Volume 6, 2019

Genomic insights from an efficient, low-cost DNA sequencing strategy could enable more sustainable cacao cultivation. Growing demand for chocolate is currently being satisfied by increasing land use. A richer understanding of this plant's genome could enable development of more productive strains, and Juan Carlos Motamayor and colleagues at Mars Chocolate have demonstrated a method for rapidly collecting such data. Most sequencing platforms produce vast multitudes of short DNA sequences which must then be assembled into a final map—a particular challenge for cacao, whose genome contains complex repetitive regions that are tough to reconstruct. Using a newer platform known as MinION, which produces far longer sequence reads, Motamayor's team assembled a detailed genome map for a widely-used cacao cultivar within months for under $5,000. This approach could facilitate genetic engineering efforts to improve crop performance.

Genetic analyses show molecular differences that could explain why curly endives taste bitterer than smooth ones. Donato Giannino of the Institute of Agricultural Biology and Biotechnology and colleagues in Italy analyzed the genetic differences between curly and smooth endives, a leafy vegetable used in salads. They found more than 3000 single sequence variations in genes distinguishing the two types from each other. Twenty six genes were involved in the biosynthesis of sesquiterpenoids, metabolites important for plant survival that also contribute to the bitter taste of endives and have antimalarial, sedative and analgesic effects when isolated for humans. Their levels were higher in curly than in smooth endives, potentially contributing to their more bitter taste. The information expands the genetic data available on endives for breeding programs.

The genetic processes that determine the colors in purple kiwifruit have been revealed by researchers in New Zealand. Anthocyanin pigments are not only essential for plant growth and development, but also provide color to make fruit attractive to pollinators and indicate ripeness for the food industry. Andrew Allan and co-workers at the University of Auckland and The New Zealand Institute for Plant and Food Research Limited examined several different kiwifruit species, and found that their color was determined by the ratio of red cyanidin-based to blue delphinidin-based anthocyanins. The team identified four biosynthetic genes that are crucial for accumulating anthocyanins, and showed that two of those genes control the red-to-blue pigment ratio. This new understanding of the anthocyanin profile could allow metabolic engineering of novel fruit colors, possibly with greater health benefits for humans.

Researchers have pinpointed key genes that make strawberries turn red when they ripen. The role of hormones in fruit ripening has been extensively studied, but questions remain about the underlying genetics. Haoru Tang at Sichuan Agricultural University in China and co-workers assembled detailed genetic profiles of two wild strawberry varieties, one with red and the other with white fruits, at three stages of ripening. They focused on long non-coding RNAs (lncRNAs), master switches of gene regulation. Identifying differences in lncRNA profiles between the varieties allowed them to trace the complex genetic networks controlling ripening and redness. They also identified two key genes that generate red pigment, which are switched off in the white fruits. These results illuminate the complex genetics underlying a key feature of one of the world's most economically important fruits. Researchers have illuminated the genetic cues that control the ripening of strawberries by comparing the genes switched on two variants, that produce red or white fruits, respectively.

Two genes have been discovered that drive the production of survival-associated molecules in plants. Proanthocyanidins (PAs) are anti-inflammatory and antioxidant molecules produced by plants that defend against pathogens and preditors. A Chinese research team led by Junmei Yin and Guangsui Yang, from the Chinese Academy of Tropical Agricultural Sciences, set out to discover the genes responsible for PA biosynthesis, finding that two proteins, AaMYB3 and AabHLH1, interact and contribute to PA biosynthesis in the tropical flower Anthurium andraeanum. Their results also showed that genetically overexpressing the two proteins caused PA accumulation in tobacco plants, with the function of AaMYB3 increased by AabHLH1. The expression pattern of the AaMYB3 and AabHLH1 genes coincided with other PA biosynthetic genes. The researchers suggest these genes may be utilized to engineer PA biosynthesis in plants.

Researchers in China have identified several genes that help chrysanthemum plants withstand waterlogging. Fadi Chen's team at Nanjing Agricultural University used high-throughput sequencing to search for correlations between genetic mutations and waterlogging tolerance in 88 chrysanthemum varieties. One analysis method identified 137 mutations linked to waterlogging tolerance, while a second uncovered 14 mutations. Comparing the two lists revealed 11 mutations common to both. Six of these mutations could improve waterlogging response by 25%, and the team found that the mutations could be combined to improve performance even further. The team developed and tested a genetic marker to identify one of the high-tolerance mutations, demonstrating how this information may help breeders. They also identified four genes linked with the 137 mutations. Altogether, these findings point the way towards breeding chrysanthemums with greater waterlogging tolerance.

Prunus mume, Chinese plum, owes its unique scent to extra gene copies. Researchers knew the main component of P. mume blooms’ prized scent, but the details of its production were unknown. Qixiang Zhang at the Beijing Forestry University and co-workers investigated the genetic basis of the scent, and uncovered an interesting evolutionary tale. A search for the scent production genes showed that P. mume has 44 copies; closely related P. persica, which lacks the special scent, has only two. Further analysis showed that the genes are clustered together, indicating they originated from duplication events, the evolutionary equivalent of accidental copying. The superfluous copies, released from their usual responsibilities, were free to evolve new functions, including scent production. These results illuminate how new plant traits can evolve, and unravel the mystery of this special scent.

A gene involved in regulating responses to chill stress in tomato plants may prove valuable in reducing crop damage caused by low temperatures. A significant limiting factor in growing certain crops is cold stress – for example, tomato and cucumber plants suffer chill damage and reduced productivity at low temperatures (0 to 12 °C). Xianggiang Zhan at the Northwest A&F University in Shaanxi, China, and co-workers demonstrated that the gene SIF3HL is a key regulator of chilling stress tolerance in tomato plants. The team generated plants with no SIF3HL expressed and found that they responded poorly at low temperatures, with higher levels of reactive oxygen species and decreased levels of metabolic enzymes. Expression levels of four cold-responsive genes were also reduced. Plants overexpressing SIF3HL, on the other hand, coped well at low temperatures.

A mutation in the tomato gene encoding UV-damaged DNA binding protein 1 (DDB1) delays fruit ripening and softening. Previous studies have established that DDB1 mutants produce fruit with high levels of carotenoids, flavonoids, and vitamin C. However, little was known about the effects of the mutation on fruit ripening processes. Yongsheng Liu at Hefei University of Technology, China, and colleagues showed that DDB1 is implicated in the synthesis of the fruit ripening hormone ethylene, the expression of ripening-associated genes, particularly during early fruit development, and cell wall-related genes. The slower ripening and increased firmness of DDB1 mutant tomatoes highlight this gene as a useful target for improving both the shelf-life and nutritional value of fleshy fruits.

Two hormones that regulate fruit ripening are more closely linked than previously thought, according to a study of ripening in peaches. Ethylene is a key ripening hormone in many fruits, and high ethylene levels turn on ethylene response factors (ERFs), genes that trigger production of sugars, pigments, and flavor compounds associated with ripening. Another hormone, abscisic acid (ABA), has recently been found to affect ripening, but its interaction with ethylene is unclear. Zhiqiang Wang and Guohuai Li at the Chinese Academy of Agricultural Sciences and coworkers investigated how ethylene and ABA interact during ripening. They found that as ethylene levels increased, ABA production was stimulated. Further investigation showed that ethylene directly triggered the ABA increase via ERFs. These results illuminate the fruit ripening process, and may help in finding ways to prolong fruit shelf life.

Uncovering the genetics behind desirable traits in petunia plants could help improve commercial cultivars. While petunia plants are a key feature of the global horticultural industry, the limited genetic variability in commercial plants makes it difficult to improve desired plant traits. Zhanao Deng at the University of Florida, US, and co-workers conducted a genome-wide QTL identification study using a crossbred population combining two petunia  species, P. integrifolia and P. axillaris. The team phenotyped the petunias in an open-air sub-tropical field rather than in an artificial environment like previous studies. They identified and characterized 17 genetic loci for seven important aesthetic traits, ranging from flower count to plant size. The petunia species had very different genetic backgrounds, likely stemming from their different geographic origins. The two species each can contribute novel genes for enhancing cultivated petunia cultivars.

Apple latent spherical virus (ALSV) offers a powerful tool to reveal strawberry gene function and induce early flowering. Preferential strawberry traits are highly influenced by their genetics; however, the specific mutations that change these traits are largely unknown. This prompted Nobuyuki Yoshikawa and his team from Iwate University, Japan, to develop ALSV to infect and introduce intended genetic material into strawberries. Infecting in vitro cultured plants at a rate of 58–100%, ALSV-vectored gene introduction proved able to ‘silence’ a natural strawberry gene, constituting a method to identify gene functions. The infection was not pathogenic and did not carry on to the plants’ progeny. The team also used ALSV to introduce a gene that induced flowering 2 months post inoculation, a technique that could be used in future to promote shorter cross-breeding times.

Researchers in the United States have developed a 3D imaging technique to quantitatively measure the shape of blueberry bushes in order to evaluate their suitability for mechanical harvesting. The team, led by Changying Li of the University of Georgia, used handheld LiDAR scanners to collect 3D data from bushes in blueberry fields. Their analysis pipeline converted these data into a description of the bushes, including height, width, volume, crown size, and parameters describing the shape. While some traits matched manual measurements better than others, the analysis described bush shape sufficiently to distinguish varieties. The team also created a tool to visualize key parameters related to suitability for mechanical harvesting. This study provides a promising tool to evaluate and manage varieties of blueberries and similar crops, though further work is needed to speed up data collection.

A broad genomic mapping effort in the common bean reveals sequence elements that may help protect this crop from plant-killing worms. The soybean cyst nematode has the potential to wreak havoc on the common bean, an important food source in many countries. Researchers led by Glen Hartman at the US Department of Agriculture conducted an extensive survey of 363 different derivatives of this crop in order to identify genetic features that might confer resistance against two different strains of this infectious worm. Their study identified regions on three different chromosomes that each appear to contribute some degree of protection against soybean cyst nematode. These offer starting points for understanding the molecular foundations of pest resistance in this crop, and could facilitate the future breeding of more robust bean strains.

A legume gene involved in determining the spatial pattern of leaflets seems to have evolved this function earlier than previously thought. Xin Li from Nanjing Agricultural University, China, and coworkers studied a mutant variety of mungbean in which the plant's leaves display a simple architecture instead of the usual compound arrangement, with several leaflets joined to a single stem. They discovered a mutation in the mungbean version of a gene called LEAFY. This gene, together with others, proved pivotal in compound leaf development in mungbeans. The results run counter to prior data showing that, outside of a small group of related legume species, LEAFY plays only to play a minor role in compound leaf development in these agriculturally important plants. The findings could thus inform breeding efforts in legumes generally.

The mystery of how pigmenting anthocyanins are transported to intracellular storage is starting to be revealed. Alongside giving fruit their color, anthocyanins confer benefits to plant and human health. Glutathione S-transferases (GSTs) are responsible for transporting anthocyanins to storage vacuoles, yet research is lacking on how GSTs are regulated. Xuesen Chen, from China's Shandong Agricultural University, and his team analyzed the activity of 23 GST genes in apple, finding one, MdGSTF6, was most highly active in the fruit-coloration stage of apple development. MdGSTF6 expression correlated with fruit anthocyanin levels and also restored anthocyanin levels in transport-suppressed plants, confirming its function. Chen's team then discovered that MdGSTF6 expression is activated by the protein MdMYB1. The MdMYB1 gene is the major regulatory gene in anthocyanin synthesis, and is now revealed to also influence their transport.

The fungus Trichoderma harzianum induces differentiated protein production in tomato roots that benefits plant nutrition and survivability. Microorganisms advantageous to plants have long been exploited in agriculture; however, with limited studies into the interface of Trichoderma fungus and plants—the roots. Italian researchers, led by the Research Centre for Vegetable and Ornamental Crops' Nunzio D'Agostino and the National Research Council's Marina Tucci, inoculated tomato plant roots with T. harzianum over 72 h, finding over 1200 examples of differential gene expression and post-expression modification that resulted in improved plant growth and immune system regulation. The interaction also induces a root change that likely promotes further interaction with the fungus and increased stress tolerance via promoting antioxidation and defensive activity. The team's work provides early evidence of the molecular mechanisms behind root–fungus symbiosis and may help to inform crop breeding and fertilisation strategies.

A newly-acquired collection of gene regulatory elements gives researchers a powerful toolbox for studying fruit production in strawberry plants. Tissue-specific gene expression is governed by DNA sequences known as promoters, and researchers led by Rachel Shahan and Zhongchi Liu at the University of Maryland recently set out to identify promoters that regulate the initiation of strawberry formation. Most fruits form in the plant ovary, but strawberries originate from the same ‘receptacle’ structure that gives rise to flowers. Liu and Shahan therefore used RNA sequencing to identify genes that are expressed specifically in this tissue but not elsewhere in the strawberry plant. Their efforts uncovered seven promoters that appear to operate in a highly receptacle-specific fashion. Armed with these sequences, researchers can now begin to manipulate and thereby dissect the genetic mechanisms governing strawberry fruit formation.

Next-generation sequencing of loquat fruit stored in different ways reveals the genes and proteins that help reduce fruit spoil. Loquat fruit become rigid and woody during cold storage, thanks to the build-up of lignin polymers in the fruit flesh. Lignification can be prevented with exposure to heat or preconditioning to cool temperatures before cold storage. Zhangjin Fei at Cornell University, New York, US, Qingbiao Wu at Zhejiang University in Hangzhou, China, and co-workers used comparative RNA sequencing to explore the molecular mechanisms inherent in lignification. The team placed three loquat groups in post-harvest cold storage for 8 days: one pre-treated with heat, one conditioned at cool temperatures, and one with no pre-treatment. They identified key genetic differences between the groups and several protein families that may regulate lignification.

Researchers in China have discovered the first region of the grapevine genome known to confer resistance to ripe rot, a fruit disease caused by fungal pathogens. A team led by Shiren Song and Jiang Lu from Shanghai Jiao Tong University crossbred a European grape species that's susceptible to ripe rot with a Chinese grape species that's resistant to the disease. They inoculated the progeny's leaves with the fungus and searched for genetic differences that could explain variation in rot symptoms. In this way, the researchers identified a segment of chromosome 14 from the Chinese Amur grape, Vitis amurensis ‘Shuang Hong’, that accounted for about 20% of difference in resistance capacity between the two grape species. This information could help breeders select more rot-resistant grapevines in the future.

Researchers in China have identified the genes involved in strawberry ripening. Mizhen Zhao led a team at the Jiangsu Academy of Agricultural Sciences which used long-read sequencing to investigate gene expression during six stages of strawberry fruit development, from small green fruit through whitening to large red fruit. They identified thousands of genes which are activated or repressed during fruit development, including 527 transcription factors – genes which regulate the activity of other genes. The analysis also revealed that genes related to the plant hormone auxin were downregulated in developing fruits, while those related to abscisic acid were upregulated, clarifying the role of the two hormones during strawberry ripening. This work not only provides a high-quality reference transcriptome for future strawberry work but also highlights genes related to ripening for further study.

Protein regulators of anthocyanin production have been identified in tomato and tobacco plants. Endogenously produced anthocyanins confer protective benefits to plants, and there is growing evidence of their health benefits to humans. Researchers from China, led by Chongqing University's Guoping Chen, analyzed tobacco and genetically modified tomato plants grown under high- and low-light conditions to discern the cellular processes modulating anthocyanin production. The team found a number of interacting metabolites that promoted anthocyanin, in particular a complex of three proteins, and evidence of a negative-feedback loop to prevent over-accumulation. These results provide insight into the biosynthesis of plant nutrients, could inform future efforts to genetically engineer more nutritious and valuable fruit, and also validates the team's mutant tomato plant as a strong model to study anthocyanin production.

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.

The interplay between various non-protein-coding RNA molecules plays a critical role in managing tomato plants’ defenses against infection. Long non-coding RNA (lncRNA) molecules can modulate gene function by binding to other, complementary RNA molecules. Researchers led by Jun Meng and Yushi Luan at the Dalian University of Technology recently set out to identify lncRNAs that contribute to tomato resistance to the pathogen that causes late blight. Their team specifically sought lncRNAs targeting another RNA molecule known as miR482b, which they had previously found to weaken plant resistance to infection. They found that one such molecule, lncRNA23468, can counter the effects of miR482b and protect tomatoes against late blight by boosting the activity of genes involved in the immune response. These results thus offer important insights into the mechanisms underlying disease resistance in this important crop.

Researchers in the USA reveal a link between cell wall composition and splitting skin in ripe tomatoes, known as cracking. To unravel the mechanism behind cracking, a team led by Elizabeth Mitcham of the University of California, Davis, compared wild-type tomato plants, mutant plants with increased soluble solids, and mutant plants with altered cell wall structure. They treated the three lines with the hormone ABA to induce cracking and measured several traits in the fruit. ABA treatment did not affect cracking incidence in the cell wall mutant but increased its frequency in the other two lines. Cell wall composition and thickness were the traits with the strongest correlation with cracking rate. Altogether, these findings show that cell wall structure is a major determinant of cracking and point the way towards reducing skin splitting in tomatoes.

Turnips show physiological and molecular signs of hypocotyl-tuber development as early as 16 days after sowing, a finding that could help farmers improve the performance of this important food and feed crop. A team led by Guusje Bonnema from Wageningen University and Research in the Netherlands
 compared the early anatomy of turnips and another closely related subspecies of Brassica rapa, the non-tuber–forming pak choi. They documented differences in the cellular organization of the xylem by day-16 after seed planting. Gene expression profiling between 1–6 weeks after sowing revealed many genes involved in hypocotyl-tuber initiation and growth. These genes affect a range of biological processes, from carbohydrate transport and metabolism to cell-wall growth to hormone regulation. Tissue culture experiments also showed that auxin, a plant growth hormone, promoted early hypocotyl-tuber development.

The discovery of genetic traits that make certain apple trees resistant to soil pathogens may help generate hardier crops. After apple orchards are replanted, some trees succumb to pathogens and fungi that have accumulated in the soil. To ensure the longevity of orchard sites, researchers want to clarify the genetic makeup of resistant trees. Yanmin Zhu at the United States Department of Agriculture in Wenatchee, US, and co-workers conducted comparative genetic analysis of two apple genotypes (one susceptible, one resistant) during infection with the plant pathogen Pythium ultimum. They found that the genotypes have multiple differentially-expressed genes. Key genes and signaling pathways in the susceptible tree's roots were suppressed 48 h after infection when the tree was most vulnerable, whereas the resistant tree responded within 24 h, upregulating genes that strengthen roots and fight disease.

A high-throughput method for determining plant characteristics offers a viable way to track competitive traits in the field. Increasingly difficult agricultural conditions are spurring plant breeding programs to prioritize plants with strong adaptations for healthy metabolism, but no current technologies can rapidly assess plant traits in the field. Now, Benoît Pallas, of the French National Institute for Agricultural Research, and his team have adapted tools such as infrared and laser-light scanning, and drone imagery, to take define and correlate metrics of 1000 apple trees, such as measurements of volume, leaf area, photosynthetic activity, and water usage. With these results and prior knowledge of the trees’ genotype, the team was able to group the trees into six classes with distinct physical and functional trait combinations. These techniques may open doors for discovering the genetic bases of plant traits.

The use of an interstock from a dwarf cultivar lowers the water conductance and affects hormone signal metabolism and transport of the sweet persimmon (Diospyros kaki Thunb.), resulting in smaller and more manageable fruit-bearing trees. Shenchun Qu from Nanjing Agricultural University, China, and colleagues compared ‘Kanshu’ persimmon scions grafted on a ‘Diospyros lotus’ rootstock with and without an interstock from a rare dwarf cultivar called ‘Nantong-xiaofangshi’. The interstock-grafted plants moved water less efficiently through their stems. The same plants also exhibited gene activity patterns that correlated with lower levels of the key growth hormones auxin and gibberellic acid. Expressing one of those putative hormone-repressor genes in transgenic tobacco caused the plants to grow shorter. By helping elucidate the mechanisms of interstock-induced dwarfing, the findings could help improve future persimmon cultivation.

Apple trees sprayed with a plant growth hormone called gibberellic acid develop seedless fruit that show morphological differences explained by changes in gene expression profiles. Ann Callahan from the US Department of Agriculture in Kearneysville, West Virginia, and colleagues showed that gibberellic acid induces flowers
of the ‘Honeycrisp’ apple
variety to develop fruit without fertilization, a process known as parthenocarpy. These fruit were seedless, with a thinner ovary at the fruit's core and a lower acid content compared
to normally pollinated controls. The researchers analyzed gene activity patterns 18 days after hormone treatment. They found differences in the expression levels of genes involved in cell division, hormone metabolism and cell wall dynamics, plus lower levels of an acidity-associated gene during early ovary development. The findings show that parthenocarpic Honeycrisp apples are possible, although they exhibit quality differences.

Understanding the metabolic variations of different types of sweet potato could help improve their nutritional value. Sweet potato is one of the world's major food crops but recurrent breeding of high yielding lines is reducing their genetic diversity. A study led by Paul D. Fraser, Royal Holloway University of London, UK, examined the chemical differences between 25 types of sweet potato, including orange and purple varieties. They show that there is little correlation between the chemicals found in the leaves and storage root material and that there are significant differences in metabolism between varieties that produce different pigments in their storage roots. Their findings highlight the importance of metabolite profiling for identifying those varieties that produce the highest levels of starch and health-promoting compounds such as carotenoids.

Genomic sleuthing reveals insights into an ancestral chromosomal duplication event from the early evolution of the pear tree. Such ‘whole-genome duplication’ is common among plants, and can arise from the combination of genetic material of plants from either the same (autopolyploid) or different (allopolyploid) species. The pear is known to have undergone a duplication event 30 million years ago, and Shaoling Zhang and colleagues at Nanjing Agricultural University in China set out to assess the nature of this genome expansion. After analysis of pear genome data and comparison against other fruit plant species, the researchers determined that the pear is an autopolyploid, and that genes found in just one ‘subgenome’ have subsequently evolved expression profiles that differ noticeably from those genes that are present as multiple homologues amongst the duplicated chromosomes.

Different selection pressure on duplicate genes explains how willow and poplar diverged from a common progenitor with four copies of their genome. A study by Tongming Yin and colleagues at Nanjing Forestry University in China compared the genomes of these two fast-growing trees to shed light on how they lost ancestral genes to retain only two copies of their genome. They found an uneven selection pressure on different genomic regions and a faster loss of duplicated genes in willow. This could explain why willow evolved more nascent and gave rise to over 300 species, whereas there are only about 29 species of poplar. Differences in gene density in the sex chromosomes are also key to the divergent evolution of these two sister lineages.

Crown rot results in major economic losses for strawberry growers; now three regions of the strawberry genome have been identified which are associated with resistance to the disease. A better understanding of these genetic mechanisms may lead to the development of more crown rot-resistant plants. Richard Harrison at NIAB EMR in Kent, UK, and colleagues used quantitative trait loci mapping to pinpoint specific regions of the cultivated strawberry genome associated with resistance to Phytophthora cactorum, the water-borne pathogen that causes crown rot. These regions appear to influence disease susceptibility independently of one another, but together account for 37% of variance in resistance to P. cactorum. A further genome wide association study identified another locus associated with rot resistance. Further work is needed to elucidate the mechanism by which genes clustering in these regions affect disease susceptibility.

Researchers in the US have uncovered how rootstocks affect scions following grafting, which will help to develop more resilient crops. A team led by Allison Miller of Saint Louis University grafted the ‘Chambourcin’ grape variety onto three different rootstocks and investigated the effect on leaf shape, ion concentration, and gene expression in the scion. They discovered that the rootstock influenced how leaf shape changed in response to different irrigation conditions. A similar irrigation-dependent effect of rootstock was found for the ion composition in the shoot. The team also identified roughly 100 genes with altered expression in each of the grafted vines, including five genes which were altered by all three graft combinations. These findings are a first step toward understanding the relationship between rootstocks and scions and modulating it to produce crops better adapted to challenging environments.

Numerous genes, including many involved in the production and signaling of key growth hormones, regulate the on-tree maturation and postharvest ripening of pear fruit. Fabrizio Costa from the Edmund Mach Foundation in San Michele All'adige, Italy, and colleagues identified nearly 9,000 genes that were differentially expressed across four maturation stages of the Abate Fetel cultivar of European pear (Pyrus communis). From this long list of genes, the researchers selected 12 involved in hormone signaling, cell wall metabolism or aromatic volatile compound production, and evaluated their expression pattern with and without application of a chemical added to delay ripening during postharvest storage. Six of the genes, five of which controlled the activity of the hormones auxin and ethylene, showed differential expression, and could be informative as molecular biomarkers for improving fruit quality in pears.

A small molecule, miR396, plays a big role in how plants respond to salt stress, a growing constraint on global crop yield. Salt stress prevents plants from absorbing nutrients, causes oxidative stress, and destroys key cellular machinery; some plants cope better than others. Hong Luo at Clemson University in South Carolina, USA and coworkers investigated how creeping bentgrass handles high salinity, focusing on the microRNA miR396, previously implicated in salt tolerance. Artificially elevating miR396 improved bentgrass’ salt tolerance. Further investigation showed that miR396 triggered increases in proteins that pump excess salt out of cells, others that prevent water loss, and antioxidant production. miR396 was found to be a master regulator that orchestrates many lines of defense against excess salt. Understanding how these pathways are activated and integrated could help in breeding more salt-tolerant crops.

Researchers in China have created a toolkit to easily mutate genes in tomato using the CRISPR gene modification technology. Zhengguo Li of Chongqing University developed the system in response to the lack of an open, standardized, reliable gene editing tool in tomato. The toolkit is designed according to an open-source, modular standard known as Biobrick. It consists of several molecular building blocks which can be used to target up to eight genes for editing or deletion. The kit also includes software to help researchers determine the DNA sequences necessary to copy genes of interest and prepare them for the CRISPR reactions. Li's team tested the toolkit by using it to successfully simultaneously mutate multiple genes involved in tomato ripening. The new toolkit will enable researchers to rapidly and easily manipulate genes in this important crop.

Studying how the wild grape Vitis amurensis copes with cold may help in breeding grape varieties that can grow at lower temperatures. To prevent frost damage, plants can increase cells’ sugar and protein contents, lowering the freezing point, and preventing ice crystal formation. V. amurensis, a wild grape native to Asia, grows well at low temperatures, but its cold-tolerance compounds have yet to be identified. Haiping Xin and Shaohua Li at the Chinese Academy of Sciences and co-workers profiled the compounds present in V. amurensis and V. vinifera cv. Muscat of Hamburg, a wine grape, following cold stress. V. amurensis cells were richer in a dozen compounds, including amino acids, organic acids, and putrescine, a component of the odor of decaying flesh. These results may help in developing grape varieties with increased cold tolerance.

Chinese researchers have optimized transient gene manipulation (TGM) to probe the function of genes in strawberries. In TGM, the expression of a gene is temporarily altered and the effect on plant development measured. TGM experiments can be conducted in days rather than the months needed for experiments involving stable transformation. A team led by Jia Wensuo of China Agriculture University evaluated how the use of TGM in strawberry fruits was affected by various conditions, including different delivery vectors, temperatures, time periods, and fruit stages. They found that the correct delivery vector, temperature, and fruit stage were crucial for the success of TGM. The team also developed a TGM analysis method to quantify and compare the contribution of different genes. The techniques developed in this study provide valuable tools for the genetic analysis of strawberry ripening.

Investigations have yielded early insights into the genetic basis of strawberry taste and nutrition. Such information informs efforts to selectively breed the fruit to maximize these qualities. A team of researchers from Spain and Germany, led by the University of Malaga's Sonia Osorio and the IFAPA´s Iraida Amaya, found 133 locations within strawberry DNA that correlated to variation in metabolic pathways and desirable traits including acidity, sugar content, and the concentration of l-ascorbic acid (vitamin C). Only a small number of associations persisted over the 2 years of investigations, suggesting that environmental factors also wield a significant influence over the strawberry fruit's molecular makeup. The team then used their data to identify a series of candidate genes that may be functionally linked to strawberry qualities; however, further research is needed to validate those connections.

Different apple varieties, such as ‘Gala’ and ‘Empire,’ defend themselves against fire blight in different ways, and studying how they do it may help in breeding varieties with better resistance. Fire blight is a devastating bacterial disease that can destroy entire orchard blocks in a single season. Breeding for increased resistance is one of the most efficient ways to combat it. Some apple varieties are naturally more resistant than others, but the underlying genetics are not well understood. Awais Khan at Cornell University in New York and co-workers investigated how the ‘Gala’ and ‘Empire’ varieties defend themselves in the first 72 h after infection. ‘Empire’ showed stronger resistance than ‘Gala,’ with many distinct resistance mechanisms. The researchers identified several resistance genes in each variety, which may eventually be used in breeding more blight-resistant apple varieties.

Genetic analysis of 179 types of vine has revealed regions of the genome and associated genes and proteins that control many of the key traits in the grapes. These traits are crucial for determining fruit quality and yield, in addition to conferring flavors that are highly valued by consumers and wine makers. Researchers in China, led by Da-Long Guo at Henan University of Science and Technology, used DNA sequencing to analyze genetic markers in a mixture of ancient, traditionally cultivated and modern grape varieties. The analysis identified specific regions of the genome linked to grape fruit development, weight, texture, skin color and flavor. The molecular basis of the effects of the identified genetic regions were also explored. The findings will help generate new varieties of grapes for the food and wine industries.

The fruiting season of a cherry is short and sweet, but at least it's relatively consistent across different environments, a new genetic analysis suggests. The development of additional early- and late-maturing sweet cherry cultivars is a major objective for cherry-breeders, but the influence of the environment on the timing of fruit maturity—which could reduce the accuracy of selective breeding efforts - was unclear. So, Craig Hardner at the University of Queensland in St Lucia and colleagues used DNA markers to  model relationships among individuals and examined the dates at which their fruit ripened at four different locations in Europe and the USA across two seasons. The timing of fruit maturity was relatively stable between related individuals across similar environments, suggesting that new cherry cultivars could be developed without having to test them at multiple sites.

Researchers in China have shown that the gene-editing system CRISPR/Cas9 can be used to efficiently mutate genes of interest in cabbage. Cabbage plants normally do not self-pollinate, making the use of traditional mutagens difficult. Hongyuan Song of Southwest University therefore turned to CRISPR/Cas9, a system which can introduce precise mutations into specific genes. Song's team targeted three genes: one related to coloration, another to self-incompatibility, and a third involved in pollen development. They began by mutating each gene separately to test the system's efficiency. Next, they built a CRISPR/Cas9 construct that would simultaneously mutate the pollen gene and the self-incompatibility gene. One-third of the plants produced using the construct had mutations in both of the target genes. These findings demonstrate that CRISPR/Cas9 is a valuable tool for trait improvement and genetic research in cabbage.

Improving the taste, colour, and disease resistance of apple varieties will now be easier, thanks to a set of genetic markers that can be used to select the best individuals to breed. Although many crop genomes have been sequenced, the information must be translated into inexpensive and easy-to-use tests for particular traits before it is practical to apply it in breeding programs. David Chagné at The New Zealand Institute for Plant & Food Research and co-workers have developed a set of markers for apple trees that indicate fruit quality, and disease and pest resistance. Using these markers, breeders will be able to peer inside the genomes of parent and offspring trees to determine whether or not they possess desirable traits. This approach shows promise to improve breeding programs for apples and other crops.

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.

The plums grown today for dried prunes likely originated from hybrid crosses and artificial selection by early agrarian societies, a genetic analysis shows. Chris Dardick from the US Department of Agriculture's Appalachian Fruit Research Laboratory in Kearneysville, West Virginia, and coworkers sequenced more than 100,000 single DNA letters scattered across the genomes of 405 different samples of the European plum (Prunus domestica). The plants clustered genetically into four groups that corresponded with known plum varieties, such as greengages and mirabelles, but not with others, including damsons. Overall, the cultivated plums harbored a low level of genetic diversity, suggestive of repeated inbreeding from a small number of founder plants. The data also point to the European plum originating from a hybrid cross between the cherry plum (Prunus cerasifera) and blackthorn (Prunus spinosa).

Long-term treatment with an anti-ripening agent inhibits the expression of regulatory genes that normally break down the cell wall of the papaya fruit. A team from Guangzhou's South China Agricultural University led by Xueping Li and Weixin Chen applied a hormone inhibitor to papayas at the breaker stage of fruit ripening. 1 h of treatment delayed ripening, whereas 16 h of treatment caused the fruit to become rubbery, with significantly higher levels of cellulose and lignin, both structural components of the cell wall. The researchers identified two genes with reduced expression following extended hormone-blocking treatment. Both normally encode proteins that aid in degrading the cell wall to promote fruit ripening. The findings thus offer a molecular explanation for why misuse of anti-ripening agents on papaya fruits can lead to undesirable characteristics.

Genes likely involved in DNA replication, immune defenses, stress response, and more occur during development within the plum plant tissue that transports molecules such as nutrients, genetic material, and hormones. The genes underlying this tissue, called phloem, are sparsely understood, inspiring a US team of researchers—led by the University of Maryland's James Culver—to categorize their activity. Using a technique that “traps” cell-specific genetic material in the process of translation, the team analyzed plum phloem gene expression at 2, 4, and 6 weeks after the induction of leaf development. Finding reduced activity associated with DNA replication activity and an increase in activity associated with immune response, response to nutrients, and transport of sugars among others. These findings could power investigations into phloem processes and how they could be manipulated for enhanced crop production.

An updated annotation of the wild strawberry genome includes over nine thousand new genes. Since the genome sequence of the wild strawberry was first published in 2011, technological improvements have led to various refinements and updates. Chunying Kang and colleagues at Huazhong Agricultural University in Wuhan, China, found that a large number of genes were either absent or inaccurately described in the annotation of the latest wild strawberry genome. They annotated 5,419 more protein-coding genes, including 139 transcription factor and 92 protein kinase encoding genes, and carried out a comprehensive analysis of the expression patterns of all genes in the new annotation. They also identified microRNAs that contribute to regulate gene expression. These data will aid future comparative and functional studies in widely grown hybrid strawberry species.

A single gene has been identified in tomatoes that regulates multiple aspects of fruit quality, including levels of health-promoting anthocyanins, opening the door to engineering more nutritious and better-tasting tomatoes. Fruit breeders have long-manipulated genes to enhance traits like yield or disease resistance, but it is rare to find a single gene that can improve multiple aspects of fruit quality. In this study, Zhengguo Li at Chongquing University in China and colleagues show that over-expressing a transcription factor called SIMYB75 results in striking deep purple tomatoes enriched in anthrocyanins–antioxidants thought to be protective against various diseases - which tomatoes are usually devoid of. They also had higher levels of other health-promoting phytochemicals and enhanced production of aroma volatiles, which can influence the taste and flavor of fruit.

Calcium may hold the key to growing peonies with stronger, straighter stems, by enabling the construction of reinforced cell walls, which impart structural support. Peonies are a popular kind of cut flowers, and those with straight stems are more sought after. Although recent studies have hinted at the importance of calcium ions, the mechanism was unclear. To investigate, Jun Tao at Yangzhou University in Jiangsu, China, and colleagues treated herbaceous peonies with ethyl glycol tetraacetic acid (EGTA), a chemical that binds to and removes calcium ions. This resulted in the reduced deposition of a structural protein called lignin in the walls of xylem cells and more pliable stems. Further analysis revealed altered expression of 43 proteins, including those involved in calcium-ion sensing and construction of ‘secondary’ walls in xylem cells within the stem.

The bacteria Candidatus Liberibacter asiaticus (CaLas) causes orange trees to produce poor-tasting fruit thanks to the decreased production of flavour-enhancing proteins, sugars, and metabolites. The University of Florida's Frederick Gmitter and his team of US and Chinese scientists profiled the proteins and metabolites of healthy Valencia sweet orange trees infected with CaLas, a bacterial pathogen that causes the citrus disease Huanglongbing and reduces the quantity and quality of fruit and juice. The researchers found 123 differentially-expressed proteins and decreased numbers of taste-enhancing constituents, including those mediated by key energy-producing processes. This degradation involved a class of chemicals called terpenoids, which the authors link to poor quality fruit. These results provide insights into the pathogenesis of CaLas infection and could empower future studies to prevent the impact of the bacteria and Huanglongbing infection.

Researchers in China have uncovered the genetic factors through which the plant hormone ABA controls strawberry ripening. Zisheng Luo's team at Zhejiang University used high-throughput sequencing to compare gene expression in strawberry plants after they were treated with ABA or an ABA-blocker. They discovered that ABA changes the expression of genes related to other hormones, metabolite synthesis, and breaking down cell walls. The team also checked the expression of short RNA molecules which regulate gene expression, known as microRNAs (miRNAs). They found 26 miRNAs which changed expression in response to ABA, six of which were novel, and identified 18 genes regulated by these miRNAs, including a cell wall gene which may be involved in fruit enlargement. These findings clarify the molecular mechanisms linking ABA with strawberry ripening and lay the groundwork for detailed functional studies.

The ability of citrus trees to tolerate alkaline soils may hinge upon plant hormones called auxins which regulate root growth. The discovery could aid the development of more resilient rootstocks. Alkaline stress, caused by e.g. industrial run-off, is a growing problem worldwide because it reduces the growth and survival of crops – including the most widely used citrus rootstock in China, Poncirus trifoliata. To better understand the mechanisms underpinning tolerance to soil alkalinity, Hualin Yi at Huazhong Agricultural University in Wuhan, China, and colleagues used next-generation sequencing to profile the transcription products of P. trifolata seedlings and those of an alkaline-tolerant rootstock, Ziyang xiangcheng, when they were grown in three different nutrient solutions. Auxin homeostasis appears to be a key element of citrus adaption to alkaline stress, they found - probably by encouraging lateral root branching.

Studies in cabbage plants shed new light on self-incompatibility mechanisms to avoid self-fertilization. In Brassica, self-incompatibility is controlled by the expression of dominant and recessive genetic variants in the S-locus region. These variants encode proteins that mediate the rejection of self-pollen, but little is known about how the dominance relationship is established between them. Takeshi Nishio at Tohoku University in Japan and colleagues have examined the sequence, expression pattern and dominance relationships of the gene encoding the pollen-coat protein SCR-22. Despite sharing features with dominant SCR variants, SCR-22 can act in a recessive manner. Interestingly, unlike other recessive SCR variants, the suppression of SCR-22 expression does not depend on the addition of methyl groups that prevent transcription factor binding. This finding suggests the dominance hierarchy is governed by different mechanisms.

Researchers in New Zealand have produced a map of genetic variants linked with red skin color in pears, opening the door to identifying the genes responsible. Satish Kumar and others at the New Zealand Institute for Plant and Food Research Limited measured the skin color of 550 hybrid pear seedlings and sequenced their genomes. Combining these data produced a map of 7,500 variants throughout the genome and identified those associated with red skin color. The most significant variant accounted for about 15% of the color variation. Further analysis of that genomic region revealed several genes which might be related to red skin color. The genomic map produced by this study will improve breeding efficiency by making it possible to screen seedlings for fruit color, but further research is necessary to characterize the candidate genes.

China accounts for nearly half of the total global production of carrots and advances in genetic technologies are contributing to improve both crop quality and yield. Cultivated carrot is the second most popular vegetable in the world after potato; this can be largely attributed to their taste and their nutritional benefits. Ai-Sheng Xiong and colleagues at Nanjing Agricultural University, China, review the latest studies on the origin and breeding of carrots. Understanding the genetic sequence and gene expression patterns in carrot plants provides valuable insights into their evolution as well as into the mechanisms underlying their resistance to disease, production of healthy carotenoids and environmental stress tolerance. Future application of gene editing technologies will help to further improve crop production and the nutritional value of carrots.

Detailed genomic maps from the fruit-bearing trees of the Prunus genus should greatly accelerate the breeding of superior cultivars. These plants produce a variety of popular fruits, but until relatively recently, breeders had only limited genetic information with which to work. Pere Arús of Spain's Institute of Agrifood Research and Technology and colleagues have now reviewed the rapid advances in Prunus genomics that have taken place since 2010, when researchers completed the first genome assembly for this genus. In the ensuing decade, increasingly high-quality genomes from the peach, Japanese apricot, and cherry have allowed scientists to home in on chromosomal regions associated with key traits such as fruit quality and disease resistance. These data also offer valuable genetic markers that agronomists can use to guide the production of healthier trees and more commercially desirable fruits.

Modifying the structure and dynamics of plasmodesmata (PD), channels that directly connect the cytoplasm of neighboring plant cells, could improve the growth and productivity of horticultural crops. Xu Chen and colleagues at Fujian Agriculture and Forestry University, China, review recent understanding of the mechanisms regulating the opening and closing of PD and potential applications of this knowledge. Changes in the levels of the sugar polymer callose or phospholipids lining the membrane of PD, or disrupted delivery and transport of PD-associated proteins affect the channels’ permeability. Modulating PD dynamics could not only enhance plant survival, by preventing the spread of pathogens and improving their response to changing environmental conditions, but also influence crop yield by aiding the transport of nutrients into fruits and the establishment beneficial symbioses.

Almost 10 years since the first draft of the apple genome was published, the insights it has afforded are being used to improve crops, while next generation DNA sequencing is enabling the breeding value of individual plants to be more rapidly assessed. In this review, Cameron Peace at Washington State University in Pullman, US, and colleagues describe the impact whole genome sequencing of the Golden Delicious apple has had on our understanding of how cultivated apples evolved, and the genomic regions controlling fruit firmness and flavor, tree growth dynamics, responses to water and nutrient availability, and other such traits. These early discoveries have also paved the way for trait-predictive tests which should further accelerate the breeding of improved apple trees, and epigenetic studies to better understand how environmental factors trigger heritable changes in apple characteristics.