Ethylene promotes fruit ripening initiation by downregulating photosynthesis, enhancing abscisic acid and suppressing jasmonic acid in blueberry (Vaccinium ashei).

BACKGROUND: Blueberry fruit exhibit atypical climacteric ripening with a non-auto-catalytic increase in ethylene coincident with initiation of ripening. Further, application of ethephon, an ethylene-releasing plant growth regulator, accelerates ripening by increasing the proportion of ripe (blue) fruit as compared to the control treatment. To investigate the mechanistic role of ethylene in regulating blueberry ripening, we performed transcriptome analysis on fruit treated with ethephon, an ethylene-releasing plant growth regulator. RESULTS: RNA-Sequencing was performed on two sets of rabbiteye blueberry ('Powderblue') fruit: (1) fruit from divergent developmental stages; and (2) fruit treated with ethephon, an ethylene-releasing compound. Differentially expressed genes (DEGs) from divergent developmental stages clustered into nine groups, among which cluster 1 displayed reduction in expression during ripening initiation and was enriched with photosynthesis related genes, while cluster 7 displayed increased expression during ripening and was enriched with aromatic-amino acid family catabolism genes, suggesting stimulation of anthocyanin biosynthesis. More DEGs were apparent at 1 day after ethephon treatment suggesting its early influence during ripening initiation. Overall, a higher number of genes were downregulated in response to ethylene. Many of these overlapped with cluster 1 genes, indicating that ethylene-mediated downregulation of photosynthesis is an important developmental event during the ripening transition. Analyses of DEGs in response to ethylene also indicated interplay among phytohormones. Ethylene positively regulated abscisic acid (ABA), negatively regulated jasmonates (JAs), and influenced auxin (IAA) metabolism and signaling genes. Phytohormone quantification supported these effects of ethylene, indicating coordination of blueberry fruit ripening by ethylene. CONCLUSION: This study provides insights into the role of ethylene in blueberry fruit ripening. Ethylene initiates blueberry ripening by downregulating photosynthesis-related genes. Also, ethylene regulates phytohormone-metabolism and signaling related genes, increases ABA, and decreases JA concentrations. Together, these results indicate that interplay among multiple phytohormones regulates the progression of ripening, and that ethylene is an important coordinator of such interactions during blueberry fruit ripening.

PbrbZIP15 promotes sugar accumulation in pear via activating the transcription of the glucose isomerase gene PbrXylA1.

The composition and abundance of soluble sugars in mature pear (Pyrus) fruit are important for its acceptance by consumers. However, our understanding of the genes responsible for soluble sugar accumulation remains limited. In this study, a S1-group member of bZIP gene family, PbrbZIP15, was characterized from pear genome through the combined analyses of metabolite and transcriptome data followed by experimental validation. PbrbZIP15, located in nucleus, was found to function in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli. After analyzing the expression profiles of sugar-metabolism-related genes and the distribution of cis-acting elements in their promoters, the glucose isomerase 1 gene (PbrXylA1), whose corresponding protein catalyzed the isomerization of glucose and fructose in vitro, was identified as a downstream target gene of PbrbZIP15. PbrbZIP15 could directly bind to the G-box element in PbrXylA1 promoter and activate its transcription, as evidenced by chromatin immunoprecipitation-quantitative PCR, yeast one-hybrid, electrophoretic mobility shift assay, and dual-luciferase assay. PbrXylA1, featuring a leucine-rich signal peptide in its N-terminal, was localized to the endoplasmic reticulum. It was validated to play a significant role in fructose, sucrose, and total soluble sugar accumulation in pear fruit and calli, which was associated with the upregulated fructose/glucose ratio. Further studies revealed a positive correlation between the sucrose content and the expression levels of several sucrose-biosynthesis-related genes (PbrFRK3/8, PbrSPS1/3/4/8, and PbrSPP1) in PbrbZIP15-/PbrXylA1-transgenic fruit/calli. In conclusion, our results suggest that PbrbZIP15-induced soluble sugar accumulation during pear development is at least partly attributed to the activation of PbrXylA1 transcription.

Cadmium exposure is associated with increased transcript abundance of multiple heavy metal associated transporter genes in roots of hemp (Cannabis sativa L.).

Industrial hemp (Cannabis sativa L.) has demonstrated promise for phytoremediation due to an extensive root system, large biomass, and ability to survive under relatively high levels of heavy metals. However, little research has been conducted to determine the impact of heavy metal uptake in hemp grown for medicinal use. This study evaluated the potential for cadmium (Cd) uptake and its impact on growth, physiological responses, and transcript expression of metal transporter genes in a hemp variety grown for flower production. The cultivar 'Purple Tiger' was exposed to 0, 2.5, 10, and 25 mg·L-1 Cd in a greenhouse hydroponic study in two independent experiments. Plants exposed to 25 mg·L-1 Cd displayed stunted plant growth characteristics, reduced photochemical efficiency, and premature senescence suggesting Cd toxicity. At the two lower concentrations of Cd (2.5 and 10 mg·L-1 Cd), plant height, biomass, and photochemical efficiency were not affected, with chlorophyll content index (CCI) being slightly lower at 10 mg·L-1 Cd, compared to 2.5 mg·L-1 Cd. There were no consistent differences between the two experiments in total cannabidiol (CDB) and tetrahydrocannabinol (THC) concentrations in flower tissues at 2.5 and 10 mg·L-1 Cd, compared to the control treatment. Root tissue accumulated the highest amount of Cd compared to other tissues for all the Cd treatments, suggesting preferential root sequestration of this heavy metal in hemp. Transcript abundance analysis of heavy metal-associated (HMA) transporter genes suggested that all seven members of this gene family are expressed in hemp, albeit with higher expression in the roots than in the leaves. In roots, CsHMA3 was up-regulated at 45 and 68 d after treatment (DAT), and CsHMA1, CsHMA4, and CsHMA5 were upregulated only under long term Cd stress at 68 DAT, at 10 mg·L-1 Cd. Results suggest that expression of multiple HMA transporter genes in the root tissue may be upregulated in hemp exposed to 10 mg·L-1 Cd in a nutrient solution. These transporters could be involved in Cd uptake in the roots via regulating its transport and sequestration, and xylem loading for long distance transport of Cd to shoot, leaf, and flower tissues.

Carbon dioxide and light curves and leaf gas exchange responses to shade levels in bell pepper (Capsicum annuum L.).

Vegetable crops grown under shade nets typically show increased yield and quality. However, little is known about the photosynthetic responses at various CO2 and light levels under nets. This study aimed to determine carbon dioxide (A/Cc) and light (A/I) curves and leaf gas exchange response of bell pepper plants grown under nets at various shade levels. Experiments were conducted in the spring-summer of 2016 and 2018 in Tifton, Georgia (GA), USA, with five shade treatments [0 % (open field), 30 %, 47 %, 63 %, and 80 %]. The A/Cc curves revealed that plants grown at 30 % shade and in the open field had similar carboxylation, electron transport, and triose phosphate utilization rates. The A/I curves showed that gross and net photosynthesis were highest at 30 % shade. The 30 % shade had similar stomatal conductance, intercellular CO2, electron transport rate, and water use efficiency compared to the open field. The A/Cc and A/I curves and the leaf gas exchange parameters explained the intrinsic causes for the higher net photosynthesis at 30 % shade than in open-field bell pepper. The information from A/Cc-curves, A/I-curves, and leaf gas exchange is applicable in modeling photosynthesis and predicting primary productivity for C3 plants in elevated-CO2 and altered-light environments.

Full-length fruit transcriptomes of southern highbush (Vaccinium sp.) and rabbiteye (V. virgatum Ait.) blueberry.

BACKGROUND: Blueberries (Vaccinium sp.) are native to North America and breeding efforts to improve blueberry fruit quality are focused on improving traits such as increased firmness, enhanced flavor and greater shelf-life. Such efforts require additional genomic resources, especially in southern highbush and rabbiteye blueberries. RESULTS: We generated the first full-length fruit transcriptome for the southern highbush and rabbiteye blueberry using the cultivars, Suziblue and Powderblue, respectively. The transcriptome was generated using the Pacific Biosciences single-molecule long-read isoform sequencing platform with cDNA pooled from seven stages during fruit development and postharvest storage. Raw reads were processed through the Isoseq pipeline and full-length transcripts were mapped to the 'Draper' genome with unmapped reads collapsed using Cogent. Finally, we identified 16,299 and 15,882 non-redundant transcripts in 'Suziblue' and 'Powderblue' respectively by combining the reads mapped to Northern Highbush blueberry 'Draper' genome and Cogent analysis. In both cultivars, > 80% of sequences were longer than 1,000 nt, with the median transcript length around 1,700 nt. Functionally annotated transcripts using Blast2GO were > 92% in both 'Suziblue' and 'Powderblue' with overall equal distribution of gene ontology (GO) terms in the two cultivars. Analyses of alternative splicing events indicated that around 40% non-redundant sequences exhibited more than one isoform. Additionally, long non-coding RNAs were predicted to represent 5.6% and 7% of the transcriptomes in 'Suziblue' and 'Powderblue', respectively. Fruit ripening is regulated by several hormone-related genes and transcription factors. Among transcripts associated with phytohormone metabolism/signaling, the highest number of transcripts were related to abscisic acid (ABA) and auxin metabolism followed by those for brassinosteroid, jasmonic acid and ethylene metabolism. Among transcription factor-associated transcripts, those belonging to ripening-related APETALA2/ethylene-responsive element-binding factor (AP2/ERF), NAC (NAM, ATAF1/2 and CUC2), leucine zipper (HB-zip), basic helix-loop-helix (bHLH), MYB (v-MYB, discovered in avian myeloblastosis virus genome) and MADS-Box gene families, were abundant. Further we measured three fruit ripening quality traits and indicators [ABA, and anthocyanin concentration, and texture] during fruit development and ripening. ABA concentration increased during the initial stages of fruit ripening and then declined at the Ripe stage, whereas anthocyanin content increased during the final stages of fruit ripening in both cultivars. Fruit firmness declined during ripening in 'Powderblue'. Genes associated with the above parameters were identified using the full-length transcriptome. Transcript abundance patterns of these genes were consistent with changes in the fruit ripening and quality-related characteristics. CONCLUSIONS: A full-length, well-annotated fruit transcriptome was generated for two blueberry species commonly cultivated in the southeastern United States. The robustness of the transcriptome was verified by the identification and expression analyses of multiple fruit ripening and quality-regulating genes. The full-length transcriptome is a valuable addition to the blueberry genomic resources and will aid in further improving the annotation. It will also provide a useful resource for the investigation of molecular aspects of ripening and postharvest processes.

Atypical Climacteric and Functional Ethylene Metabolism and Signaling During Fruit Ripening in Blueberry (Vaccinium sp.).

Climacteric fruits display an increase in respiration and ethylene production during the onset of ripening, while such changes are minimal in non-climacteric fruits. Ethylene is a primary regulator of ripening in climacteric fruits. The ripening behavior and role of ethylene in blueberry (Vaccinium sp.) ripening is controversial. This work aimed to clarify the fruit ripening behavior and the associated role of ethylene in blueberry. Southern highbush (Vaccinium corymbosum hybrids) and rabbiteye (Vaccinium ashei) blueberry displayed an increase in the rate of respiration and ethylene evolution, both reaching a maxima around the Pink and Ripe stages of fruit development, consistent with climacteric fruit ripening behavior. Increase in ethylene evolution was associated with increases in transcript abundance of its biosynthesis genes, AMINOCYCLOPROPANE CARBOXYLATE (ACC) SYNTHASE1 (ACS1) and ACC OXIDASE2 (ACO2), implicating them in developmental ethylene production during ripening. Blueberry fruit did not display autocatalytic system 2 ethylene during ripening as ACS transcript abundance and ACC concentration were not enhanced upon treatment with an ethylene-releasing compound (ethephon). However, ACO transcript abundance was enhanced in response to ethephon, suggesting that ACO was not rate-limiting. Transcript abundance of multiple genes associated with ethylene signal transduction was upregulated concomitant with developmental increase in ethylene evolution, and in response to exogenous ethylene. As these changes require ethylene signal transduction, fruit ripening in blueberry appears to involve functional ethylene signaling. Together, these data indicate that blueberry fruit display atypical climacteric ripening, characterized by a respiratory climacteric, developmentally regulated but non-autocatalytic increase in ethylene evolution, and functional ethylene signaling.

Indigenous and commercial isolates of arbuscular mycorrhizal fungi display differential effects in Pyrus betulaefolia roots and elicit divergent transcriptomic and metabolomic responses.

Background: Arbuscular mycorrhizal fungi (AMF) are beneficial soil fungi which can effectively help plants with acquisition of mineral nutrients and water and promote their growth and development. The effects of indigenous and commercial isolates of arbuscular mycorrhizal fungi on pear (Pyrus betulaefolia) trees, however, remains unclear. Methods: Trifolium repens was used to propagate indigenous AMF to simulate spore propagation in natural soils in three ways: 1. the collected soil was mixed with fine roots (R), 2. fine roots were removed from the collected soil (S), and 3. the collected soil was sterilized with 50 kGy 60Co γ-radiation (CK). To study the effects of indigenous AMF on root growth and metabolism of pear trees, CK (sterilized soil from CK in T. repens mixed with sterilized standard soil), indigenous AMF (R, soil from R in T. repens mixed with sterilized standard soil; S, soil from S in T. repens mixed with sterilized standard soil), and two commercial AMF isolates (Rhizophagus intraradices(Ri) and Funneliformis mosseae (Fm)) inoculated in the media with pear roots. Effects on plant growth, root morphology, mineral nutrient accumulation, metabolite composition and abundance, and gene expression were analyzed. Results: AMF treatment significantly increased growth performance, and altered root morphology and mineral nutrient accumulation in this study, with the S treatment displaying overall better performance. In addition, indigenous AMF and commercial AMF isolates displayed common and divergent responses on metabolite and gene expression in pear roots. Compared with CK, most types of flavones, isoflavones, and carbohydrates decreased in the AMF treatment, whereas most types of fatty acids, amino acids, glycerolipids, and glycerophospholipids increased in response to the AMF treatments. Further, the relative abundance of amino acids, flavonoids and carbohydrates displayed different trends between indigenous and commercial AMF isolates. The Fm and S treatments altered gene expression in relation to root metabolism resulting in enriched fructose and mannose metabolism (ko00051), fatty acid biosynthesis (ko00061) and flavonoid biosynthesis (ko00941). Conclusions: This study demonstrates that indigenous AMF and commercial AMF isolates elicited different effects in pear plants through divergent responses from gene transcription to metabolite accumulation.

Blossom-end rot: a century-old problem in tomato (Solanum lycopersicum L.) and other vegetables.

Blossom-end rot (BER) is a devastating physiological disorder affecting vegetable production worldwide. Extensive research into the physiological aspects of the disorder has demonstrated that the underlying causes of BER are associated with perturbed calcium (Ca2+) homeostasis and irregular watering conditions in predominantly cultivated accessions. Further, Reactive Oxygen Species (ROS) are critical players in BER development which, combined with unbalanced Ca2+ concentrations, greatly affect the severity of the disorder. The availability of a high-quality reference tomato genome as well as the whole genome resequencing of many accessions has recently permitted the genetic dissection of BER in segregating populations derived from crosses between cultivated tomato accessions. This has led to the identification of five loci contributing to BER from several studies. The eventual cloning of the genes contributing to BER would result in a deeper understanding of the molecular bases of the disorder. This will undoubtedly create crop improvement strategies for tomato as well as many other vegetables that suffer from BER.

Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato.

KEY MESSAGE: Blossom-End Rot is Quantitatively Inherited and Maps to Four Loci in Tomato. Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit; however, the genetic basis of this disorder remains unknown. To investigate the genetic basis of BER, two F2 and F3:4 populations along with a BC1 population that segregated for BER occurrence were evaluated in the greenhouse. Using the QTL-seq approach, quantitative trait loci (QTL) associated with BER Incidence were identified at the bottom of chromosome (ch) 3 and ch11. Additionally, linkage-based QTL mapping detected another QTL, BER3.1, on ch3 and BER4.1 on ch4. To fine map the QTLs identified by QTL-seq, recombinant screening was performed. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 to 1.58 Mbp with a 1.5-LOD support interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Further, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval comprising of 141 candidate genes. Taken together, our results identified and fine mapped the first loci for BER resistance in tomato that will facilitate marker-assistant breeding not only in tomato but also in many other vegetables suffering for BER.

Temporal expression patterns of fruit-specific α- EXPANSINS during cell expansion in bell pepper (Capsicum annuum L.).

BACKGROUND: Expansins (EXPs) facilitate non-enzymatic cell wall loosening during several phases of plant growth and development including fruit growth, internode expansion, pollen tube growth, leaf and root development, and during abiotic stress responses. In this study, the spatial and temporal expression patterns of C. annuum α- EXPANSIN (CaEXPA) genes were characterized. Additionally, fruit-specific CaEXPA expression was correlated with the rate of cell expansion during bell pepper fruit development. RESULTS: Spatial expression patterns revealed that CaEXPA13 was up-regulated in vegetative tissues and flowers, with the most abundant expression in mature leaves. Expression of CaEXPA4 was associated with stems and roots. CaEXPA3 was expressed abundantly in flower at anthesis suggesting a role for CaEXPA3 in flower development. Temporal expression analysis revealed that 9 out of the 21 genes were highly expressed during fruit development. Of these, expression of six genes, CaEXPA5, CaEXPA7, CaEXPA12, CaEXPA14 CaEXPA17 and CaEXPA19 were abundant 7 to 21 days after anthesis (DAA), whereas CaEXPA6 was strongly expressed between 14 and 28 DAA. Further, this study revealed that fruit growth and cell expansion occur throughout bell pepper development until ripening, with highest rates of fruit growth and cell expansion occurring between 7 and 14 DAA. The expression of CaEXPA14 and CaEXPA19 positively correlated with the rate of cell expansion, suggesting their role in post-mitotic cell expansion-mediated growth of the bell pepper fruit. In this study, a ripening specific EXP transcript, CaEXPA9 was identified, suggesting its role in cell wall disassembly during ripening. CONCLUSIONS: This is the first genome-wide study of CaEXPA expression during fruit growth and development. Identification of fruit-specific EXPAs suggest their importance in facilitating cell expansion during growth and cell wall loosening during ripening in bell pepper. These EXPA genes could be important targets for future manipulation of fruit size and ripening characteristics.

Nexus Between Spermidine and Floral Organ Identity and Fruit/Seed Set in Tomato.

Polyamines (PAs) constituting putrescine (Put), spermidine (Spd), and spermine (Spm) are ubiquitous in all organisms and play essential roles in the growth and developmental processes in living organisms, including plants. Evidences obtained through genetic, biochemical, and transgenic approaches suggest a tight homeostasis for cellular PA levels. Altered cellular PA homeostasis is associated with abnormal phenotypes. However, the mechanisms involved for these abnormalities are not yet fully understood, nor is it known whether cellular ratios of different polyamines play any role(s) in specific plant processes. We expressed a yeast spermidine synthase gene (ySpdSyn) under a constitutive promoter CaMV35S in tomato and studied the different phenotypes that developed. The constitutive expression of ySpdSyn resulted in variable flower phenotypes in independent transgenic lines, some of which lacked fruit and seed set. Quantification of PA levels in the developing flowers showed that the transgenic plants without fruit and seed set had significantly reduced Spd levels as well as low Spd/Put ratio compared to the transgenic lines with normal fruit and seed set. Transcript levels of SlDELLA, GA-20oxidase-1, and GA-3oxidase-2, which impact gibberellin (GA) metabolism and signaling, were significantly reduced in bud tissue of transgenic lines that lacked fruit and seed set. These findings indicate that PAs, particularly Spd, impact floral organ identity and fruit set in tomato involving GA metabolism and signaling. Furthermore, we suggest that a nexus exists between PA ratios and developmental programs in plants.

Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching.

BACKGROUND: Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. RESULTS: Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. CONCLUSIONS: In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.