchi-Shiobara F, Youssefian S, Berberich T, Tomonobu Kusan T (2013) Rice DEP1, encoding a highly cysteine-rich G protein γ subunit, confers cadmium tolerance on yeast cells and plants. J Exp Bot 64(14):4517–4527. https://doi.org/10.1093/jxb/ert267
Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H, Kyozuka J (2007) Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature 445:652–655. https://doi.org/10.1038/nature05504
Li J, Yuan L (2000) Hybrid rice: genetics, breeding, and seed production. Plant Breed Rev 17:15–158
Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li J (2003) Control of tillering in rice. Nature 422:618621. https://doi.org/10.1038/nature01518
Li J, Xiao J, Grandillo S, Jiang L, WanY DQ, Yuan L, McCouch SR (2004) QTL detection for rice grain quality traits using an interspecific back-cross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice. Genome 47:697–704. https://doi.org/10.1139/g04-029
Li C, Potuschak T, Colon-Carmona A, Gutierrez RA, Doerner P (2005) Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci 102(36):12978–12983. https://doi.org/10.1073/pnas.0504039102
Li S, Qian Q, Fu Z, Zeng D, Meng X, Kyozuka J, Maekawa M, Zhu X, Zhang J, Li J, Wang Y (2009) Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. Plant J 58:592–605. https://doi.org/10.1111/j.1365-313X.2009.03799.x
Li YB, Fan CC, Xing YZ, Jiang YH, Luo LJ, Sun L, Shao D, Xu CJ, Li XH, Xiao JH, He YQ, Zhang QF (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269. https://doi.org/10.1038/ng.977
Li J, Chu H, Zhang Y, Mou T, Wu C, Zhang Q, Xu J (2012) The rice HGW gene encodes a ubiquitin- associated (UBA) domain protein that regulates heading date and grain weight. PLoS ONE 7:e34231. https://doi.org/10.1371/journal.pone.0034231
Li S, Zhao B, Yuan D, Duan M, Qian Q, Tang L, Wanga B, Liu X, Zhang J, Wanga J, Suna J, Liud Z, Feng YQ, Yuan L, Li C (2013) Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression. Proc Natl Acad Sci 110(8):3167–3172. https://doi.org/10.1073/pnas.1300359110
Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H (2016) Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci 7:3. https://doi.org/10.3389/fpls.2016.00377
Li X, Tao Q, Miao J, Yang Z, Gu M, Liang G, Zhou Y (2019) Evaluation of differential qPE9-1/DEP1 protein domains in rice grain length and weight variation. Rice 12(1):1–10. https://doi.org/10.1186/s12284-019-0263-4
Li M, Pan X, Li H (2022) Pyramiding of gn1a, gs3, and ipa1 exhibits complementary and additive effects on rice yield. Int J Mol Sci 23(20):12478. https://doi.org/10.3390/ijms232012478
Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L (2023) Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice. Nat Plants 9(7):1130–1142. https://doi.org/10.1038/s41477-023-01449-2
Lian L, Xu H, Zhang H, He W, Cai Q, Lin Y, Wei L, Pan L, Xie X, Zheng Y, Wei Y, Zhu Y, Xie H, Zhang J (2020) Overexpression of OsSPL14 results in transcriptome and physiology changes in indica rice ‘MH86.’ Plant Growth Regul 90:265–278. https://doi.org/10.1007/s10725-019-00569-0
Liao Z, Yu H, Duan J, Yuan K, Yu C, Meng X, Kou L, Chen M, Jing Y, Liu G, Smith SM, Li J (2019) SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice. Nat Commun 10:2738. https://doi.org/10.1038/s41467-019-10667-2
Liao S, Yan J, Xing H, Tu Y, Zhao H, Wang G (2021) Genetic basis of vascular bundle variations in rice revealed by genome-wide association study. Plant Sci 302:110715. https://doi.org/10.1016/j.plantsci.2020.110715
Lin H, Wang R, Qian Q, Yan M, Meng X, Fu Z, Yan C, Jiang B, Su Z, Li J, Wang Y (2009) DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth. Plant Cell 21:1512–1525. https://doi.org/10.1105/tpc.109.065987
Lin Q, Wang D, Dong H, Gu S, Cheng Z, Gong J, Qin R, Jiang L, Li G, Wang JL, Wu F, Guo X, Zhang X, Lei C, Wang H, Wan J (2012) Rice APC/CTE controls tillering by mediating the degradation of MONOCULM 1. Nat Commun 3(1):752. https://doi.org/10.1038/ncomms1716
Lin Q, Wu F, Sheng P, Zhang Z, Zhang X, Guo X, Wang J, Cheng Z, Wang J, Wang H, Wan J (2015) The SnRK2-APC/CTE regulatory module mediates the antagonistic action of gibberellic acid and abscisic acid pathways. Nat Commun 6(1):7981. https://doi.org/10.1038/ncomms8981
Liu T, Liu H, Zhang H, Xing Y (2013) Validation and characterization of Ghd7.1, a major quantitative trait locus with pleiotropic effects on spikelets per panicle, plant height and heading date in rice (Oryza sativa L.). J Integr Plant Biol 55:917–927. https://doi.org/10.1111/jipb.12070
Liu E, Liu Y, Wu G, Zeng S, Thi TGT, Liang L, Liang Y, Dong Z, She D, Wang H, Zaid IU, Hong D (2016) Identification of a candidate gene for panicle length in rice (Oryza sativa L) via association and linkage analysis. Front Plant Sci 7:596. https://doi.org/10.3389/fpls.2016.00596
Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y, Tian P, Cheng Z, Yu X, Zhou K, Zhang X, Guo X, Wang J, Wang H, Wan J (2017) GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nat Plants 10(3):17043. https://doi.org/10.1038/nplants.2017.43
Liu M, Shi Z, Zhang X, Wang M, Zhang L, Zheng K, Liu J, Hu X, Di C, Qian Q, He Z, Yang DL (2019) Inducible overexpression of Ideal Plant Architecture 1 improves both yield and disease resistance in rice. Nat Plants 5(4):389–400. https://doi.org/10.1038/s41477-019-0383-2
Liu R, Feng Q, Li P, Lou G, Chen G, Jiang H, Gao G, Zhang Q, Xiao J, Li X, Xiong L, He Y (2022) GLW71, a strong functional allele of Ghd7, enhances grain size in rice. Int J Mol Sci 23(15):8715. https://doi.org/10.3390/ijms23158715
Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X, Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci 106:2071–2076. https://doi.org/10.1073/pnas.0812798106
Lu L, Yan W, Xue W, Shao D, Xing Y (2012) Evolution and association analysis of Ghd7 in rice. PLoS ONE 7:e34021. https://doi.org/10.1371/journal.pone.0034021
Lu L, Shao D, Qiu X, Sun L, Yan W, Zhou X, Yang L, He Y, Yu S, Xing Y (2013a) Natural variation and artificial selection in four genes determine grain shape in rice. New Phytol 200(4):1269–1280. https://doi.org/10.1111/nph.12430
Lu Z, Yu H, Xiong G, Wang J, Jiao Y, Liu G, Jing Y, Meng X, Hu X, Qian Q, Fu X, Wang Y, Li J (2013b) Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. Plant Cell 25:3743–3759. https://doi.org/10.1105/tpc.113.113639
Luo L, Li W, Miura K, Ashikari M, Kyozuka J (2012) Control of tiller growth of rice by OsSPL14 and strigolactones, which work in two independent pathways. Plant Cell Physiol 53(10):1793–1801. https://doi.org/10.1093/pcp/pcs122
Luo LJ, Li ZK, Mei HW, Shu QY, Tabien R, Zhong DB, Ying CS, Stansel JW, Khush GS, Paterson AH (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice II grain yield components. Genetics 158(4):1755–1771. https://doi.org/10.1093/genetics/158.4.1755
Lyu J, Huang L, Zhang S, Zhang Y, He W, Zeng P, Zeng Y, Huang G, Zhang J, Ning M, Bao Y, Zhao S, Fu Q, Wade LJ, Chen H, Wang W, Hu F (2020) Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice. Nat Commun 11(1):725. https://doi.org/10.1038/s41467-019-14264-1
Ma X, Feng F, Zhang Y, Elesawi IE, Xu K, Li T, Mei H, Liu H, Gao N, Chen C, Luo L, Yu S (2019) A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population. PLoS Genet 15(5):e100819. https://doi.org/10.1371/journal.pgen.1008191
Mallikarjuna Swamy BP, Kaladhar K, Reddy GA, Viraktamath BC, Sarla N (2014) Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara. J Genet 93:643–654. https://doi.org/10.1007/s12041-014-0420-x
Mansueto L, Rommel R, Dmytro F, Frances C, Borja N, Detras J, Miguel J, Santos A, Palis K, Poliakov A, Dubchak I, Solovyev V, Sackville R, KennethL H, Nally M, Alexandrov N, Mauleon R (2016) SNP-Seek II: a resource for allele mining and analysis of big genomic data in Oryza sativa. Curr Plant Biol 7–8:16–22. https://doi.org/10.1016/j.cpb.2016.12.003
Mao HL, Sun SY, Yao JL, Wang CR, Yu SB, Xu CG, Li XH, Zhang QF (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci 107:19579–19584. https://doi.org/10.1073/pnas.1014419107
Marri PR, Reddy LV, Siddiq EA (2005) Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genom 6(1):1–14. https://doi.org/10.1186/1471-2156-6-33
Minakuchi K, Kameoka H, Yasuno N, Umehara M, Luo L, Kobayashi K, Hanada A, Ueno K, Asami T, Yamaguchi S, Kyozuka J (2010a) FINE CULM1 ( FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice. Plant Cell Physiol 51(7):1127–1135. https://doi.org/10.1093/pcp/pcq083
Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42(6):545–549. https://doi.org/10.1038/ng.592
Murai M, Iizawa M (1994) Effects of major genes-controlling morphology of panicle in rice. Jpn J Breed 44(3):247–255. https://doi.org/10.1270/jsbbs1951.44.247
Muralidharan K, Prasad GSV, Rao CS, Siddiq EA (2019) Genetic gain for yield in rice breeding and rice production in india to meet with the demand from increased human population. Curr Sci 116:544–560. https://doi.org/10.18520/cs/v116/i4/544-560
Nan J, Feng X, Wang C, Zhang X, Wang R, Liu J, Yuan Q, Jiang G, Lin S (2018) Improving rice grain length through updating the GS3 locus of an elite variety Kongyu 131. Rice 11:21. https://doi.org/10.1186/s12284-018-0217-2
Nemoto Y, Nonoue Y, Yano M, Izawa T (2016) Hd1, a CONSTANS ortholog in rice, functions as an Ehd1 repressor through interaction with monocot-specific CCT-domain protein Ghd7. Plant J 86:221–233. https://doi.org/10.1111/tpj.13168
Ngangkham U, Samantaray S, Yadav MK, Kumar A, Chidambaranathan P, Katara JL (2018) Effect of multiple allelic combinations of genes on regulating grain size in rice. PLoS ONE 13(1):e0190684. https://doi.org/10.1371/journal.pone.0190684
Nishimura A, Ito M, Kamiya N, Sato Y, Matsuoka M (2002) OsPNH1 regulates leaf development and maintenance of the shoot apical meristem in rice. Plant J 30:189–201. https://doi.org/10.1046/j.1365-313X.2002.01279.x
Nomura T, Arakawa N, Yamamoto T, Ueda T, Adachi S, Yonemaru JI, Abe A, Takagi H, Yokoyama T, Ookawa T (2019) Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1. PLoS ONE 14(8):e0221424. https://doi.org/10.1371/journal.pone.0221424
Nomura T, Seki Y, Matsuoka M, Yano K, Chigira K, Adachi S, Piñera-Chavez FJ, Reynolds M, Ohkubo S, Ookawa T (2021) Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons. Sci Rep 11(1):15780. https://doi.org/10.1038/s41598-021-95268-0
Oikawa T, Kyozuka J (2009) Two-step regulation of LAX PANICLE1 protein accumulation in axillary meristem formation in rice. Plant Cell 21(4):1095–1108. https://doi.org/10.1105/tpc.108.065425
Ookawa T, Hobo T, Yano M, Murata K, Ando T, Miura H, Asano K, Ochiai Y, Ikeda M, Nishitani R, Ebitani T, Ozaki H, Angeles ER, Hirasawa T, Matsuoka M (2010) New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat Commun 1:132. https://doi.org/10.1038/ncomms1132
Ookawa T, Nomura T, Kamahora E, Jiang M, Ochiai Y, Samadi AF, Yamaguchi T, Adachi S, Katsura K, Motobayashi T (2022) Pyramiding of multiple strong-culm genes originating from indica and tropical japonica to the temperate japonica rice. Sci Rep 12(1):15400. https://doi.org/10.1038/s41598-022-19768-3
Ouyang X, Zhong X, Chang S, Qian Q, Zhang Y, Zhu X (2022) Partially functional NARROW LEAF1 balances leaf photosynthesis and plant architecture for greater rice yield. Plant Physiol 189(2):772–789. https://doi.org/10.1093/plphys/kiac135
Piao RH, Jiang WZ, Ham TH, Choi MS, Qiao YL, Chu SH, Park JH, Woo MO, Jin ZX, An G, Lee JY, Koh HJ (2009) Map-basedcloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet 119:1497–1506. https://doi.org/10.1007/s00122-009-1151-x
Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008) Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947–1959. https://doi.org/10.1104/pp.108.118778
Qi P, Lin YS, Song XJ, Shen JB, Huang W, Shan JX, Zhu MZ, Jiang L, Gao JP, Lin HX (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1; 3. Cell Res 22:1666–1680. https://doi.org/10.1038/cr.2012.151
Qiao YL, Piao RH, Shi JX, Lee SI, Jiang WZ, Kim BK, Lee JY, Han LZ, Ma WB, Koh HJ (2011) Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.). Theor Appl Genet 122:1439–1449. https://doi.org/10.1007/s00122-011-1543-6
Qin M, Zhang Y, Yang Y, Miao C, Liu S (2020) Seed-specific overexpression of SPL12 and IPA1 improves seed dormancy and grain size in rice. Front Plant Sci 11:532771. https://doi.org/10.3389/fpls.2020.532771
Ren M, Huang M, Qiu H, Chun Y, Li L, Kumar A, Fang J, Zhao J, Hi H, Li X (2021) Genome-wide association study of the genetic basis of effective tiller number in rice. Rice 14(1):1–13. https://doi.org/10.1186/s12284-021-00495-8
Rice productivity: Ricepedia (https://ricepedia.org/rice-as-a-crop/rice-productivity )
Saito H, Okumoto Y, Tsukiyama T, Xu C, Teraishi M, Tanisaka T (2019) Allelic differentiation at the E1/Ghd7 locus has allowed expansion of rice cultivation area. Plants 8(12):550. https://doi.org/10.3390/plants8120550
Scarpella E, Meijer AH (2004) Pattern formation in the vascular system of monocot and dicot plant species. New Phytol 164:209–242. https://doi.org/10.1111/j.1469-8137.2004.01191.x
Segami S, Kono I, Ando T, Yano M, Kitano H, Miura K, Iwasaki Y (2012) Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice. Rice 5:4. https://doi.org/10.1186/1939-8433-5-4
Sen P, Purkaystha S, Das D, Goswami J, Sen S, Rai P, Biswas T, Bhattacharyya PK, Bhattacharyya S (2021) Yield-enhancing SPIKE allele from the aus-subtype indica rice and its allele specific codominant marker. J Genet 100:36. https://doi.org/10.1007/s12041-021-01293-3
Sentoku N, Sato Y, Kurata N, Ito Y, Kitano H, Matsuoka M (1999) Regional expression of the rice KN1-type homeobox gene family during embryo, shoot, and flower development. Plant Cell 11:1651–1663. https://doi.org/10.1105/tpc.11.9.1651
Shao G, Lu Z, Xiong J, Wang B, Jing Y, Meng X, Liu G, Ma H, Liang Y, Chen F, Wang Y, Li J, Yu H (2019) Tiller bud formation regulators MOC1 and MOC3 cooperatively promote tiller bud outgrowth by activating FON1 expression in rice. Mol Plant 12:1090–1102. https://doi.org/10.1016/j.molp.2019.04.008
She KC, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T, Matsumoto K, Kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H (2010) A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell 22:3280–3294. https://doi.org/10.1105/tpc.109.070821
Shen L, Wang C, Fu YP, Wang JJ, Liu Q, Zhang XM, Yan CJ, Qian Q, Wang KJ (2016) QTL editing confers opposing yield performance in different rice varieties. J Integr Plant Biol 60(2):89–93. https://doi.org/10.1111/jipb.12501
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028. https://doi.org/10.1038/ng.169
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630. https://doi.org/10.1038/ng2014
Song X, Lu Z, Yu H, Shao G, Xiong J, Meng X, Jing Y, Liu G, Xiong G, Duan J, Yao XF, Liu CM, Li H, Wang Y, Li J (2017) IPA1 functions as a downstream transcription factor repressed by D53 in strigolactone signaling in rice. Cell Res 27(9):1128–1141. https://doi.org/10.1038/cr.2017.102
Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci 99(13):9043–9048. https://doi.org/10.1073/pnas.132266399
Subudhi PK, Garcia RS, Coronejo S, De Leon TB (2020) A novel mutation of the NARROW LEAF 1 gene adversely affects plant architecture in rice (Oryza sativa L.). Int J Mol Sci 21(21):8106. https://doi.org/10.3390/ijms21218106
Sudhakar T, Panigrahy M, Lakshmanaik M, Babu AP, Reddy CS, Anuradha K, Swamy BPM, Sarla N (2012) Variation and correlation of phenotypic traits contributing to high yield in KMR3: oryza rufipogon introgression lines. Int J Plant Breed Genet 6:69–82. https://scialert.net/abstract/?doi=ijpbg.2012.69.82
Sun F, Zhang W, Xiong G, Yan M, Qian Q, Li J, Wang Y (2010) Identification and functional analysis of the MOC1 interacting protein 1. J Genet Genomics 37:6977. https://doi.org/10.1038/ncomms1743
Sun H, Qian Q, Wu K, Luo J, Wang S, Zhang C, Ma Y, Liu Q, Huang X, Yuan Q, Han R, Zhao M, Dong G, Guo L, Zhu X, Gou Z, Wang W, Wu Y, Lin H, Fu X (2014a) Heterotrimeric G proteins regulate nitrogen-use efficiency in rice. Nat Genet 46(6):652–656. https://doi.org/10.1038/ng.2958
Sun L, Yang DL, Kong Y, Chen Y, Li XZ, Zeng LZ, Li Q, Wang ET, He ZH (2014b) Sugar homeostasis mediated by cell wall invertase GRAININCOMPLETE FILLING 1 (GIF1) plays a role in pre-existing and induced defense in rice. Mol Plant Pathol 15(2):161–173. https://doi.org/10.1111/mpp.12078
Sun S, Wang L, Mao H, Shao L, Li X, Xiao J, Ouyang Y, Zhang Q (2018) A G-protein pathway determines grain size in rice. Nature Commun 9(1):851. https://doi.org/10.1038/s41467-018-03141-y
Sun K, Huang M, Zong W, Xiao D, Lei C, Luo Y, Song Y, Li S, Hao Y, Luo W, Xu B, Guo X, Wei G, Chen L, Liu YG, Guo J (2022) Hd1, Ghd7, and DTH8 synergistically determine the rice heading date and yield-related agronomic traits. Acta Genet Sin 49(5):437–447. https://doi.org/10.1016/j.jgg.2022.02.018
Swamy BP, Sarla N (2008) Yield-enhancing quantitative trait loci (QTLs) from wild species. Biotechnol Adv 26(1):106–120. https://doi.org/10.1016/j.biotechadv.2007.09.005
Swamy BM, Kaladhar K, Ramesha MS, Viraktamath BC, Sarla N (2011) Molecular mapping of QTLs for yield and yield-related traits in Oryza sativa cv Swarna × O. nivara (IRGC81848) backcross population. Rice Sci 18(3):178–186. https://doi.org/10.1016/S1672-6308(11)60025-5
Swamy BM, Kaladhar K, Shobha Rani N, Prasad GSV, Viraktamath BC, Reddy GA, Sarla N (2012) QTL analysis for grain quality traits in 2 BC2F2 populations derived from crosses between Oryza sativa cv Swarna and 2 accessions of O. nivara. J Hered 103(3):442–452. https://doi.org/10.1016/J.RSCI.2018.06.003
Taguchi-Shiobara F, Kawagoe Y, Kato H, Onodera H, Tagiri A, Hara N, Miyao A, Hirochika H, Kitano H, Yano M, Toki S (2011) A loss-of-function mutation of rice dense panicle 1 causes semi- dwarfness and slightly increased number of spikelets. Breed Sci 61:17–25. https://doi.org/10.1270/jsbbs.61.17
Taguchi-Shiobara F, Ota T, Ebana K, Ookawa T, Yamasaki M, Tanabata T, Yamanouchi U, Wu J, Ono N, Nonoue Y, Nagata K, Fukuoka S, Hirabayashi H, Yamamoto T, Yano M (2015) Natural variation in the flag leaf morphology of rice due to a mutation of the narrow leaf 1 gene in Oryza sativa L. Genet 201:795–808. https://doi.org/10.1534/genetics.115.181040
Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu J, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T (2013) A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci Rep 3:2149. https://doi.org/10.1038/srep02149
Takai T, Adachia S, Fujitad D, Arai-Sanoh Y, Okamuraa M, Kondoa M, Kobayashia N (2017) Effects of yield-related QTLs SPIKE and GPS in two indica rice genetic backgrounds. Plant Prod Sci 20:467–476. https://doi.org/10.1080/1343943X.2017.1385404
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouc S (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genet 182(4):1323–1334. https://doi.org/10.1534/genetics.109.103002
Takano-Kai N, Jiang H, Powell A, McCouch S, Takamure I, Furuya N, Doi K, Yoshimura A (2013) Multiple and independent origins of short seeded alleles of GS3 in rice. Breed Sci 63(1):77–85. https://doi.org/10.1270/jsbbs.63.77
Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Ueguchi C (2003) The OsTB1 gene negatively regulates lateral branching in rice. Plant J 33:5138–5520. https://doi.org/10.1046/j.1365-313X.2003.01648.x
Teale WD, Paponov IA, Palme K (2006) Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol 7:847–859. https://doi.org/10.1038/nrm2020
Temple BR, Jones AM (2007) The plant heterotrimeric G-protein complex. Annu Rev Plant Biol 58:249–266. https://doi.org/10.1146/annurev.arplant.58.032806.103827
Terao T, Nagata K, Morino K, Hirose T (2010) A gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice. Theor Appl Genet 120:875–893. https://doi.org/10.1007/s00122-009-1218-8
Tian P, Liu J, Mou C, Shi C, Zhang H, Zhao Z, Lin Q, Wang J, Wang J, Zhang X, Guo X, Cheng Z, Zhu S, Ren Y, Lei C, Wang H, Wan J (2019) GW5 Like, a homolog of GW5, negatively regulates grain width, weight and salt resistance in rice. J Integr Plant Biol 61(11):1171–1185. https://doi.org/10.1111/jipb.12745
Tong H, Jin Y, Liu W, Li F, Fang J, Yin Y, Qian Q, Zhu L, Chu C (2009) DWARF AND LOW- TILLERING, a new member of the GRAS family, plays positive roles in brassinosteroid signaling in rice. Plant J 58(5):58803–58816. https://doi.org/10.1111/j.1365-313X.2009.03825.x
Tremousaygue D, Garnier L, Bardet C, Dabos P, Herve C, Lescure B (2003) Internal telomeric repeats and ‘TCP domain’ protein binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J 33(6):957–966. https://doi.org/10.1046/j.1365-313x.2003.01682.x
Tripathi L, Sowdhamini R (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genom 7:200. https://doi.org/10.1186/1471-2164-7-200
Tsukahara K, Sawada H, Kohno Y, Matsuura T, Mori IC, Terao T, Ioki M, Tamaoki M (2015) Ozone- induced rice grain yield loss is triggered via a change in panicle morphology that is controlled by aberrant panicle organization 1 gene. PLoS ONE 10(4):e0123308. https://doi.org/10.1371/journal.pone.0123308
Tu B, Tao Z, Wang S, Zhou L, Zheng L, Zhang C, Li X, Zhang X, Yin J, Zhu X, Yuan H, Li T, Chen W, Qin P, Ma B, Wang Y, Li S (2022) Loss of Gn1a/OsCKX2 confers heavy panicle rice with excellent lodging resistance. J Integr Plant Biol 64(1):23–38. https://doi.org/10.1111/jipb.13185
Umehara M, Hanada A, Yoshida S, Akiyama K, Arite T, Takeda-Kamiya N, Magome H, Kamiya Y, Shirasu K, Yoneyama K, Kyozuka J, Yamaguchi S (2008) Inhibition of shoot branching by new terpenoid plant hormones. Nature 455(7210):195–200. https://doi.org/10.1038/nature07272
Umehara M, Hanada A, Magome H, Takeda-Kamiya N, Yamaguchi S (2010) Contribution of strigolactones to the inhibition of tiller bud outgrowth under phosphate deficiency in rice. Plant Cell Physiol 51(7):1118–1126. https://doi.org/10.1093/pcp/pcq084
Vemireddy LR, Kadambari G, Reddy GE, Kola VSR, Ramireddy E, Puram VRR, Badri J, Eslavath SN, Bollineni SN, Naik BJ, Chintala S, Pottepalem R, Akkareddy S, Nagireddy R, Reddy LVB, Bodanapu R, Lekkala SP, Chakravartty N, Siddiq EA (2019) Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.). Sci Rep 9:8192. https://doi.org/10.1038/s41598-019-44708-z
Wan XY, Wan JM, Weng JF, Jiang L, Bi JC, Wang CM, Zhai HQ (2005) Stability of QTL for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet 110:1334–1346. https://doi.org/10.1007/s00122-005-1976-x
Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270. https://doi.org/10.1007/s00122-006-0227-0
Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008) Control of rice grain-filling and yield by a gene with potential signature of domestication. Nat Genet 40:1270–1274. https://doi.org/10.1038/ng.220
Wang E, Xu X, Zhang L, Zhang H, Lin L, Wang Q, Li Q, Ge S, Lu BR, Wang W, He Z (2010) Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evol Biol 10:108. https://doi.org/10.1186/1471-2148-10-108
Wang C, Chen S, Yu S (2011) Functional markers developed from multiple loci in GS3 for fine marker- assisted selection of grain length in rice. Theor Appl Genet 122(5):905–913. https://doi.org/10.1007/s00122-010-1497-0
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954. https://doi.org/10.1038/ng.2327
Wang J, Xu H, Li N, Fan F, Wang L, Zhu Y, Li S (2015a) Artificial selection of Gn1a plays an important role in improving rice yields across different ecological regions. Rice 8:37. https://doi.org/10.1186/s12284-015-0071-4
Wang L, Sun S, Jin J, Fu D, Yang X, Weng X, Xu C, Li X, Xiao J, Zhang Q (2015b) Coordinated regulation of vegetative and reproductive branching in rice. Proc Natl Acad Sci 112(50):15504–15509. https://doi.org/10.1073/pnas.1521949112
Wang J, Yu H, Xiong G, Lu Z, Jiao Y, Meng X, Liu G, Chen X, Wang W, Li J (2017) Tissue-specific ubiquitination by IPA1 interacting protein1 modulates IPA1 protein levels to regulate plant architecture in rice. Plant Cell 29(4):697–707. https://doi.org/10.1105/tpc.16.00879
Wang J, Zhou L, Shi H, Chern M, Yu H, Yi H, He M, Yin J, Zhu X, Li Y, Li W, Liu J, Wang J, Chen XQ, Qing H, Wang Y, Liu G, Wang W, Li P, Wu X, Zhu L, Zhou JM, Ronald PC, Li S, Li J, Chen X (2018a) A single transcription factor promotes both yield and immunity in rice. Science 361(6406):1026–1028. https://doi.org/10.1126/science.aat7675
Wang S, Ma B, Gao Q, Jiang G, Zhou L, Tu B, Qin P, Tan X, Liu P, Kang Y, Wang Y, Chen W, Liang C, Li S (2018b) Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes. Theor Appl Genet 131:1391–1403. https://doi.org/10.1007/s00122-018-3085-7
Wang YZ, Zhang N, Chen HW, Wang F, Huang YC, Jia BY, Wang S, Wang Y, Xu ZJ (2019) Effects of DEP1 on grain yield and grain quality in the background of two japonica rice (Oryza sativa) cultivars. Plant Breed 139(3):608–617. https://doi.org/10.1111/pbr.12788
Wang Y, Zhai L, Chen K, Shen C, Liang Y, Wang C, Zhao X, Wang S, Xu J (2020) Natural sequence variations and combinations of GNP1 and NAL1 determine the grain number per panicle in rice. Rice 13:1–15. https://doi.org/10.1186/s12284-020-00374-8
Wang B, Guo X, Qi X, Feng F, Zhu X, Hu Y, Li J, Zhao Q, Sun H (2022) OsSPL14 is involved in nitrogen-deficiency-induced root elongation in rice. Environ Exp Bot 198:104852. https://doi.org/10.1016/j.envexpbot.2022.104852
Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J (2010) DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153:1747–1758. https://doi.org/10.1104/pp.110.156943
Wei FJ, Droc G, Guiderdoni E, Hsing YIC (2013) International consortium of rice mutagenesis: resources and beyond. Rice 6(1):1–12. https://doi.org/10.1186/1939-8433-6-39
Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J (2008a) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18(12):1199–1209. https://doi.org/10.1038/cr.2008.307
Wu L, Wang X, Yu Z, Cui X, Xu Q (2022) Simultaneous improvement of grain yield and quality through manipulating two type CG protein gamma subunits in rice. Int J Mol Sci 23(3):14630. https://doi.org/10.3390/ijms23031463
Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol 142(1):280–293. https://doi.org/10.1104/pp.106.084475
Xu Z, Chen WF, Zhang LB, Zhang C (1995) The heredity of the erect character and relation with other characters in rice. J Shenyang Agric Univ 26:1–7 ((in Chinese))
Xu C, Wang Y, Yu Y, Duan J, Liao Z, Xiong G, Meng X, Liu G, Qian Q, Li J (2012) Degradation of monoculm 1 by APC/CTAD1 regulates rice tillering. Nat Commun 3:750. https://doi.org/10.1038/ncomms1743
Xu Q, Xu N, Xu H, Tang L, Liu J, Sun J, Wang J (2014) Breeding value estimation of the application of IPA1 and DEP1 to improvement of Oryza sativa L. ssp. japonica in early hybrid generations. Mol Breed 34:1933–1942. https://doi.org/10.1007/s11032-014-0150-z
Xu C, Liu Y, Li Y, Xu X, Xu C, Li X, Xiao J, Zhang Q (2015a) Differential expression of GS5 regulates grain size in rice. J Exp Bot 66(9):2611–2623. https://doi.org/10.1093/jxb/erv058
Xu Q, Liu T, Bi W, Wang Y, Hai XuH, Liang Tang L, Sun J, Xu Z (2015b) Different effects of DEP1 on vascular bundle- and panicle related traits under indica and japonica genetic backgrounds. Mol Breed 35:173. https://doi.org/10.1007/s11032-015-0364-8
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40(6):761–767. https://doi.org/10.1038/ng.143
Yamaguchi S, Kyozuka J (2010) Branching hormone is busy both underground and overground. Plant Cell Physiol 51(7):1091–1094. https://doi.org/10.1093/pcp/pcq088
Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S (2004) A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J Mol Biol 337(1):49–63. https://doi.org/10.1016/j.jmb.2004.01.015
Yan C, Zhou J, Yan S, Chen F, Yeboah M, Tang SZ, Liang GH, Gu MH (2007) Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theor Appl Genet 115:1093–1100. https://doi.org/10.1007/s00122-007-0635-9
Yan CJ, Yan S, Yang YC, Zeng XH, Fang YW, Zeng SY, Tian CY, Sun YW, Tang SZ, Gu MH (2009) Development of gene-tagged markers for quantitative trait loci underlying rice yield components. Euphytica 169:215–226. https://doi.org/10.1007/s10681-009-9937-0
Yan S, Zou G, Li S, Wang H, Liu H, Zhai G, Guo P, Song H, Yan C, Tao Y (2011) Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theor Appl Genet 123(7):1173–1181. https://doi.org/10.1007/s00122-011-1657-x
Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969–971. https://doi.org/10.1038/cr.2013.43
Yang Y, Shen Z, Xu C, Guo M, Li Y, Zhang Y, Zhong C, Sun S, Yan C (2020) Genetic improvement of panicle-erectness japonica rice toward both yield and eating and cooking quality. Mol Breed 40:51. https://doi.org/10.1007/s11032-020-01127-7
Yano K, Ookawa T, Aya K, Ochiai Y, Hirasawa T, Ebitani T, Takarada T (2015) Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism. Mol Plant 8:303–314. https://doi.org/10.1016/j.molp.2014.10.009
Ye ZH (2002) Vascular tissue differentiation and pattern formation in plants. Annu Rev Plant Biol 53:183–202. https://doi.org/10.1146/annurev.arplant.53.100301.135245
Ye J, Niu X, Yang Y, Wang S, Xu Q, Yuan X, Yu H, Wang Y, Wang S, Feng Y, Wei X (2018) Divergent Hd1, Ghd7, and DTH7 alleles control heading date and yield potential of japonica rice in Northeast China. Front Plant Sci 9:35. https://doi.org/10.3389/fpls.2018.00035
Yi X, Zhang Z, Zeng S, Tian C, Peng J, Li M, Lu Y, Meng Q, Gu M, Yan C (2011) Introgression of qPE9–1 allele, conferring the panicle erectness, leads to the decrease of grain yield per plant in japonica rice (Oryza sativa L). J Genet Genom 38(5):217–223. https://doi.org/10.1016/j.jgg.2011.03.011
Yoon DK, Suganami M, Ishiyama K, Kagawa T, Tanaka M, Nagao R, Takagi D, Ishida H, Suzuki Y, Mae T, Makino A, Obara M (2022) The gs3 allele from a large-grain rice cultivar, Akita 63, increases yield and improves nitrogen-use efficiency. Plant Direct 6(7):e417. https://doi.org/10.1002/pld3.417
Yue E, Li C, Li Y, Liu Z, Xu J (2017) MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa). Plant Mol Biol 94:469–480. https://doi.org/10.1007/s11103-017-0618-4
Yuyu C, Aike Z, Pao X, Xiaoxia W, Yongrun C, Beifang W, Yue Z, Liaqat S, Shihua C, Liyong C, Yingxin Z (2020) Effects of GS3 and GL3.1 for grain size editing by CRISPR/Cas9 in rice. Rice Sci 27(5):405–413. https://doi.org/10.1016/j.rsci.2019.12.010
Zeng D, Qian Q, Dong G, Zhu X, Dong F, Teng S, Guo L, Cao L, Cheng S, Xiong Z (2003) Development of isogenic lines of morphological markers in indica rice. J Integr Plant Biol 45(9):1116–1120
Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J, Zhang H (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci 109(52):21534–21539. https://doi.org/10.1073/pnas.1219776110
Zhang W, Sun P, He Q, Shu F, Wang J, Deng H (2013) Fine mapping of GS2, a dominant gene for big grain rice. Crop J. https://doi.org/10.1016/j.cj.2013.10.003
Zhang GH, Li SY, Wang L, Ye WJ, Zeng DL, Rao YC, Peng YL, Hu J, Yang YL, Xu J, Ren DY, Gao ZY, Zhu L, Dong GJ, Hu XM, Yan MX, Guo LB, Li CY, Qian Q (2014) LSCHL4 from japonica cultivar, which is allelic to NAL1, increases yield of indica super rice 93–11. Mol Plant 7(8):1350–1364. https://doi.org/10.1093/mp/ssu055
Zhang J, Zhou X, Yan W, Zhang Z, Lu L, Han Z, Zhao H, Liu H, Song P, Hu Y, He Q, Guo S, Gao G, Wang G, Xing Y, (2015) Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice. New Phytol 208:1056–1066. https://doi.org/10.1111/nph.13538
Zhang L, Yu H, Ma B, Liu GF, Wang JJ, Wang JM, Gao RC, Li JJ, Liu JY, Xu J, Zhang YY, Li Q, Huang XH, Xu J, Li JL, Qian Q, Han B, He ZH, Li JY (2017a) A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice. Nat Commun 8:14789. https://doi.org/10.1038/ncomms14789
Zhang Z, Hu W, Shen G, Liu H, Hu Y, Zhou X, Liu T, Xing Y (2017b) Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions. Sci Rep 7:5388. https://doi.org/10.1038/s41598-017-05873-1
Zhang ZH, Zhu YJ, Wang SL, Fan YY, Zhuang JY (2019b) Importance of the interaction between heading date genes Hd1 and Ghd7 for controlling yield traits in rice. Int J Mol Sci 20(3):516. https://doi.org/10.3390/ijms20030516
Zhang L, Ma B, Bian Z, Li X, Zhang C, Liu J, Li Q, Liu Q, He Z (2020a) Grain size selection using novel functional markers targeting 14 genes in rice. Rice 13:1–16. https://doi.org/10.1186/s12284-020-00427-y
Zhang LL, Li Y, Zheng YP, Wang H, Yang X, Chen JF, Zhou SX, Wang LF, Li XP, Ma XC, Zhao JQ, Pu M, Feng H, Fan J, Zhang JW, Huang YY, Wang WM (2020b) Expressing a target mimic of miR156fhl-3p enhances rice blast disease resistance without yield penalty by improving SPL14 expression. Front Genet 11:327. https://doi.org/10.3389/fgene.2020.00327
Zhang B, Liu H, Qi1 F, Zhang Z, Li Q, Han Z, Xing Y (2019a) Genetic interactions among Ghd7, Ghd8, OsPRR37 and Hd1 contribute to large variation in heading date in rice. Rice 12:48. https://doi.org/10.1186/s12284-019-0314-x
Zhao M, Sun J, Xiao Z, Cheng F, Xu H, Tang L, Chen W, Xu Z, Xu Q (2016) Variations in dense and erect panicle 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China. Breed Sci 66:599–605. https://doi.org/10.1270/jsbbs.16058
Zhao M, Zhao M, Gu S, Sun J, Ma Z, Wang L, Zheng W, Xu Z (2019) DEP1 is involved in regulating the carbon–nitrogen metabolic balance to affect grain yield and quality in rice (Oryza sativa L). PLoS ONE 14(3):e0213504. https://doi.org/10.1371/journal.pone.0213504
Zheng T, Sun J, Zhou S, Chen S, Lu J, Cui S, Tian Y, Zhang H, Cai M, Zhu S, Wu M, Wang Y, Jiang L, Zhai H, Wang H, Wan J (2019) Post transcriptional regulation of Ghd7 protein stability by phytochrome and OsGI in photoperiodic control of flowering in rice. New Phytol 224(1):306–320. https://doi.org/10.1111/nph.16010
Zhou Y, Zhu J, Li Z, Yi C, Liu J, Zhang H, Tang S, Gu M, Liang G (2009) Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication. Genetics 183(1):315–324. https://doi.org/10.1534/genetics.109.102681
Zhu K, Tang D, Yan C, Chi Z, Yu H, Chen J, Liang J, Gu M, Cheng Z (2010) Erect panicle2 encodes a novel protein that regulates panicle erectness in indica rice. Genetics 184(2):343–350. https://doi.org/10.1534/genetics.109.112045
Zhu M, He Y, Zhu M, Ahmad A, Xu S, He Z, Jiang s, Huang J, Li Z, Liu S, Hou X, Zhang Z (2022) ipa1 improves rice drought tolerance at seedling stage mainly through activating abscisic acid pathway. Plant Cell Rep 41(1):221–232. https://doi.org/10.1007/s00299-021-02804-3
Zou J, Zhang S, Zhang W, Li G, Chen Z, Zhai W, Zhao X, Pan X, Xie Q, Zhu L (2006) The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds. Plant J 48:687–698. https://doi.org/10.1111/j.1365-313X.2006.02916.x
Zuo J, Li J (2014) Molecular genetic dissection of quantitative trait loci regulating rice grain size. Annu Rev Genet 48:99–118. https://doi.org/10.1146/annurev-genet-120213-092138
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by J. Huang.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Sen, P., Chatterjee, A., Kumar, D. et al. Genetic and functional mechanisms of yield-related genes in rice. Acta Physiol Plant 46, 29 (2024). https://doi.org/10.1007/s11738-024-03667-3
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11738-024-03667-3