Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- AFLP:
-
Amplified fragment length polymorphism
- BC:
-
Back cross
- BILs:
-
Backcross inbred lines
- CAPS:
-
Cleaved amplified polymorphic sequences
- GDP:
-
Gross domestic product
- GPP:
-
Grain number per panicle
- HD:
-
Heading date
- MABB:
-
Marker assisted backcross breeding
- MAP:
-
Marker assisted gene pyramiding
- MAS:
-
Marker assisted selection
- MDP:
-
Marker data point
- mha:
-
Million hector
- NILs:
-
Near isogenic lines
- PH:
-
Plant height
- QTL:
-
Quantitative trait loci
- RAPD:
-
Randomly amplified polymorphic DNA
- RFLP:
-
Restriction fragment length polymorphism
- RILs:
-
Recombinant inbred lines
- SCAR:
-
Sequence characterized amplified region
- SNP:
-
Single-nucleotide polymorphism
- SPP:
-
Spikelet per panicle
- SSR:
-
Simple sequence repeat
- STS:
-
Sequence-tagged site
- UTR:
-
Untranslated region
- VNTR:
-
Variable number of tandem repeats
References
Ando T, Yamamoto T, Shimizu T et al (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890. https://doi.org/10.1007/s00122-008-0722-6
Anyaoha CO, Fofana M, Gracen V et al (2019) Introgression of two drought QTLs into FUNAABOR-2 early generation backcross progenies under drought stress at reproductive stage. Rice Sci 26:32–41. https://doi.org/10.1016/j.rsci.2018.04.006
Arite T, Iwata H, Ohshima K et al (2007) DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice. Plant J 51:1019–1029. https://doi.org/10.1111/j.1365-313X.2007.03210.x
Arite T, Umehara M, Ishikawa S et al (2009) d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant Cell Physiol 50:1416–1424. https://doi.org/10.1093/pcp/pcp091
Arunakumari K, Durgarani CV, Satturu V et al (2016) Marker-assisted pyramiding of genes conferring resistance against bacterial blight and blast diseases into Indian rice variety MTU1010. Rice Sci 23:306–316. https://doi.org/10.1016/j.rsci.2016.04.005
Ashikari M, Matsuoka M (2006) Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci 11:344–350. https://doi.org/10.1016/j.tplants.2006.05.008
Ashikari M, Sakakibara H, Lin S et al (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745. https://doi.org/10.1126/science.1113373
Ashikari M, Wu J, Yano M et al (1999) Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the α-subunit of GTP-binding protein. Proc Natl Acad Sci USA 96:10284–10289
Babu R, Nair SK, Prasanna BM, Gupta HS (2004) Integrating marker-assisted selection in crop breeding—prospects and challenges. Curr Sci 87:14
Balachiranjeevi CH, Naik B, Kumar A et al (2018) Marker-assisted pyramiding of two major, broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B. PLoS ONE 13:e0201271. https://doi.org/10.1371/journal.pone.0201271
Bernier J, Kumar A, Venuprasad R et al (2009) Characterization of the effect of a QTL for drought resistance in rice, qtl12. 1, over a range of environments in the Philippines and eastern India. Euphytica 166:207–217
Bishwas N, Sharma M, Hasan A et al (2016) Improvement of rice crop by marker-assisted backcross method. Magnesium 03:8
Brambilla V, Fornara F (2013) Molecular control of flowering in response to day length in rice: control of flowering in rice. J Integr Plant Biol 55:410–418. https://doi.org/10.1111/jipb.12033
Chakraborty S, Zeng ZB (2011) QTL mapping for days to flowering under drought condition in rice (Oryza sativa L.) genome. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39:58–63
Cho YC (2003) QTLs analysis of yield and its related traits in wild rice relative Oryza rufipogon. Treat Crop Res 4:19–29
Chukwu SC, Rafii MY, Ramlee SI et al (2019) Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). Biotechnol Biotechnol Equip 33:440–455. https://doi.org/10.1080/13102818.2019.1584054
Cobb JN, Biswas PS, Platten JD (2019) Back to the future: revisiting MAS as a tool for modern plant breeding. Theor Appl Genet 132:647–667. https://doi.org/10.1007/s00122-018-3266-4
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363:557–572. https://doi.org/10.1098/rstb.2007.2170
de Saint Germain A, Clavé G, Badet-Denisot M-A et al (2016) An histidine covalent receptor and butenolide complex mediates strigolactone perception. Nat Chem Biol 12:787–794. https://doi.org/10.1038/nchembio.2147
Dixit S, Yadaw RB, Mishra KK, Kumar A (2017) Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal. Euphytica 213:184. https://doi.org/10.1007/s10681-017-1976-3
Doi K, Izawa T, Fuse T et al (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936. https://doi.org/10.1101/gad.1189604
Donde R, Gupta MK, Gouda G et al (2019a) Computational characterization of structural and functional roles of DREB1A, DREB1B and DREB1C in enhancing cold tolerance in rice plant. Amino Acids 51:839–853
Donde R, Kumar J, Gouda G et al (2019b) Assessment of genetic diversity of drought tolerant and susceptible rice genotypes using microsatellite markers. Rice Sci 26:239–247. https://doi.org/10.1016/j.rsci.2019.01.004
Dreher K, Khairallah M, Ribaut J-M, Morris M (2003) Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT. Mol Breed 11:221–234. https://doi.org/10.1023/A:1022820520673
Fukushima A (2019) Varietal differences in tiller and panicle development determining the total number of spikelets per unit area in rice. Plant Prod Sci 22:192–201. https://doi.org/10.1080/1343943X.2018.1562308
Fuller DQ (2011) Pathways to asian civilizations: tracing the origins and spread of rice and rice cultures. Rice 4:78–92. https://doi.org/10.1007/s12284-011-9078-7
Gao Z, Qian Q, Liu X et al (2009) Dwarf 88, a novel putative esterase gene affecting architecture of rice plant. Plant Mol Biol 71:265–276. https://doi.org/10.1007/s11103-009-9522-x
Gao H, Jin M, Zheng X-M et al (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. PNAS 111:16337–16342. https://doi.org/10.1073/pnas.1418204111
Gomez MS, Kumar SS, Jeyaprakash P et al (2006) Mapping QTLs linked to physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.) in the target environment. Am J Biochem Biotechnol 2:161–169
Gouda G, Gupta MK, Donde R et al (2019) Computational approach towards understanding structural and functional role of cytokinin oxidase/dehydrogenase 2 (CKX2) in enhancing grain yield in rice plant. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2019.1597771
Guo S, Xu Y, Liu H et al (2013) The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun 4:1–12. https://doi.org/10.1038/ncomms2542
Guo S, Ku L, Qi J et al (2015) Genetic analysis and major quantitative trait locus mapping of leaf widths at different positions in multiple populations. PLoS ONE 10:e0119095. https://doi.org/10.1371/journal.pone.0119095
Gupta MK, Vadde R, Donde R et al (2018) Insights into the structure–function relationship of brown plant hopper resistance protein, Bph14 of rice plant: a computational structural biology approach. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2018.1462737
Gupta MK, Vadde R, Gouda G et al (2019) Computational approach to understand molecular mechanism involved in BPH resistance in Bt-rice plant. J Mol Graph Model 88:209–220. https://doi.org/10.1016/j.jmgm.2019.01.018
He G, Luo X, Tian F et al (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 16:618–626. https://doi.org/10.1101/gr.4814006
Henry A, Dixit S, Mandal NP et al (2014) Grain yield and physiological traits of rice lines with the drought yield QTL qDTY12.1 showed different responses to drought and soil characteristics in upland environments. Funct Plant Biol 41:1066–1077. https://doi.org/10.1071/FP13324
Hittalmani S, Huang N, Courtois B et al (2003) Identification of QTL for growth—and grain yield-related traits in rice across nine locations of Asia. TAG Theor Appl Genet 107:679–690. https://doi.org/10.1007/s00122-003-1269-1
Hong Z, Ueguchi-Tanaka M, Umemura K et al (2003) A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450. Plant Cell 15:2900–2910. https://doi.org/10.1105/tpc.014712
Hong Z, Ueguchi-Tanaka M, Fujioka S et al (2005) The rice brassinosteroid-deficient dwarf2 Mutant, defective in the rice homolog of arabidopsis DIMINUTO/DWARF1, is rescued by the endogenously accumulated alternative bioactive brassinosteroid, dolichosterone. Plant Cell 17:2243–2254. https://doi.org/10.1105/tpc.105.030973
Hospital F (2005) Selection in backcross programmes. Philos Trans R Soc B Biol Sci 360:1503–1511. https://doi.org/10.1098/rstb.2005.1670
Hospital F, Charcosset A (1997) Marker-assisted Introgression of quantitative trait loci. Genetics 147:1469–1485
Hua JP, Xing YZ, Xu CG et al (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162:1885–1895
Huang X, Qian Q, Liu Z et al (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497. https://doi.org/10.1038/ng.352
Huang X, Zhao Y, Wei X et al (2011) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39. https://doi.org/10.1038/ng.1018
Ikeda K, Ito M, Nagasawa N et al (2007) Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate: APO1 regulates meristem fate in rice. Plant J 51:1030–1040. https://doi.org/10.1111/j.1365-313X.2007.03200.x
Ikeda-Kawakatsu K, Maekawa M, Izawa T et al (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: Characterization of rice APO2/RFL gene. Plant J 69:168–180. https://doi.org/10.1111/j.1365-313X.2011.04781.x
Imai I, Kimball JA, Conway B et al (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
Ishikawa S, Maekawa M, Arite T et al (2005) Suppression of tiller bud activity in tillering dwarf mutants of rice. Plant Cell Physiol 46:79–86. https://doi.org/10.1093/pcp/pci022
Ishimaru K, Hirotsu N, Madoka Y et al (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45:707–711. https://doi.org/10.1038/ng.2612
Jiao Y, Wang Y, Xue D et al (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544. https://doi.org/10.1038/ng.591
Jing Z, Qu Y, Yu C et al (2010) QTL analysis of yield-related traits using an advanced backcross population derived from common wild rice (Oryza rufipogon L). Mol Plant Breed. https://doi.org/10.5376/mpb.2010.01.0001
Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240
Keurentjes JJB, Bentsink L, Alonso-Blanco C et al (2007) Development of a near-isogenic line population of arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics 175:891–905. https://doi.org/10.1534/genetics.106.066423
Khush GS (1999) Green revolution: preparing for the 21st century. Genome 42:10
Kobayashi K, Maekawa M, Miyao A et al (2010) PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice. Plant Cell Physiol 51:47–57. https://doi.org/10.1093/pcp/pcp166
Komatsu M, Maekawa M, Shimamoto K, Kyozuka J (2001) The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development. Dev Biol 231:364–373. https://doi.org/10.1006/dbio.2000.9988
Komiya R, Ikegami A, Tamaki S et al (2008) Hd3a and RFT1 are essential for flowering in rice. Development 135:767–774. https://doi.org/10.1242/dev.008631
Kumar A, Sandhu N, Dixit S et al (2018) Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought. Rice 11:35. https://doi.org/10.1186/s12284-018-0227-0
Lamont SJ, Dekkers JCM, Zhou H (2014) Chapter 11—immunogenetics and the mapping of immunological functions. In: Schat KA, Kaspers B, Kaiser P (eds) Avian immunology, 2nd edn. Academic Press, Boston, pp 205–221
Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399. https://doi.org/10.1104/pp.103.035527
Li S, Qian Q, Fu Z et al (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 F, Liu W, Tang J et al (2010) Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation. Cell Res 20:838–849. https://doi.org/10.1038/cr.2010.69
Li M, Tang D, Wang K et al (2011) Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnol J 9:1002–1013. https://doi.org/10.1111/j.1467-7652.2011.00610.x
Li J, Chu H, Zhang Y et al (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 et al (2013) Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression. Proc Natl Acad Sci USA 110:3167–3172. https://doi.org/10.1073/pnas.1300359110
Liu X, Wei X, Sheng Z et al (2016) Polycomb protein OsFIE2 affects plant height and grain yield in rice. PLoS ONE 11:e0164748. https://doi.org/10.1371/journal.pone.0164748
Luo X, Ji S-D, Yuan P-R et al (2013) QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice. Rice (N Y) 6:33. https://doi.org/10.1186/1939-8433-6-33
Ma X, Cheng Z, Qin R et al (2013) OsARG encodes an arginase that plays critical roles in panicle development and grain production in rice. Plant J 73:190–200. https://doi.org/10.1111/j.1365-313x.2012.05122.x
Ma X, Feng F, Zhang Y et al (2019) A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population. PLoS Genet 15:e1008191. https://doi.org/10.1371/journal.pgen.1008191
Mackill DJ, Ni J (2008) Molecular mapping and marker-assisted selection for major-gene traits in rice. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. World Scientific Publishing Company, USA, pp 137–151
Mishra KK, Vikram P, Yadaw RB et al (2013) qDTY12.1: a locus with a consistent effect on grain yield under drought in rice. BMC Genet 14:12. https://doi.org/10.1186/1471-2156-14-12
Miura K, Ikeda M, Matsubara A et al (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549. https://doi.org/10.1038/ng.592
Morishima H (1984) Species relationships and the search for ancestor. Biol Rice 3–30
Nan J, Feng X, Wang C et al (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
Ohsumi A, Takai T, Ida M et al (2011) Evaluation of yield performance in rice near-isogenic lines with increased spikelet number. Field crops Res 120(1):68–75. https://doi.org/10.1016/j.fcr.2010.08.013
Oladosu Y, Rafii MY, Samuel C et al (2019) Drought resistance in rice from conventional to molecular breeding: a review. Int J Mol Sci. https://doi.org/10.3390/ijms20143519
Ookawa T, Hobo T, Yano M et al (2010) New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield. Nat Commun 1:1–11. https://doi.org/10.1038/ncomms1132
Piao R, Jiang W, Ham T-H et al (2009) Map-based cloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet 119:1497–1506. https://doi.org/10.1007/s00122-009-1151-x
Qi P, Lin Y-S, Song X-J et al (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 Y, Piao R, Shi J et al (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
Ren D, Hu J, Xu Q et al (2018) FZP determines grain size and sterile lemma fate in rice. J Exp Bot 69:4853–4866. https://doi.org/10.1093/jxb/ery264
Semagn K, Bjørnstad Å, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 525(25):2540–2568
Seo H-S, Kim H-Y, Jeong J-Y et al (1995) Molecular cloning and characterization of RGA1 encoding a G protein a subunit from rice (Oryza sativa L. IR-36). Plant Mol Biol 27(6):1119–1131
Septiningsih EM, Prasetiyono J, Lubis E et al (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432. https://doi.org/10.1007/s00122-003-1373-2
Shakiba E, Edwards JD, Jodari F et al (2017) Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS ONE 12:e0172133. https://doi.org/10.1371/journal.pone.0172133
Shamsudin NAA, Swamy BPM, Ratnam W et al (2016) Marker assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219. BMC Genet 17:30. https://doi.org/10.1186/s12863-016-0334-0
Shen L, Courtois B, McNally KL et al (2001) Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theor Appl Genet 103:75–83. https://doi.org/10.1007/s001220100538
Singh VK, Ellur RK, Singh AK et al (2018) Effect of qGN4.1 QTL for grain number per panicle in genetic backgrounds of twelve different mega varieties of rice. Rice 11:8
Smith C, Simpson SP (1986) The use of genetic polymorphisms in livestock improvement. J Anim Breed Genet 103:205–217. https://doi.org/10.1111/j.1439-0388.1986.tb00083.x
Soller M, Beckmann JS (1990) Molecular mapping of quantitative genes. In: Proceedings of the world congress on genetics applied to livestock production 96
Song X-J, Huang W, Shi M et al (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:8
Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–221. https://doi.org/10.1007/s00122-005-0110-4
Suh J-P, Cho Y-C, Won Y-J et al (2015) Development of resistant gene-pyramided japonica rice for multiple biotic stresses using molecular marker-assisted selection. Plant Breed Biotech 3:333–345. https://doi.org/10.9787/PBB.2015.3.4.333
Swamy BPM, Kaladhar K, Ramesha MS et al (2011) Molecular mapping of QTLs for yield and yield-related traits in oryza sativa cv swarna × O. nivara (IRGC81848) backcross population. Rice Sci 18:178–186. https://doi.org/10.1016/S1672-6308(11)60025-5
Tabuchi H, Zhang Y, Hattori S et al (2011) LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems[W]. Plant Cell 23:3276–3287. https://doi.org/10.1105/tpc.111.088765
Taguchi-Shiobara F, Kawagoe Y, Kato H et al (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
Takahashi N (1984) Differentiation of ecotypes in Oryza Sativa L. In: Tsunoda S, Takahashi N (eds) Developments in crop science. Elsevier, Amsterdam, pp 31–67
Tanabe S, Ashikari M, Fujisawa S, Takatsuto S (2005) A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length | plant cell. http://www.plantcell.org/content/17/3/776. Accessed 13 Nov 2019
Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203. https://doi.org/10.1007/BF00223376
Tsai Y-C, Weir NR, Hill K et al (2012) Characterization of genes involved in cytokinin signaling and metabolism from rice1[W][OA]. Plant Physiol 158:1666–1684. https://doi.org/10.1104/pp.111.192765
Varshney RK, Bansal KC, Aggarwal PK et al (2011) Agricultural biotechnology for crop improvement in a variable climate: hope or hype? Trends Plant Sci 16:363–371. https://doi.org/10.1016/j.tplants.2011.03.004
Venuprasad R, Zenna N, Choi I-R, et al (2007) Identification of marker loci associated with tungro and drought tolerance in near-isogenic rice lines derived from IR64/Aday Sel. Int Rice Res Notes
Vikram P, Swamy BM, Dixit S et al (2011) qDTY 1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 12:89
Wan XY, Wan JM, Jiang L et al (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
Wan X, Weng J, Zhai H et al (2008) Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5. Genetics 179(4):2239–2252. https://doi.org/10.1534/genetics.108.089862
Wang P, Xing Y, Li Z, Yu S (2012a) Improving rice yield and quality by QTL pyramiding. Mol Breed 29:903–913. https://doi.org/10.1007/s11032-011-9679-2
Wang S, Wu K, Yuan Q, Liu X et al (2012b) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44(8):950–954
Wang J, Xu H, Li N et al (2015) 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 S-S, Chen R-K, Chen K-Y et al (2017) Genetic mapping of the qSBN7 locus, a QTL controlling secondary branch number per panicle in rice. Breed Sci 67:340–347. https://doi.org/10.1270/jsbbs.17007
Xiao YN, Li XH, George ML et al (2005) Quantitative trait locus analysis of drought tolerance and yield in Maize in China. Plant Mol Biol Rep 23:155–165. https://doi.org/10.1007/BF02772706
Xiao Y, Liu D, Zhang G et al (2017) Brassinosteroids regulate OFP1, a DLT interacting protein, to modulate plant architecture and grain morphology in rice. Front Plant Sci. https://doi.org/10.3389/fpls.2017.01698
Xie X, Song M-H, Jin F et al (2006) Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon. Theor Appl Genet 113:885–894. https://doi.org/10.1007/s00122-006-0348-5
Xie X, Jin F, Song M-H et al (2008) Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa × O. rufipogon cross. Theor Appl Genet 116:613–622. https://doi.org/10.1007/s00122-007-0695-x
Xing YZ, Tang WJ, Xue WY et al (2008) Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice. Theor Appl Genet 116:789–796. https://doi.org/10.1007/s00122-008-0711-9
Xu C, Wang Y, Yu Y et al (2012) Degradation of MONOCULM 1 by APC/CTAD1 regulates rice tillering. Nat Commun 3:750. https://doi.org/10.1038/ncomms1743
Xu H, Zhao M, Zhang Q et al (2016) The DENSE AND ERECT PANICLE 1 (DEP1) gene offering the potential in the breeding of high-yielding rice. Breed Sci 66:659–667. https://doi.org/10.1270/jsbbs.16120
Xue W, Xing Y, Weng X et al (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767. https://doi.org/10.1038/ng.143
Yan JQ, Zhu J, He CX et al (1998) Quantitative trait loci analysis for the developmental behavior of tiller number in rice (Oryza sativa L.). Theor Appl Genet 97:267–274. https://doi.org/10.1007/s001220050895
Yan W-H, Wang P, Chen H-X et al (2011) A Major QTL, Ghd8, Plays Pleiotropic Roles in Regulating Grain Productivity, Plant Height, and Heading Date in Rice. Mol Plant 4:319–330. https://doi.org/10.1093/mp/ssq070
Yano M, Katayose Y, Ashikari M et al (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484. https://doi.org/10.1105/tpc.12.12.2473
Yano K, Ookawa T, Aya K et al (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
Yao R, Wang L, Li Y et al (2018) Rice DWARF14 acts as an unconventional hormone receptor for strigolactone. J Exp Bot 69:2355–2365. https://doi.org/10.1093/jxb/ery014
Yeh S-Y, Chen H-W, Ng C-Y et al (2015) Down-regulation of cytokinin oxidase 2 expression increases tiller number and improves rice yield. Rice (N Y). https://doi.org/10.1186/s12284-015-0070-5
Yoshida A, Ohmori Y, Kitano H et al (2012) ABERRANT SPIKELET AND PANICLE1, encoding a TOPLESS-related transcriptional co-repressor, is involved in the regulation of meristem fate in rice. Plant J 70:327–339. https://doi.org/10.1111/j.1365-313X.2011.04872.x
Yuan S, Wang T, Yin L et al (2013) Cloning and expression of gene responsible for high-tillering dwarf phenotype in indica rice mutant gsor23. Rice Sci 20:320–328. https://doi.org/10.1016/S1672-6308(13)60134-1
Yue B, Cui K, Yu S et al (2006) Molecular marker-assisted dissection of quantitative trait loci for seven morphological traits in rice (Oryza Sativa L.). Euphytica 150:131–139. https://doi.org/10.1007/s10681-006-9101-z
Zhang Y, Luo L, Xu C et al (2006) Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor Appl Genet 113:361–368. https://doi.org/10.1007/s00122-006-0305-3
Zhang Y, Luo L, Liu T et al (2009) Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds. Theor Appl Genet 118:1035–1044. https://doi.org/10.1007/s00122-008-0960-7
Zhang S, Li G, Fang J et al (2010) The interactions among DWARF10, auxin and cytokinin underlie lateral bud outgrowth in rice. J Integr Plant Biol 52:626–638. https://doi.org/10.1111/j.1744-7909.2010.00960.x
Zhang Z, Li J, Yao G et al (2011) Fine mapping and cloning of the grain number per-panicle gene (Gnp4) on chromosome 4 in rice (Oryza sativa L.). Agric Sci China 10:1825–1833. https://doi.org/10.1016/S1671-2927(11)60182-X
Zhang G-H, Li S-Y, Wang L et al (2014) LSCHL4 from japonica cultivar, which Is allelic to NAL1, increases yield of indica super rice 93–11. Mol Plant 7:1350–1364. https://doi.org/10.1093/mp/ssu055
Zhang F, Tang J, Zhou Y et al (2015) Characterization and fine mapping of NGP4c(t), a novel gene controlling the number of grains per panicle in rice. J Genet 94:513–517. https://doi.org/10.1007/s12041-015-0553-6
Zhou Y, Tao Y, Zhu J et al (2017) GNS4, a novel allele of DWARF11, regulates grain number and grain size in a high-yield rice variety. Rice 10:34. https://doi.org/10.1186/s12284-017-0171-4
Zhu Y, Zhang Z, Chen J et al (2019) Fine mapping of qTGW10-20.8, a QTL having important contribution to grain weight variation in rice. Crop J. https://doi.org/10.1016/j.cj.2019.01.006
Zong G, Wang A, Wang L et al (2012) A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.). J Genet Genomics 39:335–350. https://doi.org/10.1016/j.jgg.2012.06.004
Zou J, Chen Z, Zhang S et al (2005) Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.). Planta 222:604–612. https://doi.org/10.1007/s00425-005-0007-0
Zou J, Zhang S, Zhang W et al (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
Funding
The authors acknowledge the Department of Science and Technology (DST), Government of India, New Delhi, for providing financial assistance through Grant number: DST/INSPIRE Fellowship/2013/992 to Inspire Fellow Miss. Gayatri Gouda
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
None.
Ethical statement
This article does not contain any studies with human participants or animals.
Informed consent
This article does not require consent from any individual or organisation.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Gouda, G., Gupta, M.K., Donde, R. et al. Marker-assisted selection for grain number and yield-related traits of rice (Oryza sativa L.). Physiol Mol Biol Plants 26, 885–898 (2020). https://doi.org/10.1007/s12298-020-00773-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12298-020-00773-7