Abstract
Tiller angle plays an essential role in determining plant architecture and yield in rice. In this study, we identified qTAC8c, a major quantitative trait locus (QTL) for tiller angle, through introduced introgression of a segment from Oryza rufipogon BJ-5 into indica ZH8015. The qTAC8c was mapped to a 1469.55-kb region on chromosome 8 with the basis on 8 K chip analysis and map-based cloning, and was further narrowed down to a 76.75-kb region containing eleven open reading frames (ORFs). Sequencing and expression analyzing indicated ORF1 (LOC_Os08g33530) is the causal gene for qTAC8c. A total of ten single nucleotide polymorphism (SNPs) and one insertion were detected in the 4792-bp genome in ORF1 between ZH8015 and NIL-85. ORF1 encodes a TCP family of transcription factors. Meanwhile, two SNPs (SNP5 and SNP6) in the coding region of ORF1 resulted in two amino acid changes (L125F and L180S). Interestingly, SNP1 to SNP7 affected grain traits, especially grain width. Besides, a functional marker S3 was designed to detect promoters of qTAC8c in rice varieties, which could be a useful application for marker-assisted selection (MAS) breeding of plant architecture in rice. This study provides genetic resources for plant architecture and grain size improvement in rice.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8(11):554–560. https://doi.org/10.1016/j.tplants.2003.09.010
Azizi P, Osman M, Hanafi MM, Sahebi M, Rafii MY, Taheri S, Harikrishna JA, Tarinejad AR, Mat Sharani S, Yusuf MN (2019) Molecular insights into the regulation of rice kernel elongation. Crit Rev Biotechnol 39(7):904–923. https://doi.org/10.1080/07388551.2019.1632257
Bai XF, Wu B, Xing YZ (2012) Yield-related QTLs and their applications in rice genetic improvement. J Integr Plant Biol 54(5):300–311. https://doi.org/10.1111/j.1744-7909.2012.01117.x
Barrantes W, Fernández-del-Carmen A, López-Casado G, González Sánchez MÁ, Fernández-Muñoz R, Granell A, Monforte AJ (2014) Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium. Mol Breeding 34:1817–1831. https://doi.org/10.1007/s11032-014-0141-0
Cai YY, Huang LZ, Song YQ, Yuan YD, Xu S, Wang XP, Liang Y, Zhou J, Liu GF, Li JY, Wang WG, Wang YH (2023) LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice. Plant Biotechnol J 21(6):1217–1228. https://doi.org/10.1111/pbi.14031
Chen YN, Fan XR, Song WJ, Zhang YL, Xu GH (2012) Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1. Plant Biotechnol J 10(2):139–149. https://doi.org/10.1111/j.1467-7652.2011.00637.x
Ding C, Lin X, Zuo Y, Yu Z, Baerson SR, Pan Z, Zeng R, Song Y (2021) Transcription factor OsbZIP49 controls tiller angle and plant architecture through the induction of indole-3-acetic acid-amido synthetases in rice. Plant J 108(5):1346–1364. https://doi.org/10.1111/tpj.15515
Dong HJ, Zhao H, Xie WB, Han ZM, Li GW, Yao W, Bai XF, Hu Y, Guo ZL, Lu K, Yang L, Xing YZ (2016) A novel tiller angle gene, TAC3, together with TAC1 and D2 largely determine the natural variation of tiller angle in rice cultivars. PLoS Genet 12(11):e1006412. https://doi.org/10.1371/journal.pgen.1006412
Harmoko R, Yoo JY, Ko KS, Ramasamy NK, Hwang BY, Lee EJ, Kim HS, Lee KJ, Oh DB, Kim DY, Lee S, Li Y, Lee SY, Lee KO (2016) N-glycan containing a core alpha1,3-fucose residue is required for basipetal auxin transport and gravitropic response in rice (Oryza sativa). New Phytol 212(1):108–122. https://doi.org/10.1111/nph.14031
He JW, Shao GN, Wei XJ, Huang FL, Sheng ZH, Tang SQ, Hu PS (2017) Fine mapping and candidate gene analysis of qTAC8, a major quantitative trait locus controlling tiller angle in rice (Oryza sativa L.). PLoS ONE 12(5):e0178177. https://doi.org/10.1371/journal.pone.0178177
Hu M, Lv SW, Wu WG, Fu YC, Liu FX, Wang BB, Li WG, Gu P, Cai HW, Sun CQ, Zhu ZF (2018) The domestication of plant architecture in African rice. Plant J 94(4):661–669. https://doi.org/10.1111/tpj.13887
Hu Y, Li SL, Fan XW, Song S, Zhou X, Weng XY, Xiao JH, Li XH, Xiong LZ, You AQ, Xing YZ (2020) OsHOX1 and OsHOX28 redundantly shape rice tiller angle by reducing HSFA2D expression and auxin content. Plant Physiol 184(3):1424–1437. https://doi.org/10.1104/pp.20.00536
Huang XH, Yang SH, Gong JY, Zhao Q, Feng Q, Zhan QL, Zhao Y, Li WJ, Cheng BY, Xia JH, Chen N, Huang T, Zhang L, Fan DL, Chen JY, Zhou CC, Lu YQ, Weng QJ, Han B (2016) Genomic architecture of heterosis for yield traits in rice. Nature 537(7622):629–633. https://doi.org/10.1038/nature19760
Huang LZ, Wang WG, Zhang N, Cai YY, Liang Y, Meng XB, Yuan YD, Li JY, Wu DX, Wang YH (2021) LAZY2 controls rice tiller angle through regulating starch biosynthesis in gravity-sensing cells. New Phytol 231(3):1073–1087. https://doi.org/10.1111/nph.17426
Hussain K, Zhang YX, Anley W, Riaz A, Abbas A, Rani MH, Wang H, Shen XH, Cao LY, Cheng SH (2020) Association mapping of quantitative trait loci for grain size in introgression line derived from Oryza rufipogon. Rice Sci 27(3):246–254. https://doi.org/10.1016/j.rsci.2020.04.007
Jiang JH, Tan LB, Zhu ZF, Fu YC, Liu FX, Cai HW, Sun CQ (2012) Molecular evolution of the TAC1 gene from rice (Oryza sativa L.). J Genet Genomics 39(10):551–560. https://doi.org/10.1016/j.jgg.2012.07.011
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40(11):1365–1369. https://doi.org/10.1038/ng.247
Li PJ, Wang YH, Qian Q, Fu ZM, Wang M, Zeng DL, Li BH, Wang XJ, Li JY (2007) LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17(5):402–410. https://doi.org/10.1038/cr.2007.38
Li MR, Li XX, Zhou ZJ, Wu PZ, Fang MC, Pan XP, Lin QP, Luo WB, Wu GJ, Li HQ (2016) Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci 7:377. https://doi.org/10.3389/fpls.2016.00377
Li N, Xu R, Li YH (2019) Molecular networks of seed size control in plants. Annu Rev Plant Biol 70:435–463. https://doi.org/10.1146/annurev-arplant-050718-095851
Li H, Sun HY, Jiang JH, Sun XY, Tan LB, Sun CQ (2020a) TAC4 controls tiller angle by regulating the endogenous auxin content and distribution in rice. Plant Biotechnol J 19:64–73. https://doi.org/10.1111/pbi.13440
Li Y, Li JL, Chen ZH, Wei Y, Qi YH, Wu CY (2020b) OsmiR167a-targeted auxin response factors modulate tiller angle via fine-tuning auxin distribution in rice. Plant Biotechnol J 18(10):2015–2026. https://doi.org/10.1111/pbi.13360
Liang QZ, Wen DQ, Xie JH, Liu LQ, Wei YZ, Wang YC, Shi SY (2015) A rapid and effective method for silver staining of PCR products separated in polyacrylamide gels. Electrophoresis 35(17):2520–2523. https://doi.org/10.1002/elps.201400182
Liao ZG, Yu H, Duan JB, Yuan K, Yu CJ, Meng XB, Kou LQ, Chen MJ, Jing YH, Liu GF, Smith SM, Li JY (2019) SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice. Nat Commun 10(1):2738. https://doi.org/10.1038/s41467-019-10667-2
Liu C, Ma T, Yuan DY, Zhou Y, Long Y, Li ZW, Dong ZY, Duan MJ, Yu D, Jing YZ, Bai XY, Wang YB, Hou QC, Liu SS, Zhang JS, Chen SY, Li DY, Liu X, Li ZK, Wang WS, Li JP, Wei X, Ma B, Wan XY (2022) The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice. Plant Biotechnol J 20(8):1470–1486. https://doi.org/10.1111/pbi.13825
Luan YX, Wang BS, Zhao Q, Ao GM, Yu JJ (2010) Ectopic expression of foxtail millet zip-like gene, SiPf40, in transgenic rice plants causes a pleiotropic phenotype affecting tillering, vascular distribution and root development. Sci China Life Sci 53(12):1450–1458. https://doi.org/10.1007/s11427-010-4090-5
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
Mao CZ, Ding WN, Wu YR, Yu J, He XW, Shou HX, Wu P (2007) Overexpression of a NAC-domain protein promotes shoot branching in rice. New Phytol 176(2):288–298. https://doi.org/10.1111/j.1469-8137.2007.02177.x
Meyer RS, Purugganan MD (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14(12):840–852. https://doi.org/10.1038/nrg3605
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
Okamura M, Hirose T, Hashida Y, Ohsugi R, Aoki N (2015) Suppression of starch synthesis in rice stems splays tiller angle due to gravitropic insensitivity but does not affect yield. Funct Plant Biol 42(1):31–41. https://doi.org/10.1071/FP14159
Pan XW, Li YC, Zhang HW, Liu WQ, Dong Z, Liu LC, Liu SX, Sheng XN, Min J, Huang RF, Li XX (2022) The chloroplast-localized protein LTA1 regulates tiller angle and yield of rice. Crop J 10(4):952–961. https://doi.org/10.1016/j.cj.2021.10.005
Rogers SO, Bendich AJ (1985) Extraction of D N A from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5(2):69–76. https://doi.org/10.1007/BF00020088
Sang DJ, Chen DQ, Liu GF, Liang Y, Huang LZ, Meng XB, Chu JF, Sun XH, Dong GJ, Yuan YD, Qian Q, Li JY, Wang YH (2014) Strigolactones regulate rice tiller angle by attenuating shoot gravitropism through inhibiting auxin biosynthesis. PNAS 111(30):11199–11204. https://doi.org/10.1073/pnas.1411859111
Shi CL, Dong NQ, Guo T, Ye WW, Shan JX, Lin HX (2020) A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway. Plant J 103:1174–1188. https://doi.org/10.1111/tpj.14793
Springer N (2010) Shaping a better rice plant. Nat Genet 42(6):475–476. https://doi.org/10.1038/ng0610-475
Sun B, Zhan XD, Lin ZC, Wu WX, Yu P, Zhang YX, Sun LP, Cao LY, Cheng SH (2017) Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.). Theoret Appl Genet 130(1):247–258. https://doi.org/10.1007/s00122-016-2787-y
Tan LB, Li XR, Liu FX, Sun XY, Li CG, Zhu ZF, Fu YC, Cai HW, Wang XK, Xie DX, Sun CQ (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40(11):1360–1364. https://doi.org/10.1038/ng.197
Teichmann T, Muhr M (2015) Shaping plant architecture. Front Plant Sci 6:233. https://doi.org/10.3389/fpls.2015.00233
Wang YH, Li JY (2005) The plant architecture of rice (Oryza sativa). Plant Mol Biol 59(1):75–84. https://doi.org/10.1007/s11103-004-4038-x
Wang YH, Li JY (2008) Molecular basis of plant architecture. Annu Rev Plant Biol 59(1):253–279. https://doi.org/10.1146/annurev.arplant.59.032607.092902
Wang L, Xu YY, Zhang C, Ma QB, Joo SH, Kim SK, Xu ZH, Chong K (2008) OsLIC, a novel CCCH-type zinc finger protein with transcription activation, mediates rice architecture via brassinosteroids signaling. PLoS ONE 3(10):e3521. https://doi.org/10.1371/journal.pone.0003521
Wang SS, Wu K, Qian Q, Liu Q, Li Q, Pan YJ, Ye YF, Liu XY, Wang J, Zhang JQ, Li S, Wu YJ, Fu XD (2017) Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Res 27(9):1142–1156. https://doi.org/10.1038/cr.2017.98
Wang B, Smith SM, Li JY (2018) Genetic regulation of shoot architecture. Annu Rev Plant Biol 69:437–468. https://doi.org/10.1146/annurev-arplant-042817-040422
Wang CC, Yu H, Huang J, Wang WS, Faruquee M, Zhang F, Zhao XQ, Fu BY, Chen K, Zhang HL, Tai SS, Wei C, McNally KL, Alexandrov N, Gao XY, Li J, Li ZK, Xu JL, Zheng TQ (2020) Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0. Plant Biotechnol J 18(1):1–3. https://doi.org/10.1111/pbi.13215
Wang H, Tu RR, Sun LP, Wang DF, Ruan ZY, Zhang Y, Peng ZQ, Zhou XP, Fu JL, Liu QE, Wu WX, Zhan XD, Shen XH, Zhang YX, Cao LY, Cheng SH (2022a) Tiller Angle Control 1 Is essential for the dynamic changes in plant architecture in rice. Int J Mol Sci 23(9):4997. https://doi.org/10.3390/ijms23094997
Wang WG, Gao HB, Liang Y, Li JY, Wang YH (2022b) Molecular basis underlying rice tiller angle: current progress and future perspectives. Mol Plant 15(1):125–137. https://doi.org/10.1016/j.molp.2021.12.002
Wang H, Tu RR, Ruan ZY, Chen C, Peng ZQ, Zhou XP, Sun LP, Hong YB, Chen DB, Liu QE, Wu WX, Zhan XD, Shen XH, Zhou ZP, Cao LY, Zhang YX, Cheng SH (2023) Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture. Theoret Appl Genet 136(7):160. https://doi.org/10.1007/s00122-023-04404-z
Wen X, Sun L, Chen Y, Xue P, Yang Q, Wang B, Yu N, Cao Y, Zhang Y, Gong K, Wu W, Chen D, Cao L, Cheng S, Zhang Y, Zhan X (2020) Rice dwarf and low tillering 10 (OsDLT10) regulates tiller number by monitoring auxin homeostasis. Plant Sci 297:110502. https://doi.org/10.1016/j.plantsci.2020.110502
Wing RA, Purugganan MD, Zhang QF (2018) The rice genome revolution: from an ancient grain to Green Super Rice. Nat Rev Genet 19:505–517. https://doi.org/10.1038/s41576-018-0024-z
Wu XR, Tang D, Li M, Wang KJ, Cheng ZK (2013) Loose plant architecture1, an indeterminate domain protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol 161(1):317–329. https://doi.org/10.1104/pp.112.208496
Wu YZ, Zhao SS, Li XR, Zhang BS, Jiang LY, Tang YY, Zhao J, Ma X, Cai HW, Sun CQ, Tan LB (2018) Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice. Nat Commun 9(1):4157. https://doi.org/10.1038/s41467-018-06509-2
Xu M, Zhu L, Shou HX, Wu P (2005) A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant Cell Physiol 46(10):1674–1681. https://doi.org/10.1093/pcp/pci183
Yoshihara T, Iino M (2007) Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways. Plant Cell Physiol 48(5):678–688. https://doi.org/10.1093/pcp/pcm042
Yu BS, Lin ZW, Li HX, Li XJ, Li JY, Wang YH, Zhang X, Zhu ZF, Zhai WX, Wang XK, Xie DX, Sun CQ (2007) TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J 52(5):891–898. https://doi.org/10.1111/j.1365-313X.2007.03284.x
Zhang YX, Wang Q, Jiang L, Liu LL, Wang BX, Shen YY, Cheng XN, Wan JM (2011) Fine mapping of qSTV11KAS, a major QTL for rice stripe disease resistance. Theoret Appl Genet 122(8):1591–1604. https://doi.org/10.1007/s00122-011-1557-0
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 JL, Li JM, Qian Q, Han B, He ZH, Li JY (2017) 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 N, Yu H, Yu H, Cai YY, Huang LZ, Xu C, Xiong GS, Meng XB, Wang JY, Chen HF, Liu GF, Jing YH, Yuan YD, Liang Y, Li SJ, Smith SM, Li JY, Wang YH (2018) A core regulatory pathway controlling rice tiller angle mediated by the LAZY1-dependent asymmetric distribution of auxin. Plant Cell 30:1461–1475. https://doi.org/10.1105/tpc.18.00063
Zhang WF, Tan LB, Sun HY, Zhao XH, Liu FX, Cai HW, Fu YC, Sun XY, Gu P, Zhu ZF, Sun CQ (2019) Natural variations at TIG1 encoding a TCP transcription factor contribute to plant architecture domestication in rice. Mol Plant 12:1075–1089. https://doi.org/10.1016/j.molp.2019.04.005
Zhao DD, Jang YH, Farooq M, Park JR, Kim EG, Du XX, Jan R, Kim KH, Lee SI, Lee GS, Kim KM (2022) Identification of a major QTL and validation of related genes for tiller angle in rice based on QTL analysis. Int J Mol Sci 23(9):5192. https://doi.org/10.3390/ijms23095192
Acknowledgements
The authors thank professor Wei for providing twenty parental materials.
Funding
This study was supported by Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute (CPSIBRF-CNRRI-202102), Independent project of State Key Laboratory of Rice Biology and Breeding (2020Z2KT10201), and Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-CNRRI).
Author information
Authors and Affiliations
Contributions
YF performed most of the experiments, analyzed the data, and wrote the manuscript; YZ constructed the populations; HW, XP, and HC collected the phenotypes, and revised this manuscript; WL, QL, WW, and YF conducted analysis of 8 K chip result; XZ, SC, LC, and YZ designed the experiments, and supervised and reviewed the manuscript. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
All authors declare that they have no conflict of interest.
Additional information
Handling Editor: Weiwei Qi.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
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
Fan, Y., Chen, H., Wang, H. et al. Fine Mapping of Major qTAC8c for Tiller Angle in Oryza rufipogon. J Plant Growth Regul (2024). https://doi.org/10.1007/s00344-024-11293-z
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00344-024-11293-z