Softening and internal fruit structure are traits of prime importance for tomato sensory quality, postharvest behavior and overall commercial value. It is also a major criterion in determining whether the crop is better suited for fresh consumption or the processing industry. The dynamics of fleshy fruit tissue texture is complex, and softness has always been addressed as a ripening associated process. Notably, so far, all the strategies aiming at improving fruit texture and postharvest shelf-life consisted in attenuating the ripening process which inevitably leads to losses in sensory qualities resulting from incomplete ripening. It is noteworthy that “All-flesh” tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Our group aims to understand the process determining firmness and texture.  Although the deciphering of the components underlying the softening process has been mostly addressed by focusing on late stages of fruit development, our data are consistent with the notion that a large component of texture and firmness of ripe fruit is determined at early pre-ripening stages, concomitant with the initiation of inner tissues differentiation. Using reversed genetics, ChIPseq, transcritptomic and microscopy techniques we highlighted the role of MBP3, a class-D MADS-Box, in locular gel formation by controlling cell cycle and cell expansion genes, indicating that important components of fruit softening are determined at early pre-ripening stages. Our findings brings a paradigm shift of thinking and provides new opportunities for breeding strategies aiming to design tomato varieties, and possibly other fleshy fruits, with specific texture properties (Huang et al. 2021, Nature Com.). Such new varieties will be better suited for tomato processing and the extended shelf life of the fresh fruits will contribute to reducing wastage.

In flowering plants, differentiation of reproductive organs and successful flower fertilization are among the main determinants of crop yield, and in most crop species, yield relies primarily on the number of inflorescences and of flowers per inflorescence. Fruit set is naturally triggered by flower pollination and represents another important developmental process that impacts crop yield. Using the tomato as model species, we address the mechanisms of fruit set and inflorescence differentiation as two major steps determining fruit yield.

The transition from flower to fruit, the so-called fruit set, is an important determinant of crop yield and in the face of global warming and fast-growing world population, maintaining yield stability is becoming a major challenge. We investigate the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum L.) using combined genome-wide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Our data demonstrate reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone post translational modifications rather than DNA methylation are associated with the remodeling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations (Hu et al. 2020, New Phytologist).

Understanding the mechanisms underlying differentiation of inflorescence and flower meristems is essential towards enlarging our knowledge of reproductive organ formation and to open new prospects for improving yield traits. Using CRISPR/Cas9 knock-out strategy, our recent study shows that SlDOF9 is a new modulator of floral differentiation in tomato. Our findings add a new actor to the complex mechanisms underlying reproductive organ differentiation in flowering plants and provide leads towards addressing the diversity of factors controlling the transition to reproductive organs (Hu et al 2022, Nature Plants).

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17: Deng W, Yang Y, Ren Z, Audran-Delalande C, Mila I, Wang X, Song H, Hu Y,

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18: Makhloufi E, Yousfi FE, Pirrello J, Bernadac A, Ghorbel A, Bouzayen M.

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20: Chaabouni S, Pirrello J, Liu M, El-Sharkawy I, Roustan JP, Bouzayen M.

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21: Bakshi A, Piya S, Fernandez JC, Chervin C, Hewezi T, Binder BM. Ethylene

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22: Djemal R, Mila I, Bouzayen M, Pirrello J, Khoudi H. Molecular cloning and

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23: Yu H, Soler M, Mila I, San Clemente H, Savelli B, Dunand C, Paiva JA, Myburg

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24: Su L, Bassa C, Audran C, Mila I, Cheniclet C, Chevalier C, Bouzayen M,

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25: Zouine M, Fu Y, Chateigner-Boutin AL, Mila I, Frasse P, Wang H, Audran C,

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a multi-levels post-transcriptional regulation including alternative splicing.

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26: Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li

Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA

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28: Hao Y, Hu G, Breitel D, Liu M, Mila I, Frasse P, Fu Y, Aharoni A, Bouzayen

M, Zouine M. Auxin Response Factor SlARF2 Is an Essential Component of the

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29: Breitel DA, Chappell-Maor L, Meir S, Panizel I, Puig CP, Hao Y, Yifhar T,

Yasuor H, Zouine M, Bouzayen M, Granell Richart A, Rogachev I, Aharoni A. AUXIN

RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit

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30: Yu H, Soler M, San Clemente H, Mila I, Paiva JA, Myburg AA, Bouzayen M,

Grima-Pettenati J, Cassan-Wang H. Comprehensive genome-wide analysis of the

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Epub 2015 Jan 9. PMID: 25577568.

 

31: Moummou H, Tonfack LB, Chervin C, Benichou M, Youmbi E, Ginies C, Latché A,

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32: Salma C, Alain L, Claude PJ, Mondher B. Tomato Aux/IAA3 and HOOKLESS are

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33: Moummou H, Kallberg Y, Tonfack LB, Persson B, van der Rest B. The plant

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34: Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S,

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35: Makhloufi E, Yousfi FE, Marande W, Mila I, Hanana M, Bergès H, Mzid R,

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36: Yousfi FE, Makhloufi E, Marande W, Ghorbel AW, Bouzayen M, Bergès H.

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37: Huang B, Routaboul JM, Liu M, Deng W, Maza E, Mila I, Hu G, Zouine M, Frasse

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38: Chaabouni S, Jones B, Delalande C, Wang H, Li Z, Mila I, Frasse P, Latché A,

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39: Liu M, Diretto G, Pirrello J, Roustan JP, Li Z, Giuliano G, Regad F,

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40: Liu M, Gomes BL, Mila I, Purgatto E, Peres LE, Frasse P, Maza E, Zouine M,

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41: Liu M, Pirrello J, Kesari R, Mila I, Roustan JP, Li Z, Latché A, Pech JC,

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42: Zouine M, Maza E, Djari A, Lauvernier M, Frasse P, Smouni A, Pirrello J,

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43: Louveau T, Leitao C, Green S, Hamiaux C, van der Rest B, Dechy-Cabaret O,

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44: Trapet P, Avoscan L, Klinguer A, Pateyron S, Citerne S, Chervin C, Mazurier

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45: Sagar M, Chervin C, Mila I, Hao Y, Roustan JP, Benichou M, Gibon Y, Biais B,

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46: Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latché A, Pech

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47: Bassa C, Mila I, Bouzayen M, Audran-Delalande C. Phenotypes associated with

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48: Maza E, Frasse P, Senin P, Bouzayen M, Zouine M. Comparison of normalization

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49: Egea I, Bian W, Barsan C, Jauneau A, Pech JC, Latché A, Li Z, Chervin C.

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time-lapse recording on intact live tissue. Ann Bot. 2011 Aug;108(2):291-7. doi:

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50: Pirrello J, Jaimes-Miranda F, Sanchez-Ballesta MT, Tournier B, Khalil-Ahmad

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51: Manríquez D, El-Sharkawy I, Flores FB, El-Yahyaoui F, Regad F, Bouzayen M,

Latché A, Pech JC. Two highly divergent alcohol dehydrogenases of melon exhibit

fruit ripening-specific expression and distinct biochemical characteristics.

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52: Ambrosino L, Ruggieri V, Bostan H, Miralto M, Vitulo N, Zouine M, Barone A,

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53: Barsan C, Zouine M, Maza E, Bian W, Egea I, Rossignol M, Bouyssie D,

Pichereaux C, Purgatto E, Bouzayen M, Latché A, Pech JC. Proteomic analysis of

chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled

with disrupted thylakoid biogenesis machinery and elevated energy-production

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54: Chervin C, Tira-Umphon A, Terrier N, Zouine M, Severac D, Roustan JP.

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55: El-Sharkawy I, Manríquez D, Flores FB, Regad F, Bouzayen M, Latché A, Pech

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56: Lucchetta L, Manriquez D, El-Sharkawy I, Flores FB, Sanchez-Bel P, Zouine M,

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