Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example

Coffee, an important agricultural product for tropical producing countries, is facing challenges due to climate change, including periods of drought, irregular rain distribution, and high temperatures. These changes result in plant water stress, leading to significant losses in coffee productivity and quality. Understanding the processes that affect coffee flowering is crucial for improving productivity and quality. In this chapter, we describe a protocol for transcriptome analysis using available Internet software, mainly in the Galaxy Platform, using RNA-Seq data from flowers collected from different parts of the coffee tree. The methods presented in this chapter provide a comprehensive protocol for transcriptome analysis of differentially expressed genes from flowers of coffee plant. This knowledge can be utilized in coffee genetic improvement programs, particularly in the selection of cultivars that are tolerant to water deficit.

Functional Characterization of ent-Copalyl Diphosphate Synthase and Kaurene Synthase Genes from Coffea arabica L

The biochemical profile of coffee beans translates directly into quality traits, nutraceutical and health promoting properties of the coffee beverage. Ent-kaurene is the ubiquitous precursor for gibberellin biosynthesis in plants, but it also serves as an intermediate in specialized (i.e., secondary) diterpenoid metabolism that leads to a diversity of more than 1,000 different metabolites. Nutraceutical effects on human health attributed to diterpenes include antioxidant, anticarcinogenic, and anti-inflammatory properties. Cafestol (CAF) and kahweol (KAH) are two diterpenes found exclusively in the Coffea genus. Our objective was to identify and functionally characterize genes involved in the central step of ent-kaurene production. We identified 17 putative terpene synthase genes in the transcriptome of Coffea arabica. Two ent-copalyl diphosphate synthase (CaCPS) and three kaurene synthase (CaKS) were selected and manually annotated. Transcript expression profiles of CaCPS1 and CaKS3 best matched the CAF and KAH metabolite profiles in different tissues. CaCPS1 and CaKS3 proteins were heterologously expressed and functionally characterized. CaCPS1 catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to ent-copalyl diphosphate (ent-CPP), which is converted to ent-kaurene by CaKS3. Knowledge about the central steps of diterpene formation in coffee provides a foundation for future characterization of the subsequent enzymes involved in CAF and KAH biosynthesis.

Small RNAs: Promising Molecules to Tackle Climate Change Impacts in Coffee Production

Over the centuries, human society has evolved based on the ability to select and use more adapted species for food supply, which means making plant species tastier and more productive in particular environmental conditions. However, nowadays, this scenario is highly threatened by climate change, especially by the changes in temperature and greenhouse gasses that directly affect photosynthesis, which highlights the need for strategic studies aiming at crop breeding and guaranteeing food security. This is especially worrying for crops with complex phenology, genomes with low variability, and the ones that support a large production chain, such as Coffea sp. L. In this context, recent advances shed some light on the genome function and transcriptional control, revealing small RNAs (sRNAs) that are responsible for environmental cues and could provide variability through gene expression regulation. Basically, sRNAs are responsive to environmental changes and act on the transcriptional and post-transcriptional gene silencing pathways that regulate gene expression and, consequently, biological processes. Here, we first discuss the predicted impact of climate changes on coffee plants and coffee chain production and then the role of sRNAs in response to environmental changes, especially temperature, in different species, together with their potential as tools for genetic improvement. Very few studies in coffee explored the relationship between sRNAs and environmental cues; thus, this review contributes to understanding coffee development in the face of climate change and towards new strategies of crop breeding.

Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes

BACKGROUND

The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study.

RESULTS

The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans.

CONCLUSION

Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica.

Comparative transcriptome analysis of wheat in response to corn leaf aphid, Rhopalosiphum maidis F. infestation

Aphids are one of the most important insect pests of wheat crop in all wheat growing regions of the world. Amongst various aphid species, the corn leaf aphid (Rhopalosiphum maidis F.) is considered one of the most destructive insect pests of wheat in the North Western Plains region of India. Transcriptome profiling of highly susceptible wheat Triticum durum genotype, A-9-30-1 and tolerant wheat Triticum aestivum genotype, HD2967 was performed to investigate aphid-host interactions. The results obtained from differential gene expression analysis of R. maidis on the highly susceptible genotype, A-9-30-1 plants, when compared with the tolerant genotype, HD2967, showed that 212 genes were significantly upregulated and 1009 genes were significantly downregulated. Our findings demonstrated that the genes associated with defense were significantly higher in response to R. maidis on HD2967 as compared to A-9-30-1. Additionally, various genes with physiological attributes were expressed during aphid attack. Based on gene ontology classification, three classifications, such as, cellular components (CC), molecular function (MF), and biological processes (BP) of sequences were identified. KEGG enrichment analysis revealed that twenty-five pathway genes were differentially expressed during the infestation of wheat with R. maidis. Notable changes were observed in A-9-30-1 and HD2967 transcriptomic profiling after infestation. The results obtained in the present study will help to elucidate the mechanism governing host-pest interaction and may lead to the development of new methods for increasing the resistance level of wheat against R. maidis, including over-expression of defense-related genes.

Transcriptome and carotenoid profiling of different varieties of Coffea arabica provides insights into fruit color formation

The processability and ultimate quality of coffee (C offea arabica) are determined by the composition of the matured fruits. The basis of genetic variation in coffee fruit quality could be explained by studying color formation during fruit maturation. Transcriptome profiling was conducted on matured fruits of four C. arabica varieties (orange colored fruits (ORF); purple colored fruits (PF); red colored fruits (RF) and yellow colored fruits (YF)) to identify key color-regulating genes, biosynthesis pathways and transcription factors implicated in fruit color formation. A total of 39,938 genes were identified in the transcriptomes of the four C. arabica varieties. In all, 2745, 781 and 1224 differentially expressed genes (DEGs) were detected in YF_vs_PF, YF_vs_RF and YF_vs_ORF, respectively, with 1732 DEGs conserved among the three pairwise groups. Functional annotation of the DEGs led to the detection of 28 and 82 key genes involved in the biosynthesis of carotenoids and anthocyanins, respectively. Key transcription factors bHLH, MYB, NAC, MADS, and WRKY implicated in fruit color regulation were detected. The high expression levels of gene-LOC113688784 (PSY), gene-LOC113730013 (β-CHY), gene-LOC113728842 (CCD7), gene-LOC113689681 (NCED) and gene-LOC113729473 (ABA2) in YF may have accounted for the yellow coloration. The differential expression of several anthocyanin and carotenoid-specific genes in the fruits substantially account for the purple (PF), red (RF), and orange (ORF) colorations. This study provides important insights into fruit color formation and variations in C. arabica and will help to develop coffee varieties with specific color and quality traits.

Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors

MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules, and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS genes underpin the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.

CsAGA1 and CsAGA2 Mediate RFO Hydrolysis in Partially Distinct Manner in Cucumber Fruits

A Raffinose family oligosaccharides (RFOs) is one of the major translocated sugars in the vascular bundle of cucumber, but little RFOs can be detected in fruits. Alpha-galactosidases (α-Gals) catalyze the first catabolism step of RFOs. Six α-Gal genes exist in a cucumber genome, but their spatial functions in fruits remain unclear. Here, we found that RFOs were highly accumulated in vascular tissues. In phloem sap, the stachyose and raffinose content was gradually decreased, whereas the content of sucrose, glucose and fructose was increased from pedicel to fruit top. Three alkaline forms instead of acid forms of α-Gals were preferentially expressed in fruit vascular tissues and alkaline forms have stronger RFO-hydrolysing activity than acid forms. By inducible gene silencing of three alkaline forms of α-Gals, stachyose was highly accumulated in RNAi-CsAGA2 plants, while raffinose and stachyose were highly accumulated in RNAi-CsAGA1 plants. The content of sucrose, glucose and fructose was decreased in both RNAi-CsAGA1 and RNAi-CsAGA2 plants after β-estradiol treatment. In addition, the fresh- and dry-weight of fruits were significantly decreased in RNAi-CsAGA1 and RNAi-CsAGA2 plants. In cucurbitaceous plants, the non-sweet motif within the promoter of ClAGA2 is widely distributed in the promoter of its homologous genes. Taken together, we found RFOs hydrolysis occurred in the vascular tissues of fruits. CsAGA1 and CsAGA2 played key but partly distinct roles in the hydrolysis of RFOs.

Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]

As atmospheric [CO₂] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO₂ (eCO₂) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO₂. Although many genes were found to be commonly expressed by the two genotypes under eCO₂, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO₂. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO₂ with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO₂ in these coffee genotypes.

Low-Copy Genes in Terpenoid Metabolism: The Evolution and Expression of MVK and DXR Genes in Angiosperms

Terpenoids are a diverse class of metabolites that impact plant metabolism in response to environmental cues. They are synthesized either via a predominantly cytosolic (MVA) pathway or a plastidic pathway (MEP). In Arabidopsis, several enzymes from the MVA and MEP pathways are encoded by gene families, excluding MVK and DXR, which are single-copy genes. In this study, we assess the diversity, evolution and expression of DXR and MVK genes in selected angiosperms and Coffea arabica in particular. Evolutionary analysis revealed that DXR and MVK underwent purifying selection, but the selection effect for DXR was stronger than it was for MVK. Digital gene expression (DGE) profile analysis of six species revealed that expression levels of MVK in flowers and roots were high, whereas for DXR peak values were observed in leaves. In C. arabica, both genes were highly expressed in flowers, and CaDXR was upregulated in response to methyl jasmonate. C. arabica DGE data were validated by assessing gene expression in selected organs, and by plants treated with hexanoic acid (Hx) using RT-qPCR. MVK expression was upregulated in roots treated with Hx. CaDXR was downregulated in leaves by Hx treatment in a genotype-specific manner, indicating a differential response to priming.

An innovative automated active compound screening system allows high-throughput optimization of somatic embryogenesis in Coffea arabica

Somatic embryogenesis (SE) faces many challenges in fulfilling the growing demand for elite materials. A high-throughput approach is required to accelerate the optimization of SE protocols by multiplying experimental conditions within a limited time period. For the first time in plant micropropagation, we have developed a miniaturized and automated screening system to meet high-throughput standards. Coffea arabica embryo regeneration, classically achieved in 250-ml Erlenmeyer flasks, was successfully miniaturized in 24-well plates, allowing a volume downscaling factor of 100 and a space saving of 53 cm²/well. Cell clusters were ground and filtered to fit the automated pipetting platform, leading to fast, reproducible and uniform cluster distribution (23.0 ± 5.5 cell clusters/well) and successful regeneration (6.5 ± 2.2 embryos/well). Pilot screening of active compounds on SE was carried out. Compounds belonging to the histone deacetylase inhibitor family were tested for embryo regeneration efficiency. Cells treated with 1 µM Trichostatin A showed a marked 3-fold increase in the number of regenerated embryos. When re-tested in 250-ml flasks, the same enhancement was obtained, thereby validating the miniaturized and automated screening method. These results showed that our screening system is reliable and well suited to screening hundreds of compounds, offering unprecedented perspectives in plant micropropagation.

Full moonlight-induced circadian clock entrainment in Coffea arabica

BACKGROUND

It is now well documented that moonlight affects the life cycle of invertebrates, birds, reptiles, and mammals. The lunisolar tide is also well-known to alter plant growth and development. However, although plants are known to be very photosensitive, few studies have been undertaken to explore the effect of moonlight on plant physiology.

RESULTS

Here for the first time we report a massive transcriptional modification in Coffea arabica genes under full moonlight conditions, particularly at full moon zenith and 3 h later. Among the 3387 deregulated genes found in our study, the main core clock genes were affected.

CONCLUSIONS

Moonlight also negatively influenced many genes involved in photosynthesis, chlorophyll biosynthesis and chloroplast machinery at the end of the night, suggesting that the full moon has a negative effect on primary photosynthetic machinery at dawn. Moreover, full moonlight promotes the transcription of major rhythmic redox genes and many heat shock proteins, suggesting that moonlight is perceived as stress. We confirmed this huge impact of weak light (less than 6 lx) on the transcription of circadian clock genes in controlled conditions mimicking full moonlight.

Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

Background

Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved.

Methods

Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study.

Results

A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed.

Discussion

The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.

Gene Expression Maps in Plants: Current State and Prospects

For many years, progress in the identification of gene functions has been based on classical genetic approaches. However, considerable recent omics developments have brought to the fore indirect but high-resolution methods of gene function identification such as transcriptomics, proteomics, and metabolomics. A transcriptome map is a powerful source of functional information and the result of the genome-wide expression analysis of a broad sampling of tissues and/or organs from different developmental stages and/or environmental conditions. In plant science, the application of transcriptome maps extends from the inference of gene regulatory networks to evolutionary studies. However, only some of these data have been integrated into databases, thus enabling analyses to be conducted without raw data; without this integration, extensive data preprocessing is required, which limits data usability. In this review, we summarize the state of plant transcriptome maps, analyze the problems associated with the combined analysis of large-scale data from various studies, and outline possible solutions to these problems.

Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages

BACKGROUND

Sweetpotato (Ipomoea batatas) is a hexaploid plant and generally most genotypes do not flower at all in sub-tropics. Heterografting was carried out between sweetpotato cultivar 'Xushu 18' and Japanese morning glory (Ipomoea nil). With sweetpotato as 'scion' and I. nil as 'rootstock', sweetpotato was induced flowering in the autumn. However, little is known about the molecular mechanisms underlying sweetpotato responses to grafting, especially during the full blooming stages.

OBJECTIVES

To investigate the poorly understood molecular responses underlying the grafting-induced phenotypic processes in sweetpotato at full anthesis.

METHODS

In this study, to explore the transcriptome diversity and complexity of sweetpotato, PacBio Iso-Seq and Illumina RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression of five tissues: scion flowers (SF), scion leaves (SL), scion stems (SS), own-rooted leaves (OL) and own-rooted stems (OS).

RESULTS

A total of 138,151 transcripts were generated with an average length of 2255 bp, and more than 72% (100,396) of the transcripts were full-length. During full blooming, to examine the difference in gene expression of sweetpotato under grafting and natural growth conditions, 7905, 7795 and 15,707 differentially expressed genes were detected in pairwise comparisons of OS versus SS, OL versus SL and SL versus SF, respectively. Moreover, differential transcription of genes associated with anthocyanin biosynthesis, light pathway and photosynthesis, ethylene signal transduction pathway was observed in scion responses to grafting.

CONCLUSION

Our study is useful in understanding the molecular basis of grafting-induced flowering in grafted sweetpotatoes, and will lay a foundation for further research on sweetpotato breeding in the future.

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

KEY MESSAGE

Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies.

ABSTRACT

Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq 500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500 bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.

A simple and efficient agroinfiltration method in coffee leaves (Coffea arabica L.): assessment of factors affecting transgene expression

The establishment of a simple, rapid and efficient transient expression system is a necessary tool for the functional validation of candidate genes in coffee biotechnology. The effects of Agrobacterium strain, age of the donor plant, infiltration method, and infiltration medium on transgene expression in detached coffee leaves were evaluated. Regarding the effect of Agrobacterium strain, the expression of uidA was higher in GV3101-treated coffee disks than in LBA4404 and ATHV-treated samples. On the other hand, transient expression of uidA was significantly higher in leaf disks from young plants (6-weeks-old) (13.1 ± 1.4%) than in mature tissue (12-weeks-old) (1.6 ± 1.2%). Transient uidA expression was higher in detached coffee leaf disks from young plants infiltrated with one injection of 15 µL of Agrobacterium strain GV3101::1303 suspended in MS salts supplemented with 30 g/L sucrose, 1.9 g/L MES and 200 uM AS with subsequent sanding of the abaxial epidermis. Using the optimized protocol, expression of the uidA gene was observed 6, 24 and 48 h and 5 weeks after bacterial injection. DNA was extracted from coffee disks with positive GUS expression and specific mgfp5 and uidA fragments were amplified 5 weeks post-agroinfiltration. On the other hand, using the optimized protocol, a specific cry10Aa (500 bp) fragment was amplified in the agro-infiltrated coffee leaf disks 5 weeks post-agroinfiltration with the plasmid pB427-35S-cry10Aa. Moreover, the expression of the gene cry10Aa in two infiltrated coffee leaf disks was verified by RT-PCR and an expected 500 bp fragment was amplified.

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

The coffee bean transcriptome explains the accumulation of the major bean components through ripening

The composition of the maturing coffee bean determines the processing performance and ultimate quality of the coffee produced from the bean. Analysis of differences in gene expression during bean maturation may explain the basis of genetic and environmental variation in coffee quality. The transcriptome of the coffee bean was analyzed at three stages of development, immature (green), intermediate (yellow) and mature (red). A total of more than 120 million 150 bp paired-end reads were collected by sequencing of transcripts of triplicate samples at each developmental stage. A greater number of transcripts were expressed at the yellow stage. As the beans matured the types of highly expressed transcripts changed from transcripts predominantly associated with galactomannan, triacylglycerol (TAG), TAG lipase, 11 S and 7S-like storage protein and Fasciclin-like arabinogalactan protein 17 (FLA17) in green beans to transcripts related to FLA1 at the yellow stage and TAG storage lipase SDP1, and SDP1-like in red beans. This study provides a genomic resource that can be used to investigate the impact of environment and genotype on the bean transcriptome and develop coffee varieties and production systems that are better adapted to deliver quality coffee despite climate variations.

Metabolic process of raffinose family oligosaccharides during cold stress and recovery in cucumber leaves

Raffinose family oligosaccharides (RFOs) accumulate under stress conditions in many plants and have been suggested to act as stress protectants. To elucidate the metabolic process of RFOs under cold stress, levels of RFOs, and related carbohydrates, the expression and activities of main metabolic enzymes and their subcellular compartments were investigated during low-temperature treatment and during the recovery period in cucumber leaves. Cold stress induced the accumulation of stachyose in vacuoles, galactinol in vacuoles and cytosol, and sucrose and raffinose in vacuoles, cytosol, and chloroplasts. After cold stress removal, levels of these sugars decreased gradually in the respective compartments. Among four galactinol synthase genes (CsGS), CsGS1 was not affected by cold stress, while the other three CsGSs were up-regulated by low temperature. RNA levels of acid-α-galactosidase (GAL) 3 and alkaline-α-galactosidase (AGA) 2 and 3, and the activities of GAL and AGA, were up-regulated after cold stress removal. GAL3 protein and GAL activity were exclusively located in vacuoles, whereas AGA2 and AGA 3 proteins were found in cytosol and chloroplasts, respectively. The results indicate that RFOs, which accumulated during cold stress in different subcellular compartments in cucumber leaves, could be catabolized in situ by different galactosidases after stress removal.

Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.