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Fine Mapping of Inflorescence Pruning Node Gene in Tomato (Solanum lycopersicum) Based on BSA-seq Technique |
SHI Hai-Lin1, ZHANG Dan-Dan1, GAO Qian4, YOU Yuan-Yuan1, SHU Jin-Shuai5, WANG Shuai1,2,3*, MAO Xiu-Jie1,2,3 |
1 College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China; 2 Hebei Key Laboratory of Characteristic Horticultural Germplasm Mining and Innovative Utilization, Qinhuangdao 066004, China; 3 Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Qinhuangdao 066004, China; 4 Changli Institute of Pomology, Hebei Academy of Agricultural and Forestry Sciences, Changli 066000, China; 5 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China |
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Abstract The number of main stem flowers affects the yield of self-pruning tomato (Solanum lycopersicum). In order to locate the genes associated with inflorescence pruning node, a fine mapping was carried out for laying a foundation for gene cloning and functional analysis and providing evidences for the analysis of regulation mechanism. In this study, one F2 population was constructed from the cross between AXF (low nodal self-pruning tomato strain) and GXF (nodal self-pruning tomato strain) , and linkage analysis and gene localization were performed by bulked segregant analysis sequencing (BSA-seq) and molecular marker. The results showed that the associated region from 47.56~47.59 Mb was located on chromosome 2 with the size of 25 497 bp, containing 3 candidate genes (thiosulfate sulfurtransferase 18 (TST18) (GenBank No. XM_004232452.4), MLO-like protein 4 (MLO4) (GenBank No. XM_019212390.2) and 26S proteasome non- ATPase regulatory subunit 4 (PSMD4) (GenBank No. XM_010318126.3)). 118 InDel (insertion-deletion)/ CAPS (cleaved amplified polymorphism sequences)/dCAPS (derived CAPS) primers were designed for fine mapping and a dCAPS14 molecular maker closely linked with candidate gene PSMD4 was finally delimited by further analysis. qRT-PCR analysis showed that the relative expression of the candidate gene was significantly different between AXF and GXF. The PSMD4 was involved in ubiquitin-proteasome system mediated protein degradation and served as key candidate gene. PSMD4 might play an important role in the controlling of inflorescence pruning node. These results had a significance in marker-assisted self-pruning tomato breeding for ideal architecture with easy cultivation.
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Received: 22 January 2023
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Corresponding Authors:
*wangshuai101og@126.com
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[1] 陈贤, 王其刚, 关文灵, 等 . 2007. 番茄品系产量的逐步回归分析[J]. 北方园艺 , 31(3): 8-9. (Chen X, Wang Q G, Guan W L, et al.2007. Stepwise regression analysis of tomato strain yield[J]. Northern Horticulture, 31(3): 8-9.) [2] 杜海东, 游茜, 李毅丰, 等 . 2022. 基于重测序的 3 个自封顶番茄品系基因组变异检测分析[J]. 分子植物育种, 20(03): 756-764. (Du H D, You X, Li Y F, et al.Genome variation detection and analysis of three self-pruning to‐ mato lines based on resequencing[J]. Molecular Plant Breeding, 20(03): 756-764.) [3] 杜敏敏, 周明, 邓磊, 等 . 2017. 番茄分子育种现状与展望-从基因克隆到品种改良[J]. 园艺学报, 44(03): 581-600. (Du M M, Zhou M, Deng L, et al.2017. Current status and prospects on tomato molecular breeding-from gene cloning to cultivar improvement[J]. Acta Horticulturae Sinica, 44(03): 581-600.) [4] 李景富 .2011. 中国番茄育种学[M]. 北京: 中国农业出版社, pp. 255-263. (Li J F.Chinese tomato breeding[M]. Chi‐ na Agriculture Press, Beijing, China, pp. 255-263.) [5] 毛秀杰, 王帅, 王宇, 等 . 2018. 番茄封顶花序节位的遗传差异及 SSR 分子标记研究[J]. 北方园艺, 42(21): 13-16. (Mao X J, Wang S, Wang Y, et al.2018. Genetic differ‐ ence of plant type characteristics and SSR markers asso‐ ciated with pruning inflorescence number of two self- pruning cultivar tomatoes[J]. Northern Horticulture, 42(21): 13-16.) [6] 倪晓琦, 陈锡威, 金晓锋 . 2022. E3 泛素连接酶接头蛋白 Ke‐ap1 的研究进展[J]. 生物化学与生物物理进展, 49(02): 328-348. (Ni X Q, Chen X W, Jin X F.2022. Research progress of E3 ubiquitin ligase linker protein Keap1[J]. Progress in Biochemistry and Biophysics, 49(02): 328-348.) [7] 祁世明, 梁燕 . 2020. 番茄 SELF-PRUNING 基因家族及株形调控功能研究进展[J]. 园艺学报, 47(09): 1705-1714. (Qi S M, Liang Y.2020. Advances in research of the SELF-PRUNING gene family and plant architecture regulatory functions in tomato[J]. Acta Horticultural Si‐ nica, 47(09): 1705-1714.) [8] 孙亚莉, 赵婷婷, 杨欢欢, 等 . 2019. 番茄抗叶霉病基因 Cf-12 定位及候选基因分析[J]. 分子植物育种, 17(18): 5910-5917. (Sun Y L, Zhao T T, Yang H H, et al.Cf-12 resis‐ tance gene localization and candidate gene analysis of tomato[J]. Molecular Plant Breeding, 17(18): 5910-5917.) [9] Altschul S F, Madden T L, Schäffer A A, et al.1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs[J]. Nucleic Acids Research, 25(17): 3389-3402. [10] Barbarian M, Asadi-Gharneh H A, Golabadi M.2018. Factor analysis, stepwise regression and path coefficient analy‐ ses of yield, yield-associated traits, and fruit quality in tomato[J]. International Journal of Vegetable Science, 25(5): 1-12. [11] Bradley D, Ratcliffe O, Vincent C, et al.1997. Inflorescence commitment and architecture in Arabidopsis[J]. Science, 275(5296): 80-83. [12] Carmel-Goren L, Liu Y S, Lifschitz E, Zamir D.2003. The SELF-PRUNING gene family in tomato[J]. Plant Mo‐ lecular Biology, 52(6): 1215-1222. [13] Chen L Y, Bernhardt A, Lee J H, et al.2015. Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases[J]. Molecular Plant, 8(2): 242-250. [14] Cheng M Z, Meng F Y, Mo F L, et al.2022. Slym1 control the color etiolation of leaves by facilitating the decomposi‐ tion of chlorophyll in tomato[J]. Plant Science, 324(11): 457-468. [15] Cingolani P, Platts A, Wang L L, et al.2012. A program for an‐ notating and predicting the effects of single nucleotide polymorphisms, SnpEff[J]. Fly, 6(2): 80-92. [16] Cloer E W, Siesser P F, Cousins E M, et al.2018. p62-depen‐ dent phase separation of patient-derived KEAP1 muta‐ tions and NRF2[J]. Molecular and Cellular Biology, 38(22): e00644-17. [17] Dai D Y, Wang L, Zhang JM, et al.2022. Primary mapping and analysis of the CmARM14 candidate gene for ma‐ ture fruit abscission in melon[J]. Agronomy, 12(12): 3117-3132. [18] Eliezer L, Tamar E, Alexander R, et al.2006. The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli[J]. Proceedings of the National Academy of Sci‐ ences of the USA, 103(16): 6398-6403. [19] Fekih R, Takagi H, Tamiru M, et al.2013. MutMap+ : Genetic mapping and mutant identification without crossing in rice[J]. PLOS ONE, 8(7): e68529. [20] Fridman E, Liu Y S, Carmel-Goren L, et al.2002. Two tightly linked QTLs modify tomato sugar content via different physiological pathways[J]. Molecular Genetics and Ge‐ nomics, 266(5): 821-826. [21] Hill J T, Demarest B L, Bisgrove B W, et al.2013. MMAPPR: Mutation mapping analysis pipeline for pooled RNA-seq[J]. Genome Research, 23(4): 687-697. [22] Jiang K, Liberatore K L, Park S J, et al.2013. Tomato yield heterosis is triggered by a dosage sensitivity of the flori‐gen pathway that fine-tunes shoot architecture[J]. PLoS Genetics, 9(12): e1004043. [23] Kinet J M.1977. Effect of light conditions on the develop‐ ment of the inflorescence in tomato[J]. Scientia Horti‐ culturae, 6(1): 15-26. [24] Li H, Durbin R.2009. Fast and accurate short read alignment with burrows-wheeler transform[J]. Bioinformatics, 25(14): 1754-1760. [25] Li W, Dai L Y, Wang G L.2012. PUB13, a U-box/ARM E3 li‐ gase, regulates plant defense, cell death, and flowering time[J]. Plant Signaling and Behavior, 7(8): 898-900. [26] Lifschitz E, Ayre B G, Eshed Y.2014. Florigen and anti-flori‐ gen-a systemic mechanism for coordinating growth and termination in flowering plants[J]. Frontiers in Plant Sci‐ ence, 5(465): 1-14. [27] MacAlister C A, Park S J, Jiang K, et al.2012. Synchroniza‐ tion of the flowering transition by the tomato TERMI‐ NATING FLOWER gene[J]. Nature Genetics, 44(12): 1393-1398. [28] Marincs F, Nagy T, Miró K, et al.2017. Large-scale amplicon sequencing of the SP3D gene responsible for fruit-yield heterosis in tomato[J]. Plant Gene, 9(3): 45-49. [29] McKenna A, Hanna M, Banks E, et al.2010. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data[J]. Genome Re‐ search, 20(9): 1297-1303. [30] Michelmore R W, Paran I, Kesseli R V.1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating popula‐ tions[J]. Proceedings of the National Academy of Sci‐ ences of the USA, 88(21): 9828-9832. [31] Molinero-Rosales N, Jamilena M, Zurita S, et al.1999. FAL‐ SIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meri‐ stem identity[J]. The Plant Journal, 20(6): 685-693. [32] Molinero-Rosales N, Latorre A, Jamilena M, et al.2004. SIN‐ GLE FLOWER TRUSS regulates the transition and maintenance of flowering in tomato[J]. Planta, 218(3), 427-434. [33] Park S J, Jiang K, Tal L, et al.2014. Optimization of crop pro‐ ductivity in tomato using induced mutations in the flori‐ gen pathway[J]. Nature Genetics, 46(12): 1337-1342. [34] Porebski S, Bailey L G, Baum B R.1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components[J]. Plant Molecular Biology Reporter, 15(1): 8-15. [35] Ruangrak E, Su X M, Huang Z J, et al.2018. Fine mapping of a major QTL controlling early flowering in tomato us‐ ing QTL-seq[J]. Canadian Journal of Plant Science, 98(3): 672-682. [36] Samach A, Lotan H.2007. The transition to flowering in to‐mato[J]. Plant Biotechnology, 24(1): 71-82. [37] Shalit A, Rozman A, Goldshmidt A, et al.2009. The flower‐ ing hormone florigen functions as a general systemic regulator of growth and termination[J]. Proceedings of the National Academy of Sciences of the USA, 106(20): 8392-8397. [38] Soyk S, Müller N A, Park S J, et al.2017. Variation in the flowering gene SELF PRUNING 5G promotes day-neu‐ trality and early yield in tomato[J]. Nature Genetics, 49(1): 162-168. [39] Takagi H, Abe A, Yoshida K, et al.2013. QTL ‐ seq: Rapid mapping of quantitative trait loci in rice by whole ge‐ nome resequencing of DNA from two bulked popula‐ tions[J]. The Plant Journal, 74(1): 174-83. [40] Wickland D P, Hanzawa Y.2015. The flowering locus T/TER‐ MINAL flower 1 gene family: Functional evolution and molecular mechanisms[J]. Molecular Plant, 8(7): 983-997. [41] Zhou S, Hu Z, Li F, et al.2019. Overexpression of SlOFP20 affects floral organ and pollen development[J]. Horticul‐ ture Research, 6(1): 154-169. [42] Zhu C M, Peng Q, Fu D B, et al.2018. The E3 ubiquitin li‐ gase HAF1 modulates circadian accumulation of EAR‐ LY FLOWERING3 to control heading date in rice under long-day conditions[J]. The Plant Cell, 30(10): 2352-2367. |
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