Regulating Tomato quality through Expression
Final Report Abstract
Under the Regulatome project, a high-quality near chromosome scale genome sequence of Solanum lycopersicoides (a total of 1.27G and a scaffold N50 of 93.9 Mb) has been produced with the help of additional funding leveraged from the TRIAD Foundation. Annotation of the genome with the aid of PacBio IsoSeq and Illumina RNA-Seq data resulted in 37,938 protein-coding genes. The S. lycopersicoides introgression lines into S. lycoperiscum were grown in replicated field trials and ripe fruit transcriptome profiling (RNA-Seq) was performed on all fruiting lines to generate both a gene expression reference for the fruit and to facilitate fine mapping of all wild species introgression. A subset of the population was also greenhouse grown under normal watering and drought stress with fruit subject to similar transcriptome profiling. Fruit from both trials have been examined for levels of nutrient and quality metabolites in multiple laboratories participating in the project (carotenoids, volatiles, broader metabolite profiling). The screening of the primary metabolite composition has been carried out for the S. lycopersicoides introgression line population grown in field conditions in both Israel and the USA. These trials confirmed previously characterized QTL found in other populations but more importantly identified novel QTL for the quality compound ascorbate and metabolites such as galactinol and raffinose which may play an important role under limited irrigation regimes. Additional approaches led to the identification of eQTLs and candidate genes influencing the levels of flavonols, carotenoids, flavor volatiles and vitE in tomato fruits. A number of these genes are currently being functionally tested.
Publications
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Vargas-Ortiz, Erandi; Gonda, Itay; Smeda, John R.; Mutschler, Martha A.; Giovannoni, James J.; Jander, Georg
(See online at https://doi.org/10.1038/s41598-018-24998-5) - (2019) Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato. Plant biotechnology journal 17 (1) 33–49
Yazdani, Mohammad; Sun, Zhaoxia; Yuan, Hui; Zeng, Shaohua; Thannhauser, Theodore W.; Vrebalov, Julia; Ma, Qiyue; Xu, Yimin; Fei, Zhangjun; van Eck, Joyce; Tian, Shiping; Tadmor, Yaakov; Giovannoni, James J.; Li, Li
(See online at https://doi.org/10.1111/pbi.12945) - (2019) Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. The plant genome 12 (1) 180010
Gonda, Itay; Ashrafi, Hamid; Lyon, David A.; Strickler, Susan R.; Hulse-Kemp, Amanda M.; Ma, Qiyue; Sun, Honghe; Stoffel, Kevin; Powell, Adrian F.; Futrell, Stephanie; Thannhauser, Theodore W.; Fei, Zhangjun; van Deynze, Allen E.; Mueller, Lukas A.; Giova
(See online at https://doi.org/10.3835/plantgenome2018.02.0010) - (2019) Tomato stigma exsertion induced by high temperature is associated with the jasmonate signalling pathway. Plant, cell & environment 42 (4) 1205–1221
Pan, Changtian; Yang, Dandan; Zhao, Xiaolin; Jiao, Chen; Yan, Yanqiu; Lamin-Samu, Anthony Tumbeh; Wang, Qiaomei; Xu, Xiangyang; Fei, Zhangjun; Lu, Gang
(See online at https://doi.org/10.1111/pce.13444) - (2016). Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL. Frontiers Plant Sci 7: 1671
Liu Z, Alseekh S, Brotman Y, Zheng Y, Fei Z, Tieman DM, Giovannoni JJ, Fernie AR, Klee HJ
(See online at https://doi.org/10.3389/fpls.2016.01671) - (2017) An InDel in the promoter of Al-activated malate transporter 9 selected during tomato domestication determines fruit malate content and aluminum tolerance. Plant Cell. 9:2249-2268
Ye J, Wang X, Hu T, Zhang F, Wang B, Li C, Yang T, Li H, Lu Y, Giovannoni J, Zhang Y, Ye Z
(See online at https://doi.org/10.1105/tpc.17.00211) - (2017) De novo assembly of a new Solanum pennellii accession using Nanopore sequencing. Plant Cell, Oct 29 (10): 2336-2348
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(See online at https://doi.org/10.1105/tpc.17.00521) - (2017) Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits, J. Exp. Botany. 68:4869-4884
Huang B, Routaboul J, Liu M, Deng W, Maza E, Mila I, Hu G, Zouine M, Frasse P, Vrebalov J, Giovannoni J, Li Z, van der Rest B, Bouzayen M
(See online at https://doi.org/10.1093/jxb/erx303) - (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu. Rev. Plant Biol. 68:61-84
Giovannoni, J., Nguyen, C., Ampofo, B., Zhong, S., Fei, Z.
(See online at https://doi.org/10.1146/annurev-arplant-042916-040906) - (2018) AtPDS over-expression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnol J. 16:482-494
McQuinn RP, Wong B, Giovannoni JJ
(See online at https://doi.org/10.1111/pbi.12789) - (2018) Exploring Plant Stilbenes for Healthy Skin. PhD Thesis. University of East Anglia (UK)
E. Hawkins
- (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants
Lü P, Yu S, Zhu N, Chen Y-R, Zhou B, Pan Y, Tzeng D, Fabi JP, Argyris J, Garcia-Mas J, Ye N, Zhang J, Grierson D, Xiang J, Fei Z, Giovannoni J, Zhong S
(See online at https://doi.org/10.1038/s41477-018-0249-z) - (2018) High-resolution transcriptome mapping of tomato fruit development and ripening. Nature Comm. 9:364
Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich D, Shi Y, Xu Y, Zheng Y, Snyder S, Martin L, Ruiz-may E, Thannhauser T, Chen K, Domozych D, Catala C, Fei Z, Mueller L, Giovannoni J, Rose J
(See online at https://doi.org/10.1038/s41467-017-02782-9) - (2018) Identification of transcriptional regulators determining nutritional quality of tomato. PhD Thesis. University of East Anglia (UK)
E. Fearnley
- (2018) Mechanistic elucidation of long distance mRNA movement in Nicotiana benthamiana/tomato heterografts. Plant Physiology. 77:745-758
Xia C, Zheng Y, Huang J, Zhou X, Li R, Zha M, Wang S, Huang Z, Lan H, Turgeon R, Fei Z, Zhang C
(See online at https://doi.org/10.1104/pp.17.01836) - (2018) Quantitative trait loci analysis identifies a prominent gene involved in the production of fatty-acid-derived flavor volatiles in tomato. Mol. Plant 11: 1147–1165
Garbowicz K, Liu Z, Alseekh S, Tieman D, Taylor M, Kuhalskaya A, Ofner I, Zamir D, Klee H, Fernie A, Brotman Y
(See online at https://doi.org/10.1016/j.molp.2018.06.003) - (2019) Dissecting regulatory eQTLs of the carotenoid biosynthetic pathway in tomato fruit using S.lycopersicum x S.pennellii introgression lines. PhD Thesis
J. Li
