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Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca , a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants. In flowering plants, fertilization triggers auxin synthesis in the endosperm to promote seed and fruit development. Here the authors show that an MADS-box transcription factor AGL62 is required to activate auxin synthesis in the endosperms of Fragaria vesca, a diploid strawberry, and Arabidopsis.

Auxin response factors (ARFs) encode transcriptional factors that function in the regulation of plant development processes. A tomato ARF gene, SlARF5 , was observed to be expressed at high levels in emasculated ovaries but maintained low expression levels in pollinated ovaries. The ami RNA SlARF5 lines exhibited ovary growth and formed seedless fruits following emasculation. These parthenocarpic fruits developed fewer locular tissues, and the fruit size and weight were decreased in transgenic lines compared to those of wild-type fruits. Gene expression analysis demonstrated that several genes involved in the auxin-signaling pathway were downregulated, whereas some genes involved in the gibberellin-signaling pathway were enhanced by the decreased SlARF5 mRNA levels in transgenic plants, indicating that SlARF5 may play an important role in regulating both the auxin- and gibberellin-signaling pathways during fruit set and development.

The highest quality pomegranate necessitates a tropical or subtropical environment for proper growth and development. This study evaluated two pomegranate cultivars including Rabab Poost Ghermez Neyriz (RPGN) and Makhmal Malas Shahreza (MMS) for physical traits, biochemical properties, and juice quality in their native locations as well as other warm and arid regions during two growing seasons (2019–2020 and 2020–2021) in Iran. The results showed that cultivars with the maximum redness (a*) were more likely to originate in cooler climates, and the cultivar’s responses to changing climates were also different. According to pomegranate characteristics, cultivars in different regions had different fruit, aril, and skin weights. According to these findings, pomegranate fruits cultivated in other climates than the origin climate have a smaller edible fraction. The findings also demonstrate that pomegranate fruits cultivated in mountain climates have more significant biochemical parameters such as total phenol, anthocyanin content, antioxidant capacity, and vitamin C than those produced in desert environment settings. The increased titratable acidity (TA), total soluble solids (TSS), and pH values of pomegranates produced in origin climate than the warm environment; thus, suggest that changes in pomegranate cultivar origin had a clear impact on fruit juice quality. Environmental factors, such as wind speed, altitude, and annual precipitation, had a significant correlation with a* skin, TSS, fruit weight, aril weight, edible portion, pH, TA, phenol, antioxidants, and anthocyanin content.

To ensure successful plant reproduction and crop production, the spatial and temporal control of the termination of the floral meristem must be coordinated. In Arabidopsis , the timing of this termination is determined by AGAMOUS (AG). Following its termination, the floral meristem underdoes gynoecium formation. A direct target of AG, CRABS CLAW ( CRC ), is involved in both floral meristem determinacy and gynoecium development. However, how floral meristem termination is coordinated with gynoecium formation is not understood. Here, we identify a mechanistic link between floral meristem termination and gynoecium development through fine-tuning of auxin homeostasis by CRC. CRC controls auxin homeostasis in the medial region of the developing gynoecium to generate proper auxin maxima. This regulation partially occurs via direct transcriptional repression of TORNADO2 ( TRN2 ) by CRC. Plasma membrane-localized TRN2 modulates auxin homeostasis. We propose a model describing how regulation of auxin homeostasis mediates the transition from floral meristem termination to gynoecium development. In Arabidopsis , the timing of floral meristem termination is determined by AGAMOUS. Here, the authors show that the CRC transcription factor, itself a direct target of AGAMOUS, coordinates meristem termination with subsequent gynoecium formation partly by repressing TRN2 expression and regulating auxin homeostasis.

Wangmo red ball Camellia oleifera is the main Camellia species cultivated for oil in the low-heat valley of Guizhou, China. In this study, we evaluated the comprehensive nutritional value of Wangmo C. oleifera seed oil through fatty acid and nutritional component analyses. Twenty excellent Wangmo C. oleifera plants with stable yield and disease resistance were selected from the Camellia oleifera germplasm resource garden in the low-heat valley site of Guizhou University. The unit crown yield, fatty acid content of the seed oil, fatty acid composition and functional nutrients were determined, and the oil quality was comprehensively evaluated using principal component analysis. The fatty acid content of C. oleifera seed oil was 35.03–53.47%, suggesting likely popularization and wide application prospects. The fatty acids included SFAs, MUFAs and PUFAs, and the oleic acid content was 80%, indicating a highly stable and nutritious oil. The oil was also rich in carotenoids, polyphenols, flavonoids, β-sitosterol, squalene and α-Ve, with average content of 7.404 mg/kg, 16.062 mg/kg, 0.401 g/100 g, 265.087 mg/kg, 129.315 mg/kg and 21.505 mg/100 g, respectively. However, the correlations among the nutritional indices were weak. PCA showed that germplasms GH7, GH43, GH28, GH8 and GH31 exhibited the top five nutritional qualities. The rankings in this study provide data for identifying excellent Wangmo C. oleifera plants with high nutritional quality. Additionally, this study provides a valuable reference for the research and development of high-end edible oil and a theoretical basis for the development of economic forest species in low-heat valley areas across the world.

The changes in reproductive phenology (i.e. timing of flowering and fruiting) observed in recent decades demonstrate that tree reproduction has already been altered by climate change. However, understanding the impact of these changes in reproductive success and fitness remains a major challenge for ecologists. We describe here a previously unreported phenomenon: a significant increase in the reproductive effort (seed production) of temperate oaks with increasing spring temperature, observed over the last decade. In contrast, no relationship was found between seed production and precipitation. This sensitivity of seed production to temperature was confirmed by a “space-for-time” substitution based on elevation gradients. Our findings suggest that global warming may enhanceoak reproductive effort in temperate ecosystems. Nevertheless, while fitness can be enhanced by higher levels of seed production, it also depends on the frequency and synchronization of mast seeding production, which may also be influenced by climate change.

Tomato is considered as the genetic model for climacteric fruits, in which three major players control the fruit ripening process: ethylene, ripening transcription factors, and DNA methylation. The fruitENCODE project has now shown that there are multiple transcriptional circuits regulating fruit ripening in different species, and H3K27me3, instead of DNA methylation, plays a conserved role in restricting these ripening pathways. In addition, the function of the core tomato ripening transcription factors is now being questioned. We have employed CRISPR/Cas9 genome editing to mutate the SBP - CNR and NAC - NOR transcription factors, both of which are considered as master regulators in the current tomato ripening model. These plants only displayed delayed or partial non-ripening phenotypes, distinct from the original mutant plants, which categorically failed to ripen, suggesting that they might be gain-of-function mutants. Besides increased DNA methylation genome-wide, the original mutants also have hyper-H3K27me3 in ripening gene loci such as ACS2 , RIN , and TDR4 . It is most likely that multiple genetic and epigenetic factors have contributed to their strong non-ripening phenotypes. Hence, we propose that the field should move beyond these linear and two-dimensional models and embrace the fact that important biological processes such as ripening are often regulated by highly redundant network with inputs from multiple levels. Fruit ripening: Multiple backup plans The regulatory circuits that govern the expression of genes required for ripening in tomato plants are highly redundant. Fleshy fruits that use the hormone ethylene to regulate ripening have developed independently multiple times in the history of the angiosperms. Guiqin Qu at China Agricultural University in Beijing and colleagues working on the fruitENCODE project are exploring the genetic and epigenetic basis of this convergent evolution. In tomatoes, three transcription factors have been shown to control ethylene production and regulate ripening. However, when gene editing techniques were used to introduce mutations that interfere with the function of these transcription factors, partial ripening or a delay in ripening was observed. The fact that ripening was not abolished indicates that the ripening process is more robust and complex than previously thought.

NAC (NAM, ATAF1/2, and CUC2) transcription factors play important roles in fruit ripening and quality. The watermelon genome encodes 80 NAC genes, and 21 of these NAC genes are highly expressed in both the flesh and vascular tissues. Among these genes, ClNAC68 expression was significantly higher in flesh than in rind. However, the intrinsic regulatory mechanism of ClNAC68 in fruit ripening and quality is still unknown. In this study, we found that ClNAC68 is a transcriptional repressor and that the repression domain is located in the C-terminus. Knockout of ClNAC68 by the CRISPR-Cas9 system decreased the soluble solid content and sucrose accumulation in mutant flesh. Development was delayed, germination was inhibited, and the IAA content was significantly decreased in mutant seeds. Transcriptome analysis showed that the invertase gene ClINV was the only gene involved in sucrose metabolism that was upregulated in mutant flesh, and expression of the indole-3-acetic acid-amido synthetase gene ClGH3.6 in the IAA signaling pathway was also induced in mutant seeds. EMSA and dual-luciferase assays showed that ClNAC68 directly bound to the promoters of ClINV and ClGH3.6 to repress their expression. These results indicated that ClNAC68 positively regulated sugar and IAA accumulation by repressing ClINV and ClGH3.6. Our findings provide new insights into the regulatory mechanisms by which NAC transcription factors affect fruit quality and seed development.

The maturation of green fleshy fruit to become colourful and flavoursome is an important strategy for plant reproduction and dispersal. In tomato ( Solanum lycopersicum ) and many other species, fruit ripening is intimately linked to the biogenesis of chromoplasts, the plastids that are abundant in ripe fruit and specialized for the accumulation of carotenoid pigments. Chromoplasts develop from pre-existing chloroplasts in the fruit, but the mechanisms underlying this transition are poorly understood. Here, we reveal a role for the chloroplast-associated protein degradation (CHLORAD) proteolytic pathway in chromoplast differentiation. Knockdown of the plastid ubiquitin E3 ligase SP1, or its homologue SPL2, delays tomato fruit ripening, whereas overexpression of SP1 accelerates ripening, as judged by colour changes. We demonstrate that SP1 triggers broader effects on fruit ripening, including fruit softening, and gene expression and metabolism changes, by promoting the chloroplast-to-chromoplast transition. Moreover, we show that tomato SP1 and SPL2 regulate leaf senescence, revealing conserved functions of CHLORAD in plants. We conclude that SP1 homologues control plastid transitions during fruit ripening and leaf senescence by enabling reconfiguration of the plastid protein import machinery to effect proteome reorganization. The work highlights the critical role of chromoplasts in fruit ripening, and provides a theoretical basis for engineering crop improvements. Fruit ripening is a fine-tuned process involving wholesale changes to both the structure and metabolism of the fruit. Now, the CHLORAD proteolytic pathway is shown to regulate chromoplast development, thus altering the ripening process of tomato fruits.