Regulating Tomato quality through Expression

• Applicants: Professor Zhangjun Fei, Ph.D.; Professor Alisdair Fernie, Ph.D.; Professor James Giovannoni, Ph.D.; Professor Dr. Harry Klee; Professorin Dr. Cathie Martin; Professor Dr. Björn Usadel
• Subject Area: Plant Physiology
• Term: from 2015 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 263748294

• Final Report Year: 2019

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

• (2018) Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles. Scientific reports 8 (1) 7429
  Vargas-Ortiz, Erandi; Gonda, Itay; Smeda, John R.; Mutschler, Martha A.; Giovannoni, James J.; Jander, Georg
  
• (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
  
• (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
  
• (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
  
• (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
  
• (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
  
• (2017) De novo assembly of a new Solanum pennellii accession using Nanopore sequencing. Plant Cell, Oct 29 (10): 2336-2348
  Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B
  
• (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
  
• (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.
  
• (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
  
• (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
  
• (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
  
• (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
  
• (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
  
• (2019) Dissecting regulatory eQTLs of the carotenoid biosynthetic pathway in tomato fruit using S.lycopersicum x S.pennellii introgression lines. PhD Thesis
  J. Li