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Abstract Ethylene-responsive element binding factors (ERFs) are involved in regulation of various stress responses in plants, but their biological functions in waterlogging stress are largely unclear. In this study, we identified a petunia (Petunia × hybrida) ERF gene, PhERF2, that was significantly induced by waterlogging in wild-type (WT). To study the regulatory role of PhERF2 in waterlogging responses, transgenic petunia plants with RNAi silencing and overexpression of PhERF2 were generated. Compared with WT plants, PhERF2 silencing compromised the tolerance of petunia seedlings to waterlogging, shown as 96% mortality after 4 days waterlogging and 14 days recovery, while overexpression of PhERF2 improved the survival of seedlings subjected to waterlogging. PhERF2-RNAi lines exhibited earlier and more severe leaf chlorosis and necrosis than WT, whereas plants overexpressing PhERF2 showed promoted growth vigor under waterlogging. Chlorophyll content was dramatically lower in PhERF2-silenced plants than WT or overexpression plants. Typical characteristics of programmed cell death (PCD), DNA condensation, and moon-shaped nuclei were only observed in PhERF2-overexpressing lines but not in PhERF2-RNAi or control lines. Furthermore, transcript abundances of the alcoholic fermentation-related genes ADH1-1, ADH1-2, ADH1-3, PDC1, and PDC2 were reduced in PhERF2-silenced plants, but increased in PhERF2-overexpressing plants following exposure to 12-h waterlogging. In contrast, expression of the lactate fermentation-related gene LDH was up-regulated in PhERF2-silenced plants, but down-regulated in its overexpressing plants. Moreover, PhERF2 was observed to directly bind to the ADH1-2 promoter bearing ATCTA motifs. Our results demonstrate that PhERF2 contributes to petunia waterlogging tolerance through modulation of PCD and alcoholic fermentation system.

Abstract Auxin response factors (ARFs) are involved in auxin-mediated transcriptional regulation in plants. In this study, we performed functional characterization of SlARF6A in tomato. SlARF6A is located in the nucleus and exhibits transcriptional activator activity. Overexpression of SlARF6A increased chlorophyll contents in the fruits and leaves of tomato plants, whereas downregulation of SlARF6A decreased chlorophyll contents compared with those of wild-type (WT) plants. Analysis of chloroplasts using transmission electron microscopy indicated increased sizes of chloroplasts in SlARF6A-overexpressing plants and decreased numbers of chloroplasts in SlARF6A-downregulated plants. Overexpression of SlARF6A increased the photosynthesis rate and accumulation of starch and soluble sugars, whereas knockdown of SlARF6A resulted in opposite phenotypes in tomato leaves and fruits. RNA-sequence analysis showed that regulation of SlARF6A expression altered the expression of genes involved in chlorophyll metabolism, photosynthesis and sugar metabolism. SlARF6A directly bound to the promoters of SlGLK1, CAB, and RbcS genes and positively regulated the expression of these genes. Overexpression of SlARF6A also inhibited fruit ripening and ethylene production, whereas downregulation of SlARF6A increased fruit ripening and ethylene production. SlARF6A directly bound to the SAMS1 promoter and negatively regulated SAMS1 expression. Taken together, these results expand our understanding of ARFs with regard to photosynthesis, sugar accumulation and fruit development and provide a potential target for genetic engineering to improve fruit nutrition in horticulture crops.

Crop genetics: lessons from hybrids The genetic sequence of a hybrid walnut tree sheds light on the evolution of the parental species and on some important traits. A study led by Ming-Cheng Luo and Jan Dvorak at the University of California Davis, USA, describes a new approach for producing high-quality genome assemblies of the parental species from interspecific hybrids. By applying long-read sequencing technology and optical mapping to a popular hybrid between cultivated Persian/English walnut and a wild relative that is native to North America they were able to completely assemble the genomes of these two species, gain insights into the evolution of their chromosomes and the distribution of disease-resistant genes. This approach could be used on other outcrossing crops to generate reference-quality genome assemblies and accelerate genetic improvements in commercially important crops.

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.

Crop genetics: novel gene involved in tomato ripening Chinese researchers have identified a new gene which regulates the ripening of tomatoes. Several genes known to control tomato ripening are members of the NAC family of regulators. To identify others, a team led by Daqi Fu of China Agricultural University blocked the expression of candidate NAC genes. The discovered that silencing NOR-like1 repressed ripening, leaving the tomatoes partially green. The team also engineered plants with defective copies of NOR-like1 and found that this delayed ripening and eventually resulted in partially ripe fruit and impaired seed development. RNA sequencing of these lines revealed that NOR-like1 directly regulates genes involved in ethylene synthesis, carotenoid accumluation, chlorophyll metabolism, and cell wall breakdown. These findings clearly demonstrate a key role for NOR-like1 as a positive regulator of tomato ripening and a potential tool for controlling this important process.

Abscission: Uncovering a master regulatory gene Investigations using tomato plant models provide insights into a key part of plants’ growth cycle. During healthy growth, plants deliberately drop unfertilized flowers and ripe fruit - a process called abscission. This process influences crop yields, yet the molecular mechanisms involved are not clear. Tomato plants provide a valuable model because they develop distinct abscission zones (AZ) at the stems (pedicels) attaching single flowers to the plant. Shimon Meir at the Agricultural Research Organization, The Volcani Center in Israel and co-workers uncovered the role of the tomato hybrid proline rich protein gene (THyPRP) in regulating the tomato flower AZ. Using a newly-developed microarray chip to monitor genes in the AZ, the team found that silencing THyPRP altered gene expression in the flower AZ, which in turn affected its competence to respond to ethylene signaling. They also identified several other proteins and signaling pathways involved in abscission.

Flower development: When to wilt How long flowers bloom is determined by genes that alter levels of the plant hormones ethylene and auxin. When flowers are no longer needed, plants signal them to die; the underlying genetic mechanisms are not well understood. Cai-Zhong Jiang at the University of California, Davis and co-workers used genetic analysis to determine how the signals for petal death are encoded. They studied petunia flowers at four stages: opening, pollen release, onset of wilting, and fully wilted, and identified over 5000 genes that were turned up or down. The master switches for petal death were found to be genes controlling ethylene and auxin levels. Using a virus to artificially switch off several genes, the researchers identified genes that shorten or extend flower life by up to three days. These results may be useful in plant breeding.