Guarding tomato fruit setting in adverse temperatures through the miRNA166-SlHB15A regulatory module

Abstract

Fruits are defined as mature ovaries originated from a coordinated development between ovules (precursors of seeds) and carpels (precursors of the fruit body). Disconnecting the ovule development from carpel development is a long-desired goal in agriculture to generate seedless fruits easier to consume. However, pollination and fertilization are required to promote hormone pathways—i.e., auxin and gibberellin—that are crucial for seed and fruit set (Gillaspy et al., 1993Gillaspy G. Bendavid H. Gruissem W. Fruits: a developmental perspective.Plant Cell. 1993; 5: 1439-1451Crossref PubMed Scopus (808) Google Scholar; Raghavan, 2003Raghavan V. Some reflections on double fertilization, from its discovery to the present.New Phytol. 2003; 159: 565-583Crossref PubMed Scopus (86) Google Scholar). Even though developing seeds are central for normal fruit development, examples of seedless or parthenocarpic fruits are present in wild and cultivated species (Joldersma and Liu, 2017Joldersma D. Liu Z. The making of virgin fruit: the molecular and genetic basis of parthenocarpy.J. Exp. Bot. 2017; 69: 955-962Crossref Scopus (26) Google Scholar). Given that fruit development is controlled by a network of physiological and molecular pathways, parthenocarpy—defined as the fertilization-independent seedless fruit set—may be achieved through hormone treatment or by altering specific genetic programs (Joldersma and Liu, 2017Joldersma D. Liu Z. The making of virgin fruit: the molecular and genetic basis of parthenocarpy.J. Exp. Bot. 2017; 69: 955-962Crossref Scopus (26) Google Scholar; Silva et al., 2017Silva E.M. Silva G.F.F.E. Bidoia D.B. da Silva Azevedo M. Almeida deJesus F. Pino L.E. Peres L.E.P. Carrera E. Lopez-Diaz I. Nogueira F.T.S. microRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato.Plant J. 2017; 92: 95-109Crossref PubMed Scopus (34) Google Scholar). microRNAs (miRNAs) are crucial regulators in several genetic programs and, together with their targets, configurate the so-called miRNA regulatory modules. Several miRNA regulatory modules interplay with hormone networks to regulate plant reproduction, including various stages of fruit development (Correa et al., 2018Correa J.P.O. Silva E.M. Nogueira F.T.S. Molecular control by non-coding RNAs during fruit development: from gynoecium patterning to fruit ripening.Front. Plant Sci. 2018; 9: 1760Crossref PubMed Scopus (9) Google Scholar). Thus, by altering specific miRNA regulatory modules, it is possible to generate seedless fruits (Silva et al., 2017Silva E.M. Silva G.F.F.E. Bidoia D.B. da Silva Azevedo M. Almeida deJesus F. Pino L.E. Peres L.E.P. Carrera E. Lopez-Diaz I. Nogueira F.T.S. microRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato.Plant J. 2017; 92: 95-109Crossref PubMed Scopus (34) Google Scholar). In a recent study, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar found a new miRNA regulatory module that controls ovule development and fruit setting in tomato (Solanum lycopersicum). They isolated miR166-targeted SlHB15A mutants that exhibit aberrant ovules and parthenocarpic fruits under normal and adverse temperature conditions. The miR166-targeted SlHB15A gene is expressed in the ovule integument and directly regulates auxin and ethylene signaling to prevent fruit set in the absence of fertilization (Figure 1). miRNAs are well-known orchestrators of gene expression, either post-transcriptionally or by translation inhibition (Yu et al., 2017Yu Y. Jia T. Chen X. The ‘how’ and ‘where’ of plant microRNAs.New Phytol. 2017; 216: 1002-1017Crossref PubMed Scopus (203) Google Scholar). Most miRNA regulatory modules are critical for regulating a variety of aspects in plant development. The ancient miR166 family is highly conserved among plants and targets PHABULOSA (PHB), PHAVOLUTA (PHV), REVOLUTA (REV), and ATHB-8 and -15 genes, which belong to the class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factor family. The miR166-HD-ZIPIII module plays critical roles in the shoot apical meristem establishment, lateral organ polarity, vascular patterning of the shoot and the root, and nutrition ion uptake (Sakaguchi and Watanabe, 2012Sakaguchi J. Watanabe Y. miR165⁄166 and the development of land plants.Develop. Growth Differ. 2012; 54: 93-99Crossref PubMed Scopus (37) Google Scholar). Recently, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar unveiled a novel function for the miR166-SlHB15A module in regulating an importnat agronomic trait, namely fruit set. Their work described the loss of the miR166-targeted SlHB15A function in tomato, which leads to abnormal ovule development and promotes parthenocarpic fruit set by modulating auxin and ethylene signaling. Remarkably, SlHB15A expression is subjected to gene dosage regulation, which is achieved by the induction of miR166 in response to low temperature. To our knowledge, this is likely the first report to show that recessive dosage sensitivity may be controlled by a miRNA. To reveal novel genetic tools that modulate fruit set, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar screened an ethyl methanesulfonate-based tomato mutant population exposed to non-permissive heat conditions in the field. They identified a mutant displaying a fertilization-independent fruit set, which they named parthenocarpic fruit 1 (pf1). Due to the non-fertilization-based fruit set, pf1circumvents daily temperature fluctuations (32°C/24°C day/night) and promotes fruit set and better yield compared with wild-type (WT) plants. Interestingly, the pf1 mutation was found to be located in a miR166-targeted HD-ZIPIII transcription factor, named SlHB15A. In addition, after performing allelic tests, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar confirmed that the classic parthenocarpic tomato mutant pat (Mazzucato et al., 1998Mazzucato A. Taddei A.R. Soressi G.P. The parthenocarpic fruit (pat) mutant of tomato (Lycopersicon esculentum Mill.) sets seedless fruits and has aberrant anther and ovule development.Development. 1998; 125: 107-114Crossref PubMed Google Scholar) is a mutant allele of the miR166-targeted SlHB15A. Exposure to low temperature represents a threat for fruit set in some species (Zhao et al., 2017Zhao C. Liu B. Piao S. Wang X. Lobell D.B. Huang Y. Huang M. Yao Y. Bassu S. Ciais P. et al.Temperature increase reduces global yields of major crops in four independent estimates.Proc. Natl. Acad. Sci. U S A. 2017; 114: 9326-9331Crossref PubMed Scopus (809) Google Scholar). Under cold conditions (15°C day/12°C night), SlHB15A loss-of-function alleles (pf1/pf1) promote parthenocarpy and even increase the fruit set rate in 70% compared with pollinated WT plants. Interestingly, heterozygous plants carrying the pf1alleles proved to be parthenocarpic under cold stress, whereas they did not produce parthenocarpic fruits under optimal or heat conditions. These observations suggest that a fine-tune regulation of the SlHB15A transcript levels is fundamental to modulate cold-induced fruit set in tomato. In fact, the authors showed that cold-induced miR166 acts as a switch of SlHB15A-dosage sensitivity under cold stress. To support this idea, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar identified plants harboring a miR166-resistant SlHB15A allele (pf1-6) not parthenocarpic under normal or low temperatures, and constructed compound-heterozygote hybrids by crossing pf1-6 with the pf1 (SlHB15A loss-of-function) mutant. After cold exposure, none of these hybrids were able to produce fruits without fertilization. Altogether, the genetic and molecular data of the study support the idea that miR166 is induced in response to cold exposure, leading to haploinsufficiency or recessive dosage sensitivity of SlHB15A during fruit development. miRNA-based repression of GAMYB expression has been previously reported to interfere with ovule development and promote obligatory parthenocarpy in tomato by modulating auxin and gibberellin responses (Silva et al., 2017Silva E.M. Silva G.F.F.E. Bidoia D.B. da Silva Azevedo M. Almeida deJesus F. Pino L.E. Peres L.E.P. Carrera E. Lopez-Diaz I. Nogueira F.T.S. microRNA159-targeted SlGAMYB transcription factors are required for fruit set in tomato.Plant J. 2017; 92: 95-109Crossref PubMed Scopus (34) Google Scholar). In their study, Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar concluded that the loss of SlHB15A function leads to aberrant ovule formation with aborted integument remaining at the base of the nucellus, which fully correlates with parthenocarpy. The authors show that unpollinated pf1 abnormal ovules display a similar transcriptomic profile when compared with WT pollinated ovules, and that SlHB15A directly inhibits auxin signaling and induces ethylene-associated genes, preventing fruit set in the absence of fertilization. However, it remains to be determined how the fertilization process alleviates the SlHB15A-mediated inhibition of ovary development. In summary, the study showed compelling evidences that the miR166-SlHB15A module is essential to control hormone responses during tomato fruit development under normal and non-permissive temperatures (Figure 1). Oscillations in temperature represent a major threat to crop yield around the world. Due to the current climate change scenario, it is pivotal to anticipate new strategies to expand the agricultural cultivation areas to reduce risks to food safety in the near future. Given that extreme (low or high) temperatures may prevent fruit set (Zhao et al., 2017Zhao C. Liu B. Piao S. Wang X. Lobell D.B. Huang Y. Huang M. Yao Y. Bassu S. Ciais P. et al.Temperature increase reduces global yields of major crops in four independent estimates.Proc. Natl. Acad. Sci. U S A. 2017; 114: 9326-9331Crossref PubMed Scopus (809) Google Scholar), parthenocarpy could be a big help to mitigate yield losses. Thus, parthenocarpic fruits are considered a highly desirable agronomic trait. Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar have shown that, by altering the miR166-SlHB15A module, it is possible not only to modulate fruit set but also to increase tomato yield in non-permissive temperatures. Incorporating this knowledge into tomato breeding programs may help expand tomato cultivation areas to locations subjected to extreme fluctuations in temperature for most of the year, which would significantly increase tomato production worldwide. Considering that the miR166 regulatory module is highly conserved (Sakaguchi and Watanabe, 2012Sakaguchi J. Watanabe Y. miR165⁄166 and the development of land plants.Develop. Growth Differ. 2012; 54: 93-99Crossref PubMed Scopus (37) Google Scholar), the work by Clepet et al., 2021Clepet C. Ravi S.D. Boumlik R. Hao Y. Motin H. Marcel F. Verdenaud M. Mania B. Brisou G. Citerne S. et al.The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.05.005Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar also opens a new venue to explore this regulatory module to increase the cultivation areas not only for other Solanaceae (e.g., pepper, eggplant) but also for other important fruit crops (e.g., citrus, papaya) potentially threatened by global temperature fluctuations.