Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset

Background  

Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset.     

Chill-responsive dehydrins in blueberry: Are they associated with cold hardiness or dormancy transitions?

To survive winters, woody perennials of temperate zones must enter into endodormancy. Resumption of spring growth requires sufficient exposure to low temperature (chill units, CUs) in winter (chilling requirement), which also plays a role in the development of cold hardiness (cold acclimation). Physiological studies on dormancy breaking have focused on identifying markers, such as appearance or disappearance of proteins in response to varying degrees of chill unit accumulation. However, whether these changes are associated with dormancy transitions or cold acclimation is not clear. In the present study, greenhouse-grown blueberry (Vaccinium section Cyanococcus) plants were used to address this question. Three blueberry cultivars, Bluecrop, Tifblue, and Gulfcoast having chilling requirement of approximately 1 200, 900 and 600 CUs, respectively, were first exposed to 4°C for long enough to provide chill units equivalent to one-half of their respective chilling requirement. This treatment was expected to result in cold acclimation. A fraction of plants was then subjected to a 15/12°C (light/dark) regime for 2 weeks, a treatment expected to be “dormancy-neutral” but cause deacclimation. Before and after each treatment, cold hardiness and dormancy status of floral buds were determined; proteins were extracted from the buds collected on the same sampling date, and separated by one-dimensional SDS-PAGE. Dehydrin-like proteins were identified by immunoblotting, using anti-dehydrin antiserum. Results indicate that the chilling treatment resulted in cold acclimation as indicated by increased bud hardiness in all three cultivars. Data also indicate a distinct accumulation of three dehydrin-like proteins of 65, 60, and 14 kDa during cold acclimation. The cold hardiness and levels of dehydrin proteins decreased during the exposure to 15/12°C for 2 weeks. Results also confirmed that this treatment had no negative effect on chill unit accumulation. Densitometric scans of protein gels indicated a close association between the abundance of dehydrins and degree of cold hardiness in these cultivars. In addition, levels of the dehydrin proteins and cold hardiness remained about the same between 100% and >100% satisfaction of chilling requirement. These results suggest that changes in dehydrin expression are more closely associated with cold hardiness than with dormancy transitions.     

Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

Background  

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community.     

The Arabidopsis THADA homologue modulates TOR activity and cold acclimation

• Low temperature is one of the most important environmental factors that affect global survival of humans and animals and equally importantly the distribution of plants and crop productivity. Survival of metazoan cells under cold stress requires regulation of the sensor‐kinase Target Of Rapamycin (TOR). TOR controls growth of eukaryotic cells by adjusting anabolic and catabolic metabolism. Previous studies identified the Thyroid Adenoma Associated (THADA) gene as the major effect locus by positive selection in the evolution of modern human adapted to cold. Here we investigate the role of THADA in TOR signaling and cold acclimation of plants.
• We applied BLAST searches and homology modeling to identify the AtTHADA (AT3G55160) in Arabidopsis thaliana as the highly probable orthologue protein. Reverse genetics approaches were combined with immunological detection of TOR activity and metabolite profiling to address the role of the TOR and THADA for growth regulation and cold acclimation.
• Depletion of the AtTHADA gene caused complete or partial loss of full‐length mRNA, respectively, and significant retardation of growth under non‐stressed conditions. Furthermore, depletion of AtTHADA caused hypersensitivity towards low‐temperatures. Atthada displayed a lowered energy charge. This went along with decreased TOR activity, which offers a molecular explanation for the slow growth phenotype of Atthada. Finally, we used TOR RNAi lines to identify the de‐regulation of TOR activity as one determinant for sensitivity towards low‐temperatures.
• Taken together our results provide evidence for a conserved function of THADA in cold acclimation of eukaryotes and suggest that cold acclimation in plants requires regulation of TOR.

     

Characterization of wild bee communities in apple and blueberry orchards

1. Wild bees provide invaluable ecosystem services in agricultural landscapes such as pollination. However, in recent decades, pollinator biodiversity, especially in wild bees, is declining on a global scale, with potentially far‐reaching consequences for crop production. Thus, there is an urgent need to determine whether wild bees are present in agricultural systems, such as fruit orchards.
2. In the present study, we examined the wild bee fauna at species and community levels during the period of bee activity (May to August) in apple and high‐bush blueberry orchards in New England.
3. Bee communities are crop‐specific and dominated by very few species, which fluctuate according to crop and season. The blueberry associated bee fauna was more diverse. In apple, communities were phylogenetically clustered at the genus level and dominated by solitary ground nesting bees within the genus Andrena. Species fluctuated widely in presence and abundance throughout the season, leading to differences in community composition and functional trait structure.
4. The results obtained in the present study show that apple and blueberry harbour a distinct and diverse bee fauna that performs vital pollination services in orchards. Our results provide essential baseline data for wild bees in blueberry and apple orchards and this can be used to improve management and conservation strategies for wild bee preservation in these crops.

     

Native bees with floral sonication behaviour can achieve high-performance pollination of highbush blueberry in Chile

1. Blueberry is one of the most relevant buzz-pollinated crops worldwide and Chile is the most important global producer of fresh blueberries during wintertime in the Northern Hemisphere. Thousands of exotic Bombus terrestris are imported from Europe to pollinate blueberries. However, no study has investigated the performance of the native Chilean fauna to pollinate blueberry or other crops. Therefore, we aimed to compare the performance of native Chilean floral visitors with managed visitors to pollinate highbush blueberry.
2. Per-visit pollination performance (stigmatic pollen deposition) and floral visitation were measured and the presence of sonication behaviour of flower visitors was evaluated for five cultivars in two blueberry orchards located in southern Chile.
3. Floral visitors showed a preference for one or more blueberry cultivars, instead of visiting all cultivars equally. Floral visits with sonication deposited more conspecific pollen on stigmas than visits without sonication. Some native sonicating bees (Cadeguala and Bombus), especially Cadeguala occidentalis, were efficient pollen vectors of blueberry and better pollinators than honeybees (5.8 times more pollen transferred) similar to that of the managed bee B. terrestris.
4. The results indicate that some Chilean native bee species, especially those with sonication behaviour, can provide pollination service to highbush blueberry crops.

     

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (<Emphasis Type="Italic">Medicago sativa</Emphasis>) using microsatellite and AFLP markers

Background  

Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population.     

Surveys reveal a complex association of phytoplasmas and viruses with the blueberry stunt disease on Canadian blueberry farms

Surveys for phytoplasmas and viruses were conducted during September 2014 and 2015 on highbush blueberry farms in the Région Montérégie, Quebec. Total DNA and RNA were extracted from blueberry bushes showing blueberry stunt (BBS) symptoms and from symptomless blueberry bushes, and utilised as templates for PCR and RT‐PCR assays, respectively. Phytoplasma DNA was amplified with universal phytoplasma primers that target the 16S rRNA, secA and secY genes from 12 out of 40 (30%) plants tested. Based on 16S rRNA, secA and secY gene sequence identity, phylogenetic clustering, actual and in silico RFLP analyses, phytoplasma strains associated with BBS disease in Quebec were identified as ‘Candidatus Phytoplasma asteris’‐related strains, closely related to the BBS Michigan phytoplasma strain (16SrI‐E). The secY gene sequence‐based single nucleotide polymorphism analysis revealed that one of the BBS phytoplasma strains associated with a leaf marginal yellowing is a secY‐I RFLP variant of the subgroup 16SrI‐E. Two viruses were detected in blueberry bushes. The Blueberry Red Ringspot Virus (BRRV) was found in a single infection in the cultivar Bluecrop with no apparent typical BRRV symptoms. The Tobacco Ringspot Virus (TRSV) was found singly infecting blueberry plants and co‐infecting a BBS phytoplasma‐infected blueberry cv. Bluecrop plant. This is the first report of TRSV in the cv. Bluecrop in Quebec. The Quebec BBS phytoplasma strain was identified in the leafhopper Graphocephala fennahi, which suggests that G. fennahi may be a potential vector for the BBS phytoplasma. The BBS disease shows a complex aetiology and epidemiology; therefore, prompt actions must be developed to support focused BBS integrated management strategies.     

Generation and analysis of 9792 EST sequences from cold acclimated oat, <Emphasis Type="Italic">Avena sativa</Emphasis>

Background  

Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required.     

The expression of a rab-related gene,rab 18, is induced by abscisic acid during the cold acclimation process of Arabidopsis thaliana (L.) Heynh

Erratum

The expression of a rab-related gene, rab 18, is induced by abscisic acid during the cold acclimation process of Arabidopsis thaliana (L.) Heynh     

Proteomic analysis of shoot tissue during photoperiod induced growth cessation in <Emphasis Type="Italic">V. riparia</Emphasis> Michx. grapevines

Background  

Growth cessation, cold acclimation and dormancy induction in grapevines and other woody perennial plants native to temperate continental climates is frequently triggered by short photoperiods. The early induction of these processes by photoperiod promotes winter survival of grapevines in cold temperate zones. Examining the molecular processes, in particular the proteomic changes in the shoot, will provide greater insight into the signaling cascade that initiates growth cessation and dormancy induction. To begin understanding transduction of the photoperiod signal, Vitis riparia Michx. grapevines that had grown for 35 days in long photoperiod (long day, LD, 15 h) were subjected to either a continued LD or a short photoperiod (short day, SD, 13 h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis.     

The oatmeal nematode <Emphasis Type="Italic">Panagrellus redivivus</Emphasis> survives moderately low temperatures by freezing tolerance and cryoprotective dehydration

The cold tolerance abilities of only a few nematode species have been determined. This study shows that the oatmeal nematode, Panagrellus redivivus, has modest cold tolerance with a 50% survival temperature (S ₅₀) of −2.5°C after cooling at 0.5°C min⁻¹ and freezing for 1 h. It can survive low temperatures by freezing tolerance and cryoprotective dehydration; although freezing tolerance appears to be the dominant strategy. Freezing survival is enhanced by low temperature acclimation (7 days at 5°C), with the S ₅₀ being lowered by a small but significant amount (0.42°C). There is no cold shock or rapid cold hardening response under the conditions tested. Cryoprotective dehydration enhances the ability to survive freezing (the S ₅₀ is lowered by 0.55°C, compared to the control, after 4 h freezing at −1°C) and this effect is in addition to that produced by acclimation. Breeding from survivors of a freezing stress did not enhance the ability to survive freezing. The cold tolerance abilities of this nematode are modest, but sufficient to enable it to survive in the cold temperate environments it inhabits.     

Molecular cloning and characterization of Polygalacturonase-Inhibiting Protein and Cinnamoyl-Coa Reductase genes and their association with fruit storage conditions in blueberry (Vaccinium corymbosum)

Blueberry is a widely grown and easily perishable fruit crop. An efficient post-harvest handling is critical, and for that purpose gene technology methods have been part of ongoing programmes to improve crops with high food values such as blueberry. Here we report the isolation, cloning, characterization and differential expression levels of two cDNAs encoding Polygalacturonase-Inhibitor Protein (PGIP) and Cinnamoyl-Coa Reductase (CCR) from blueberry fruits in relation to various storage conditions. The open reading frame of PGIP and CCR encodes a polypeptide of 329 and 347 amino acids, respectively. To assess changes in the expression of blueberry PGIP and CCR after harvest, a storage trial was initiated. The northern blots hybridization showed a clear differential expression level of PGIP and CCR between freshly harvested and stored fruits as well as between fruits stored under various storage conditions. Although the prospects of exploiting such a strategy for crop improvement are limited, the results provide further insight into the control of the quality over the storage period at the molecular level.     

TRUNCATULIX – a data warehouse for the legume community

Background  

Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database – hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data.     

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Background  

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph.     

The SNF1-type serine-threonine protein kinase <Emphasis Type="Italic">SAPK4</Emphasis>regulates stress-responsive gene expression in rice

Background  

Plants respond to extracellularly perceived abiotic stresses such as low temperature, drought, and salinity by activation of complex intracellular signaling cascades that regulate acclimatory biochemical and physiological changes. Protein kinases are major signal transduction factors that have a central role in mediating acclimation to environmental changes in eukaryotic organisms. In this study, we characterized the function of the sucrose nonfermenting 1-related protein kinase2 (SnRK2) SAPK4 in the salt stress response of rice.