JIA-2022-0308 SlGH9-15通过激素和非生物胁迫响应顺式元件调节番茄果实开裂

doi:10.1016/j.jia.2022.09.013

摘要/Abstract

摘要：

在发育后期，如遇到不适宜的环境条件，果实极易发生开裂。裂果严重影响果实的生产和销售。本研究利用混池转录组测序（BSR- seq）技术发掘到番茄果实开裂的关键调控基因。研究通过BSR-Seq鉴定到与不规则裂果性状相关的两个区域，分别位于第9和第11号染色体，共包含127个候选基因。进一步通过差异表达分析以及在耐裂和易裂番茄中的qRT-PCR分析，筛选到显著差异表达的候选基因SlGH9-15 (Solyc09g010210)。对GH9基因家族进行生物信息学分析，发现20个SlGH9基因被分为3组。系统发育分析表明，SlGH9-15与细胞壁结构相关基因AtGH9B1, AtGH9B6, OsGH9B1和OsGH9B3密切相关。启动子顺式作用元件分析表明，SlGH9-15可被不同激素(乙烯和脱落酸)及非生物胁迫诱导表达。表达模式分析表明，13个SlGH9基因，特别是SlGH9-15在易裂果基因型中高表达，且随着果实发育成熟，表达量逐渐增加，在红熟期表达量达到最大值。此外，与耐裂果番茄相比，易裂果番茄中纤维素酶活性较高，纤维素含量较低，在红熟期两基因型中该基因表达差异更为显著。本研究首次鉴定到SlGH9-15基因，推测为番茄果实开裂的关键调控基因。研究为阐明番茄裂果的分子机制及其复杂的调控网络提供了新视野。

Abstract:

Fruit cracking occurs easily during the late period of fruit development when plants encounter an unsuitable environment, dramatically affecting fruit production and marketing. This study conducted the bulked segregant RNA-Seq (BSR) to identify the key regulatory gene of fruit cracking in tomatoes. BSR-Seq analysis illustrated that two regions associated with irregularly cracking were located on chromosomes 9 and 11, containing 127 candidate genes. Further, through differentially expression analysis and qRT-PCR in cracking-susceptible and cracking-resistant genotypes, the candidate gene SlGH9-15 (Solyc09g010210) with significantly differential expression levels was screened. Bioinformatics analysis of the GH9 gene family revealed that 20 SlGH9 genes were divided into three groups. The phylogenetic analysis showed that SlGH9-15 was closely related to cell wall construction-associated genes AtGH9B1, AtGH9B6, OsGH9B1, and OsGH9B3. The cis-acting elements analysis revealed that SlGH9-15 was activated by various hormones (ethylene and ABA) and abiotic stresses. The expression pattern indicated that 13 SlGH9 genes, especially SlGH9-15, were highly expressed in the cracking-susceptible genotype. Its expression level gradually increased during fruit development and achieved maximum value at the red ripe stage. Additionally, the cracking-susceptible tomato showed higher cellulase activity and lower cellulose content than the cracking-resistant tomato, particularly at the red ripe stage. This study identified SlGH9-15 as a key gene associated with fruit cracking in tomatoes for the first time and gives new insights for understanding the molecular mechanism and complex regulatory network of fruit cracking

Key words: tomato , irregular cracking , BSR-Seq , GH9-15

. JIA-2022-0308 SlGH9-15通过激素和非生物胁迫响应顺式元件调节番茄果实开裂 [J]. Journal of Integrative Agriculture, 2023, 22(2): 447-463.

LIN Hao-wei, WU Zhen, ZHOU Rong, CHEN Bin, ZHONG Zhao-jiang, JIANG Fang-ling.

SlGH9-15 regulates tomato fruit cracking with hormonal and abiotic stress responsiveness cis-elements [J]. Journal of Integrative Agriculture, 2023, 22(2): 447-463.

参考文献

Balbontín C, Ayala H, Bastías R M, Tapia G, Ellena M, Torres C, Yuri J A, Quero-Garcia J, Rios J C, Silva H. 2013. Cracking in sweet cherries: A comprehensive review from a physiological molecular and genomic perspective. Chilean Journal of Agricultural Research, 73, 66–72.
Bargel H, Neinhuis C. 2004. Altered tomato (Lycopersicon esculentum Mill.) fruit cuticle biomechanics of a pleiotropic non ripening mutant. Plant Growth Regulation, 23, 61–75.
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of Royal Statistical Soceity Series Bstatistical Methodology, 57, 289–300.
Cao J K, Jiang W B, Zhao Y M. 2007. Experiment Guidance of Postharvest Physiology and Biochemistry of Fruits and Vegetables. China Light Industry Press, Beijing, China. (in Chinese)
Capel C, Yuste-Lisbona F J, López-Casado G, Angosto T, Cuartero J, Lozano R, Capel J. 2017. Multi-environment QTL mapping reveals genetic architecture of fruit cracking in a tomato RIL Solanum lycopersicum × S. pimpinellifolium population. Theoretical & Applied Genetics, 130, 213–222.
Chapman M H, Bonnet J, Grivet L, Lynn J, Graham N, Smith R, Sun G P, Walley P G, Poole M, Causse M, King G J, Baxter C, Seymour G B. 2012. High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus. Plant Physiology, 159, 1644–1657.
Chen B, Wu Z, Wen J Q, Lin H W, Yu L, Xue L Z, Zhou R, Jiang F L. 2021. QTL mapping and candidate gene analysis for irregular fruit dehiscence traits in tomato. Journal of Horticulture, 48, 1329–1339.
Considine J, Brown K. 1981. Physical aspects of fruit growth: Theoretical analysis of distribution of surface growth forces in relation to cracking and splitting. Plant Physiology, 68, 371–376.
Correia S, Schouten R, Silva A P, Gonçalves B. 2018. Sweet cherry fruit cracking mechanisms and prevention strategies: A review. Scientia Horticulturae, 240, 369–377.
Cosgrove D J. 2000. Loosening of plant cell walls by expansins. Nature, 407, 321–326.
Cui L P, Qiu Z K, Wang Z R, Gao J C, Guo Y M, Huang Z J, Du Y C, Wang X X. 2017. Fine mapping of a gene (ER4.1) that causes epidermal reticulation of tomato fruit and characterization of the associated transcriptome. Frontiers in Plant Science, 8, 1254.
Davarpanah S, Tehranifar A, Abadía J, Val J, Davarynejad G, Aran M, Khorassani R. 2018. Foliar calcium fertilization reduces fruit cracking in pomegranate (Punica granatum cv. Ardestani). Scientia Horticulturae, 230, 86–91.
Demirsoy L, Demirsoy H. 2004. The epidermal characteristics of fruit skin of some sweet cherry cultivars in relation to fruit cracking. Pakistan Journal of Botany, 36, 725–731.
Dorais M, Demers D A, Papadopoulos A P. 2004. Greenhouse tomato fruit cuticle cracking. Horticultural Reviews, 30, 163–184.
Du H, Zhu J, Su H, Huang M, Wang H W, Ding S C, Zhang B L, Luo A, Wei S D, Tian X H. 2017. Bulked segregant RNA-seq reveals differential expression and SNPs of candidate genes associated with waterlogging tolerance in Maize. Frontiers in Plant Science, 8, 1022.
Gao J, Zhang Y X, Li Z G, Liu M C. 2020. Role of ethylene response factors (ERFs) in fruit ripening. Food Quality and Safety, 4, 5.
Gao Y, Zhang Y P, Fan Z Q, Jing Y, Chen J Y, Grierson D, Yang R, Fu D Q. 2021. Mutagenesis of SlNAC4 by CRISPR/Cas9 alters gene expression and softening of ripening tomato fruit. Vegetable Research, 1, 8.
Gine-Bordonaba J, Echeverria G, Ubach D, Aguilo-Aguayo I, Lopez M L, Larrigaudiere C. 2017. Biochemical and physiological changes during fruit development and ripening of two sweet cherry varieties with different levels of cracking tolerance. Plant Physiology and Biochemistry, 111, 216–225.
Giovannoni J. 2004. Genetic regulation of fruit development and ripening. The Plant Cell, 16, doi: 10.1105/tpc.019158.
Hahn F. 2011. Fuzzy controller decreases tomato cracking in greenhouses. Computers and Electronics Agriculture, 77, 21–27.
Huang J F, Li Y, Wang Y T, Chen Y Y, Liu M Y, Wang Y M, Zhang R, Zhou S G, Li J Y, Tu Y Y, Hao B, Peng L C, Xia T. 2017. A precise and consistent assay for major wall polymer features that distinctively determine biomass saccharifcation in transgenic rice by near infrared spectroscopy. Biotechnol Biofuels, 10, 294.
Huang J F, Xia T, Li G H, Li X L, Li Y, Wang Y T, Wang Y M, Chen Y Y, Xie G S, Bai F W, Peng L C, Wang L Q. 2019. Overproduction of native endo-β-1,4-glucanases leads to largely enhanced biomass saccharification and bioethanol production by specific modification of cellulose features in transgenic rice. Biotechnol Biofuels, 12, 11.
Huang Z, Peng G, Liu X, Deora A, Falk K C, Gossen B D, McDonald M R, Yu F Q. 2017. Fine mapping of a clubroot resistance gene in Chinese cabbage using SNP markers identified from bulked segregant RNA sequencing. Frontiers in Plant Science, 8, 1448.
Hudson I W. 1956. The inheritance of resistance to fruit cracking in the tomato (Lycopersicon esculentum L). MSc thesis, Oregon State College, America.
Jiang F L, Lopez A, Jeon S, Freitas S, Yu Q, Wu Z, Labavitch J, Tian S, Powell A, Mitcham E. 2019. Disassembly of the fruit cell wall by the ripening-associated polygalacturonase and expansin influences tomato cracking. Horticulture Research, 6, 17.
Khadivi-Khub A. 2015. Physiological and genetic factors influencing fruit cracking. Acta Physiologiae Plantarum, 37, 1718.
Lai A, Santangelo E, Soressi G P, Fantoni R. 2007. Analysis of the main secondary metabolites produced in tomato (Lycopersicon esculentum Mill.) epicarp tissue during fruit ripening using fluorescence techniques. Postharvest Biology and Technology, 43, 335–342.
Li H J. 2016. Genetic analysis and QTL mapping of tomato fruit cracking traits. MSc thesis, Northeast Agricultural University, China. (in Chinese)
Li J S, Dai X H, Zhao Y D. 2006. A role for auxin response factor 19 in auxin and ethylene signaling in Arabidopsis. Plant Physiology, 140, 899–908.
Li M, Li B, Guo G, Chen Y X, Xie J Z, Lu P, Wu Q H, Zhang D Y, Zhang H Z, Yang J. 2018. Mapping a leaf senescence gene els1 by BSR-Seq in common wheat. The Crop Journal, 6, 236–243.
Li Y, Jones L, McQueen-Mason S. 2003. Expansins and cell growth. Current Opinion in Plant Biology, 6, 603–610.
Liao N Q, Hu Z Y, Li Y Y, Hao J F, Chen S N, Xue Q, Ma Y Y, Zhang K J, Mahmoud A, Ali A, Malangisha G K, Lyu X L, Yang J H, Zhang M F. 2020. Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon. Plant Biotechnology Journal, 18, 1066–1077.
Lin M M, Fang J B, Hu C G, Qi X J, Sun S H, Chen J Y, Sun L M, Zhong Y P. 2020. Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole genome re-sequencing. PLoS ONE, 15, e0219884.
Liszkay A. 2004. Production of reactive oxygen intermediates (O2–·, H2O2, and ·OH) by maize roots and their role in wall loosening and elongation growth. Plant Physiology, 136, 3114–3123.
Liu S, Yeh C T, Tang H M, Nettleton D, Schnable P S. 2012. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS ONE, 7, 0036406.
Liu Y, Lv J, Liu Z, Wang J, Yang B Z, Chen W C, Ou L J, Dai X Z, Zhang Z Q, Zhou X X. 2020. Integrative analysis of metabolome and transcriptome reveals the mechanism of color formation in pepper fruit (Capsicum annuum L.). Food Chemistry, 306, 125629.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–ΔΔCt method. Methods, 25, 402–408.
Lu K, Li T, He J, Chang W, Zhang R, Liu M, Yu M N, Fan Y H, Ma J Q, Sun W, Qu C M, Liu L Z, Li N N, Liang Y, Wang R, Qian W, Tang Z L, Xu X F, Lei B, Zhang K, et al. 2018. qPrimerDB: A thermodynamics-based gene-specific qPCR primer database for 147 organisms. Nucleic Acids Research, 46, 1229–1236.
Moctezuma E, Smith D L, Gross K C. 2003. Antisense suppression of a β-galactosidase gene (TBG6) in tomato increases fruit cracking. Journal of Experimental Botany, 54, 2025–2033.
Robinson M D, McCarthy D J, Smyth G K. 2010. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139–140.
Sano O, Hikawa M, Imanishi S. 2018. Reduction of radial fruit cracking by single spraying of forchlorfenuron 1-(2-chloro-4-pyridyl)-3-phenylurea of fruit clusters in tomato production under rain shelter. Horticulture Research, 17, 87–93.
Shi H Y, Cao L W, Xu Y, Yang X, Liu S L, Liang Z S, Li G C, Yang Y P, Zhang Y X, Chen L. 2021. Transcriptional profiles underlying the effects of salicylic acid on fruit ripening and senescence in pear (Pyrus pyrifolia Nakai). Journal of Integrative Agriculture, 20, 2424–2437.
Tsabary G, Shani Z, Roiz L, Levy I, Riov J, Shoseyov O. 2003. Abnormal ‘wrinkled’ cell walls and retarded development of transgenic Arabidopsis thaliana plants expressing endo-1,4-beta-glucanase (cell) antisense. Plant Molecular Biology, 51, 213–224.
Vaidyanathan S, Harrigan G. 2005. Metabolome Analyses: Strategies for Systems Biology. Springer, Berlin/Heidelberg, Germany.
Vicente A R, Powell A, Creve L C, Labavitch J M. 2007. Cell wall disassembly events in boysenberry (Rubus idaeus L×Rubusursinus Cham&Schldl) fruit development. Functional Plant Biology, 34, 614–623.
Wang C N, Luan F S, Liu H Y, Davis A R, Zhang Q A, Dai Z Y, Liu S. 2021. Mapping and predicting a candidate gene for flesh color in watermelon. Journal of Integrative Agriculture, 20, 2100–2111.
Wei B, Wang L, Bosland P W, Zhang G Y, Zhang R. 2019. Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration. BMC Genomics, 20, 837.
Xue L Z, Sun M T, Wu Z, Yu L, Yu Q H, Tang Y P, Jiang F L. 2020. LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network. BMC Plant Biology, 20, 162.
Yamaguchi M, Sato I, Ishiguro M. 2002. Influences of epidermal cell sizes and flesh firmness on cracking susceptibility in sweet cherry (Prunus avium L.) cultivars and selections. Journal of the Japanese Society for Horticultural Science, 71, 738–746.
Zhu Y, Fan L N, Huang Z J, Du Y C, Guo Y M, Li J M, Liu L, Shu J D, Wang X X. 2020. Fine mapping of tomato dehiscence resistance gene Cr3a. Acta Horticulturae Sinica, 47, 275–286. (in Chinese)