Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color

A transcription factor, PbWRKY24, contributes to russet skin formation in pear fruits by modulating lignin accumulation

Skin color is one of the major traits of fruit appearance quality in pear (Pyrus) that affects the fruit commodity value. Russet skin protects pear fruits from environmental stresses and its formation process is closely linked to lignin accumulation. However, the molecular regulatory networks underlying russet skin formation in pear fruits involve complex secondary metabolic pathways and remain elusive. Here, we explored the regulatory mechanisms underlying lignin accumulation in pear skin based on transcriptome sequencing, co-expression network analysis, and gene expression profiling. We identified a WRKY transcription factor gene, PbWRKY24, that regulates russet skin formation in pear fruits. The relative expression of PbWRKY24 in russet pear skin was significantly correlated with lignin content. We then verified the function of PbWRKY24 in lignin accumulation via genetic transformation. DNA affinity purification sequencing revealed that PbWRKY24 directly binds to the promoter of a lignin biosynthesis gene, PbPRX4. This binding was confirmed by yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays. Overexpression of PbPRX4 in pear skin stimulated lignin accumulation and consequently promoted russet skin formation. This study provides a glimpse into the intricate lignin biosynthesis mechanisms during russet skin formation in pear fruits, which is of practical significance to pear breeding for fruit quality.

Combined transcriptome and metabolome analysis revealed the molecular mechanisms of fruit skin coloration in pink strawberry

Elucidating the key genes and metabolites responsible for fruit skin color is essential for the breeding of strawberry varieties with beautiful fruit color. Here, transcriptome and metabolome analyses were used to identify the key genes and metabolites associated with fruit skin color in strawberry accessions of red skin (Kaorino), white skin (2012-W02), and the pink skin (Fenyu NO.1, the F1 hybrid of Kaorino and 2012-W02). The metabolomic data showed that the content of anthocyanin-related metabolites, such as p-Coumaroyl quinic acid, 5-Hydroxyconiferyl alcohol and Coumestrol were significantly higher in red-skinned strawberry line Kaorino than in the white-skinned line 2012-W02. The flavonoids and isoflavonoids such as syringetin and 2,7,4'-trihydroxy-isoflavone, were less expressed in the Kaorino than in the other two accessions. Transcriptome analysis revealed that the expression of genes involved in anthocyanin biosynthesis, such as BZ1, F3H, CHS, CHI, DFR, 4CL, PAL, CCR, 4CL, F5H, REF1 and UGT72E, were also significantly upregulated in the red-skinned line Kaorino compared to the white-skinned line 2012-W02, while the HCT, CYP75B1, FG3, HIDH, IF7MAT, I2'H, and VR was downregulated in Kaorino. Combined transcriptome and metabolome analyses revealed that the pathways of isoflavonoid biosynthesis and flavone and flavonol biosynthesis, and the phenylpropanoid biosynthesis pathway essential for anthocyanin synthesis were commonly enriched by DRMs and DEGs. In addition, the metabolites of peonidin 3-O-glucoside, 2'-hydroxydaidzein and daidzin, and the genes of CYP93B2_16 and UGT73C6 were detected and most accumulated in pink-skinned Fenyu NO.1. This result suggested that the main strategy for obtaining a red skin color is to enhance the upstream pathway of anthocyanin biosynthesis, including the phenylpropanoid biosynthesis pathway, and to restrict the downstream steps in the flavonoid biosynthesis pathway, such as the branch pathway of flavone and flavonol biosynthesis and isoflavonoid biosynthesis.

Physiological and Molecular Responses of Pyrus pyraster Seedlings to Salt Treatment Analyzed by miRNA and Cytochrome P450 Gene-Based Markers

Physiological and molecular marker-based changes were studied in the tissues of two-year-old Pyrus pyraster (L.) Burgsd. seedlings under salt treatment. For 60 days, 5 mL of 100 mM NaCl solution was applied to each plant per day to a cumulative volume of 300 mL in the substrate. In response to osmotic stress, the seedlings increased their water use efficiency (WUE) on day 20 of regular NaCl application and maintained a stable net photosynthetic rate (An) per unit area. Under conditions of increasing salinity, the young plants maintained a balanced water regime of the leaf tissues (Ψwl). The seedlings invested mass to their root growth (R/S), retained a substantial portion (72%) of Na+ ions in the roots, and protected their leaves against intoxication and damage. A significant decrease in the leaf gas exchange parameters (gs, E, An) was manifested on day 60 of the experiment when the cumulative NaCl intake was 300 mL per plant. The variability in the reactions of the seedlings to salinity is related to the use of open-pollinated progeny (54 genotypes) in the experiment. Lus-miR168 showed tissue- and genotype-specific genome responses to the applied stress. Polymorphic miRNA-based loci were mostly detected in the root samples on the 20th and 35th days of the experiment. The cumulative effect of the salt treatment was reflected in the predominance of polymorphic loci in the leaves. We can confirm that miRNA-based markers represent a sensitive detection tool for plant stress response on an individual level. The screening and selection of the optimal type of miRNA for this type of research is crucial. The cytochrome P450-Based Analog (PBA) techniques were unable to detect polymorphism among the control and treated seedlings, except for the primer pair CYP2BF+R, where, in the roots of the stressed plant, insertions in the amplicons were obtained. The expression ratios of cytochrome P450 in the salt-stressed plants were higher in the roots in the case of 20/100 mL and in the leaves with higher doses. The observed physiological and molecular responses to salinity reflect the potential of P. pyraster seedlings in adaptation to osmotic and ionic stress.

Identification and Characterization of ABCG15-A Gene Required for Exocarp Color Differentiation in Pear

Exocarp color is a commercially essential quality for pear which can be divided into two types: green and russet. The occurrence of russet color is associated with deficiencies and defects in the cuticular and epidermal layers, which affect the structure of the cell wall and the deposition of suberin. Until now, the genetic basics triggering this trait have not been well understood, and limited genes have been identified for the trait. To figure out the gene controlling the trait of exocarp color, we perform a comprehensive genome-wide association study, and we describe the candidate genes. One gene encoding the ABCG protein has been verified to be associated with the trait, using an integrative analysis of the metabolomic and transcriptomic data. This review covers a variety of omics resources, which provide a valuable resource for identifying gene-controlled traits of interest. The findings in this study help to elucidate the genetic components responsible for the trait of exocarp color in pear, and the implications of these findings for future pear breeding are evaluated.

Comparative transcriptome analysis of Veratrum maackii and Veratrum nigrum reveals multiple candidate genes involved in steroidal alkaloid biosynthesis

Veratrum (Melanthiaceae; Liliales) is a genus of perennial herbs known for the production of unique bioactive steroidal alkaloids. However, the biosynthesis of these compounds is incompletely understood because many of the downstream enzymatic steps have yet to be resolved. RNA-Seq is a powerful method that can be used to identify candidate genes involved in metabolic pathways by comparing the transcriptomes of metabolically active tissues to controls lacking the pathway of interest. The root and leaf transcriptomes of wild Veratrum maackii and Veratrum nigrum plants were sequenced and 437,820 clean reads were assembled into 203,912 unigenes, 47.67% of which were annotated. We identified 235 differentially expressed unigenes potentially involved in the synthesis of steroidal alkaloids. Twenty unigenes, including new candidate cytochrome P450 monooxygenases and transcription factors, were selected for validation by quantitative real-time PCR. Most candidate genes were expressed at higher levels in roots than leaves but showed a consistent profile across both species. Among the 20 unigenes putatively involved in the synthesis of steroidal alkaloids, 14 were already known. We identified three new CYP450 candidates (CYP76A2, CYP76B6 and CYP76AH1) and three new transcription factor candidates (ERF1A, bHLH13 and bHLH66). We propose that ERF1A, CYP90G1-1 and CYP76AH1 are specifically involved in the key steps of steroidal alkaloid biosynthesis in V. maackii roots. Our data represent the first cross-species analysis of steroidal alkaloid biosynthesis in the genus Veratrum and indicate that the metabolic properties of V. maackii and V. nigrum are broadly conserved despite their distinct alkaloid profiles.

Advances in Understanding the Causes, Molecular Mechanism, and Perspectives of Russeting on Tree Fruit

The external quality of fruit is one of its most important qualities; good external quality attracts consumers easily and increases the value of fruit. Fruit russeting is one of the factors that influences the external quality of fruit and has been studied in most horticultural plants. However, the molecular mechanism of russeting has never been discussed so far. In this review, we summarize the research progress on fruit russeting, including causes, microscopic histomorphology, composition, genetics, and regulation and made a series of elaboration on the current research on fruit russeting. This study aims to provide insights into the mechanisms underlying fruit russeting. It also puts forward ideas for research on fruit russeting, which may provide a reference for future research.

An autopolyploid-suitable polyBSA-seq strategy for screening candidate genetic markers linked to leaf blight resistance in sugarcane

An autopolyploid-suitable polyBSA-seq strategy was developed for screening candidate genetic markers linked to leaf blight resistance in sugarcane. Due to the complex genome architecture, the quantitative trait loci mappings and linkage marker selections for agronomic traits of autopolyploid crops were mainly limited to the time-consuming and cost intensive construction of genetic maps. To map resistance-linked markers for sugarcane leaf blight (SLB) caused by Stagonospora tainanensis, the autopolyploid-suitable bulk-segregant analysis based on the sequencing (polyBSA-seq) strategy was successfully applied for the first time. Resistant- and susceptible-bulks (R- and S-bulks) constructed from the extreme-phenotypic sugarcane F₁ lines of YT93-159 × ROC22 were deep sequenced with 195.0 × for bulks and 74.4 × for parents. Informative single-dose variants (ISDVs) present as one copy in one parent and null in the other parent were detected based on the genome sequence of LA Purple, an autooctoploid Saccharum officinarum, to screen candidate linkage markers (CLMs). The proportion of the number of short reads harboring ISDVs in the total short reads covering a given genomic position was defined as ISDV index and the ISDVs with indices met the threshold set in this study (0.04-0.14) were selected as CLMs. In total, three resistance- and one susceptibility-related CLMs for SLB resistance were identified by the polyBSA-seq. Among them, two markers on chromosome 10 were less than 300 Kb apart. Furthermore, the RNA-seq was used to calculate the expression level of genes within 1.0 Mb from the aforementioned four CLMs, which demonstrated that twelve genes were differentially expressed between resistant and susceptible clones, including a receptor-like kinase and an ethylene-responsive transcription factor. This is the first reported polyBSA-seq in autopolyploid sugarcane, which specifically tailored for the fast selection of the CLMs and causal genes associated with important agronomic traits.

An ARF1-binding factor triggering programmed cell death and periderm development in pear russet fruit skin

Plants have a cuticular membrane (CM) and periderm membrane (PM), which act as barriers to terrestrial stresses. The CM covers primary organs with a continuous hydrophobic layer of waxes embedded in cutin, while the PM stacks with suberized cells outermost to the secondary tissues. The formation of native periderm is regulated by a postembryonic meristem phellogen that produces suberized phellem (cork) outwardly. However, the mechanism controlling phellogen differentiation to phellem remains to be clarified. Here, map-based cloning in a pear F1 population with segregation for periderm development in fruit skin facilitated the identification of an aspartic acid repeat deletion in Pyrus Periderm Programmed Cell Death 1.1 (PyPPCD1.1) that triggers phellogen activity for cork formation in pear russet fruit skin. PyPPCD1.1 showed preferential expression in pear fruit skin, and the encoded protein shares a structural similarity to that of the viral capsid proteins. Asp deletion in PyPPCD1.1 weakened its nuclear localization but increased its accumulation in the chloroplast. Both PyPPCD1.1 and its recessive allele directly interact with ADP-ribosylation factor 1 (ARF1). PyPPCD1.1 triggered PCD in an ARF1-dependent manner. Thus, this study identified the switch gene for PCD and periderm development and provided a new molecular regulatory mechanism underlying the development of this trait.

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".

Dissecting the molecular mechanism of russeting in sand pear (Pyrus pyrifolia Nakai) by metabolomics, transcriptomics, and proteomics

Brown coloration and a rough appearance as russet and semi-russet (partial russet) are features unique to the popular Asian sand pear (Pyrus pyrifolia Nakai). The degree of russeting is different between different genotypes. Russeting is sensitive to water fluctuations, where excessive rainwater can trigger/stimulate its development. However, the molecular mechanism of russeting is currently unclear. Here, we employed multi-omics, i.e., metabolomics, transcriptomics, and proteomics, and analyzed the effect of different sand pear genotypes and artificial rainfall on russeting of pear fruits. This led to the identification of 79, 64, and 29 differentially produced/expressed metabolites, transcripts, and proteins that are involved in the biosynthesis of suberin, phenylpropane, cutin, and waxes. Further analysis of these differentially expressed genes and their encoded proteins revealed that four of them exhibited high expression at both transcript and protein levels. Transient expression of one such gene, PbHHT1 (accession number 103966555), which encodes ω-hydroxypalmitate-O-feruloyl transferase, in young green non-russet fruits triggered premature suberization in the russeting pear genotypes. This coincided with increased production of 16-feruloyloxypalmitic acid, a conjugated compound between phenols and esters during the polymerization for suberin formation. Collectively, our data from the combined three omics demonstrate that russeting in sand pear is a complex process involving the biosynthesis and transport of suberin and many other secondary metabolites.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia)

Fruit color is one of the most important external qualities of pear (Pyrus pyrifolia) fruits. However, the mechanisms that control russet skin coloration in pear have not been well characterized. Here, we explored the molecular mechanisms that determine the russet skin trait in pear using the F₁ population derived from a cross between russet skin ('Niitaka') and non-russet skin ('Dangshansu') cultivars. Pigment measurements indicated that the lignin content in the skin of the russet pear fruits was greater than that in the non-russet pear skin. Genetic analysis revealed that the phenotype of the russet skin pear is associated with an allele of the PpRus gene. Using bulked segregant analysis combined with the genome sequencing (BSA-seq), we identified two simple sequence repeat (SSR) marker loci linked with the russet-colored skin trait in pear. Linkage analysis showed that the PpRus locus maps to the scaffold NW_008988489.1: 53297-211921 on chromosome 8 in the pear genome. In the mapped region, the expression level of LOC103929640 was significantly increased in the russet skin pear and showed a correlation with the increase of lignin content during the ripening period. Genotyping results demonstrated that LOC103929640 encoding the transcription factor MYB36 is the causal gene for the russet skin trait in pear. Particularly, a W-box insertion at the PpMYB36 promoter of russet skin pears is essential for PpMYB36-mediated regulation of lignin accumulation and russet coloration in pear. Overall, these results show that PpMYB36 is involved in the regulation of russet skin trait in pear.

An integrated metabolic and transcriptomic analysis reveals the mechanism through which fruit bagging alleviates exocarp semi-russeting in pear fruit

Fruit semi-russeting is an undesirable quality trait that occurs in fruit production. It is reported that preharvest fruit bagging could effectively alleviate fruit exocarp semi-russeting, but the physiological and molecular mechanisms remain unclear. In the present study, we performed an in-depth investigation into pear fruit semi-russeting from morphologic, metabolic and transcriptomic perspectives by comparing control (semi-russeted) and bagged (non-russeted) 'Cuiguan' pear fruits. The results showed that significant changes in cutin and suberin resulted in pear fruit semi-russeting. Compared with the skin of bagged fruits, the skin of the control fruits presented reduced cutin contents accompanied by an accumulation of suberin, which resulted in fruit semi-russeting; α, ω-dicarboxylic acids accounted for the largest proportion of typical suberin monomers. Moreover, combined transcriptomic and metabolic analysis revealed a series of genes involved in cutin and suberin biosynthesis, transport and polymerization differentially expressed between the two groups. Furthermore, the expression levels of genes involved in the stress response and in hormone biosynthesis and signaling were significantly altered in fruits with contrasting phenotypes. Finally, a number of transcription factors, including those of the MYB, NAC, bHLH and bZIP families, were differentially expressed. Taken together, the results suggest that the multilayered mechanism through which bagging alleviates pear fruit semi-russeting is complex, and the large number of candidate genes identified provides a good foundation for future functional studies.

Long-Term Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Berry Transcriptome

Viticulture is one of the horticultural systems in which antifungal treatments can be extremely frequent, with substantial economic and environmental costs. New products, such as biofungicides, resistance inducers and biostimulants, may represent alternative crop protection strategies respectful of the environmental sustainability and food safety. Here, the main purpose was to evaluate the systemic molecular modifications induced by biocontrol products as laminarin, resistance inducers (i.e., fosetyl-Al and potassium phosphonate), electrolyzed water and a standard chemical fungicide (i.e., metiram), on the transcriptomic profile of ‘Nebbiolo’ grape berries at harvest. In addition to a validation of the sequencing data through real-time polymerase chain reaction (PCR), for the first-time the expression of some candidate genes in different cell-types of berry skin (i.e., epidermal and hypodermal layers) was evaluated using the laser microdissection approach. Results showed that several considered antifungal treatments do not strongly affect the berry transcriptome profile at the end of season. Although some treatments do not activate long lasting molecular defense priming features in berry, some compounds appear to be more active in long-term responses. In addition, genes differentially expressed in the two-cell type populations forming the berry skin were found, suggesting a different function for the two-cell type populations.

Lignin and Quercetin Synthesis Underlies Berry Russeting in 'Sunshine Muscat' Grape

In order to further explore the mechanism of 'sunshine muscat' grape russet formation, transcriptomic and metabolomic analyses were performed on 'sunshine muscat' grape peels with and without russet. A total of 1491 differentially expressed genes (DEGs) were discovered based on these analyses. The phenylpropane synthesis pathway was the key metabolic pathway identified, and 28 DEGs related to phenylpropane synthesis pathway were screened, of which 16 were related to lignin synthesis. In addition, 60 differential metabolites were screened. There were 29 phenolic substances among the differential metabolites, which were all up-regulated and 10 were quercetin-related glycosides. Our results indicate that phenols likely play a dominant role in the formation of 'sunshine muscat' grape russet, and the synthesis of lignin and quercetin may be the key factors underlying russet formation.

Proteome and transcriptome profile analysis reveals regulatory and stress-responsive networks in the russet fruit skin of sand pear

The epidermal tissues of the cuticular membrane (CM) and periderm membrane (PM) confer first-line protection from environmental stresses in terrestrial plants. Although PM protection is essentially ubiquitous in plants, the protective mechanism, the function of many transcription factors and enzymes, and the genetic control of metabolic signaling pathways are poorly understood. Different microphenotypes and cellular components in russet (PM-covered) and green (CM-covered) fruit skins of pear were revealed by scanning and transmission electron microscopy. The two types of fruit skins showed distinct phytohormone accumulation, and different transcriptomic and proteomic profiles. The enriched pathways were detected by differentially expressed genes and proteins from the two omics analyses. A detailed analysis of the suberin biosynthesis pathways identified the regulatory signaling network, highlighting the general mechanisms required for periderm formation in russet fruit skin. The regulation of aquaporins at the protein level should play an important role in the specialized functions of russet fruit skin and PM-covered plant tissues.

Developmental and Environmental Regulation of Cuticular Wax Biosynthesis in Fleshy Fruits

The aerial parts of land plants are covered by a hydrophobic layer called cuticle that limits non-stomatal water loss and provides protection against external biotic and abiotic stresses. The cuticle is composed of polymer cutin and wax comprising a mixture of very-long-chain fatty acids and their derivatives, while also bioactive secondary metabolites such as triterpenoids are present. Fleshy fruits are also covered by the cuticle, which has an important protective role during the fruit development and ripening. Research related to the biosynthesis and composition of cuticles on vegetative plant parts has largely promoted the research on cuticular waxes in fruits. The chemical composition of the cuticular wax varies greatly between fruit species and is modified by developmental and environmental cues affecting the protective properties of the wax. This review focuses on the current knowledge of the cuticular wax biosynthesis during fleshy fruits development, and on the effect of environmental factors in regulation of the biosynthesis. Bioactive properties of fruit cuticular waxes are also briefly discussed, as well as the potential for recycling of industrial fruit residues as a valuable raw material for natural wax to be used in food, cosmetics and medicine.

Selection and validation of suitable reference genes for qRT-PCR analysis in pear leaf tissues under distinct training systems

Training systems generally alter tree architecture, which modulates light microclimate within the canopy, for the purpose of improving photosynthetic efficiency and fruit quality. Gene expression quantification is one of the most important methods for exploring the molecular mechanisms underlying the influence of training systems on pear photosynthesis, and suitable reference genes for gene expression normalization are a prerequisite for this method. In this study, the expression stability of nine common and four novel candidate genes were evaluated in 14 different pear leaf samples in two training systems, including those at four developmental stages (training_period) and from different parts of the trees (training_space), using two distinct algorithms, geNorm and NormFinder. Our results revealed that SKD1 (Suppressor of K⁺Transport Growth Defect1)/ YLS8 (Yellow Leaf Specific 8) and ARM (Armadillo) were the most stable single reference genes for the ‘training_period’ and ‘training_space’ subsets, respectively, although these single genes were not as stable as the optimal pairs of reference genes, SKD1+YLS8 and ARM+YLS8, respectively. Furthermore, the expression levels of the PpsAPX (Ascorbate peroxidase) gene showed that the arbitrary use of reference genes without previous testing could lead to misinterpretation of data. This work constitutes the first systematic analysis regarding the selection of superior reference genes in training system studies, facilitating the elucidation of gene function in pear and providing valuable information for similar studies in other higher plants.

Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)

Breeding of fruit trees is hindered by their large size and long juvenile period. Genome-wide association study (GWAS) and genomic selection (GS) are promising methods for circumventing this hindrance, but preparing new large datasets for these methods may not always be practical. Here, we evaluated the potential of breeding populations evaluated routinely in breeding programs for GWAS and GS. We used a pear parental population of 86 varieties and breeding populations of 765 trees from 16 full-sib families, which were phenotyped for 18 traits and genotyped for 1,506 single nucleotide polymorphisms (SNPs). The power of GWAS and accuracy of genomic prediction were improved when we combined data from the breeding populations and the parental population. The accuracy of genomic prediction was improved further when full-sib data of the target family were available. The results suggest that phenotype data collected in breeding programs can be beneficial for GWAS and GS when they are combined with genome-wide marker data. The potential of GWAS and GS will be further extended if we can build a system for routine collection of the phenotype and marker genotype data for breeding populations.

Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues

The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

Stone cell content is thought to be one of the key determinants for fruit quality in pears. However, the molecular mechanism of stone cell development remains poorly understood. In this study, we found that the stone cell clusters (SCCs) distribution and area in ‘Dangshan Su’ (with abundant stone cells) were higher as compared to ‘Lianglizaosu’ (low stone cell content bud sport of ‘Dangshan Su’) based on the histochemical staining, and the correlations of lignin content with stone cell content and SCC area was significant. The fruits of ‘Dangshan Su’ and ‘Lianglizaosu’ at three different developmental stages (23 and 55 days after flowering and mature) were sampled for comparative transcriptome analysis to explore the metabolic pathways associated with stone cell development. A total of 42444 unigenes were obtained from two varieties, among which 7203 differentially expressed genes (DEGs) were identified by comparison of the six transcriptomes. Specifically, many DEGs associated with lignin biosynthesis were identified, including coumaroylquinate 3-monooxygenase (C3H), shikimate O-hydroxycinnamoyltransferase (HCT), ferulate 5-hydroxylase (F5H), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD), as well as genes related to carbon metabolism, such as sorbitol dehydrogenase-like (SDH-like) and ATP-dependent 6-phosphofructokinase (ATP-PFK). At the peak of the stone cell content (55 days after flowering), the expression level of these genes in ‘Dangshan Su’ was significantly increased compared with ‘Lianglizaosu’, indicating that these genes were closely related to stone cell development. We validated the transcriptional levels of 33 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The results were consistent with the transcriptome analysis, indicating the reliability of transcriptome data. In addition, subcellular localization analysis of three DEGs in lignin synthesis (PbC3H, PbF5H and PbPOD) revealed that these proteins are mainly distributed in the cell membrane and cytoplasm. These results provide new insights into the molecular mechanism of stone cell formation.

MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins

A comparison of the transcriptomes of russeted vs nonrusseted apple skins previously highlighted a tight relationship between a gene encoding an MYB-type transcription factor, MdMYB93, and some key suberin biosynthetic genes. The present work assesses the role of this transcription factor in the suberization process. A phylogenetic analysis of MdMYB93 and Arabidopsis thaliana MYBs was performed and the function of MdMYB93 was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight the MdMYB93-regulated genes. Ultraperformance liquid chromatography-triple time-of-flight (UPLC-TripleTOF) and GC-MS were used to investigate alterations in phenylpropanoid, soluble-free lipid and lipid polyester contents. A massive accumulation of suberin and its biosynthetic precursors in MdMYB93 agroinfiltrated leaves was accompanied by a remobilization of phenylpropanoids and an increased amount of lignin precursors. Gene expression profiling displayed a concomitant alteration of lipid and phenylpropanoid metabolism, cell wall development, and extracellular transport, with a large number of induced transcripts predicted to be involved in suberin deposition. The present work supports a major role of MdMYB93 in the regulation of suberin deposition in russeted apple skins, from the synthesis of monomeric precursors, their transport, polymerization, and final deposition as suberin in primary cell wall.

RNA-Seq Expression Analysis of Enteric Neuron Cells with Rotenone Treatment and Prediction of Regulated Pathways

The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson's disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes. The functional categorization revealed that the DEGs were involved in the regulation of cell differentiation and development, response to various stimuli, and regulation of neurogenesis. In addition, the pathway and network analysis showed that the Mitogen Activated Protein Kinase (MAPK), Toll-like receptor, Wnt, and Ras signaling pathways were intensively involved in the effect of rotenone on the ENS. Additionally, the quantitative real-time polymerase chain reaction result for the selected seven DEGs matched those of the RNA-seq analysis. Our results present a significant step in the identification of DEGs and provide new insight into the progression of PD in the rotenone-induced model.

Bulked sample analysis in genetics, genomics and crop improvement

Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.

The role of polyamines during exocarp formation in a russet mutant of 'Dangshansuli' pear (Pyrus bretschneideri Rehd.)

Differential genes of suberin, polyamine and transcription factors in transcriptome sequences and the contents of H 2 O 2 , spermidine, spermine, and putrescine changed significantly after treating with MGBG. Russeting is a commercially important process that restores the control of water loss through the skin via the formation of a waterproofing periderm just beneath the microcracked skin of pear primary fruit. A spontaneous russet skin mutant, the yellow-green 'Dangshansuli' pear, has been identified. To understand the role of polyamines in the formation of the russet skin of the mutant-type (MT) pear, it was treated with methylglyoxal-bis-(guanylhydrazone) (MGBG) for 4 weeks after full bloom. One week later, differentially expressed genes among the wild-type (WT), MT, and MGBG-treated MT pears were screened, hydrogen peroxide (H2O2) was localized using CeCl3, and the contents of H2O2 and polyamine were measured. A total of 57,086,772, 61,240,014, and 67,919,420 successful reads were generated from the transcriptomes of WT, MT, and MGBG-treated MT, with average unigene lengths of 701, 720, and 735 bp, respectively. Differentially expressed genes involved in polyamine metabolism and suberin synthesis were screened in 'Dangshansuli' and in the mutant libraries, and their relative expression was found to be significantly altered after treatment with MGBG, which was confirmed by real-time PCR. The expression patterns of differentially expressed transcription factors were identified and were found to be similar to those of the polyamine- and suberin-related genes. The results indicated that the H2O2 generated during polyamine metabolism might contribute to russet formation on the exocarp of the mutant pear. Furthermore, the contents of H2O2, spermidine, spermine, and putrescine and H2O2 localization provided a comprehensive transcriptomic view of russet formation in the mutant pear.

Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.)

Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. "Starkrimson" (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'

BACKGROUND

Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru).

RESULTS

In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'.

CONCLUSIONS

A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple.

Apple russeting as seen through the RNA-seq lens: strong alterations in the exocarp cell wall

Russeting, a commercially important defect in the exocarp of apple (Malus × domestica), is mainly characterized by the accumulation of suberin on the inner part of the cell wall of the outer epidermal cell layers. However, knowledge on the underlying genetic components triggering this trait remains sketchy. Bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties. This experimental design was chosen to lower the impact of genotype on the obtained results. Validation by qPCR was carried out on representative genes and additional varieties. Gene ontology enrichment revealed a repression of lignin and cuticle biosynthesis genes in russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R(2) = 0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of cuticle biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. The large number of candidate genes identified in this study provides a solid foundation for further functional studies.

The cinnamyl alcohol dehydrogenase gene family in melon (Cucumis melo L.): bioinformatic analysis and expression patterns

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. However, little was known about CADs in melon. Five CAD-like genes were identified in the genome of melons, namely CmCAD1 to CmCAD5. The signal peptides analysis and CAD proteins prediction showed no typical signal peptides were found in all CmCADs and CmCAD proteins may locate in the cytoplasm. Multiple alignments implied that some motifs may be responsible for the high specificity of these CAD proteins, and may be one of the key residues in the catalytic mechanism. The phylogenetic tree revealed seven groups of CAD and melon CAD genes fell into four main groups. CmCAD1 and CmCAD2 belonged to the bona fide CAD group, in which these CAD genes, as representative from angiosperms, were involved in lignin synthesis. Other CmCADs were distributed in group II, V and VII, respectively. Semi-quantitative PCR and real time qPCR revealed differential expression of CmCADs, and CmCAD5 was expressed in different vegetative tissues except mature leaves, with the highest expression in flower, while CmCAD2 and CmCAD5 were strongly expressed in flesh during development. Promoter analysis revealed several motifs of CAD genes involved in the gene expression modulated by various hormones. Treatment of abscisic acid (ABA) elevated the expression of CmCADs in flesh, whereas the transcript levels of CmCAD1 and CmCAD5 were induced by auxin (IAA); Ethylene induced the expression of CmCADs, while 1-MCP repressed the effect, apart from CmCAD4. Taken together, these data suggested that CmCAD4 may be a pseudogene and that all other CmCADs may be involved in the lignin biosynthesis induced by both abiotic and biotic stresses and in tissue-specific developmental lignification through a CAD genes family network, and CmCAD2 may be the main CAD enzymes for lignification of melon flesh and CmCAD5 may also function in flower development.

Morphology and quantitative monitoring of gene expression patterns during floral induction and early flower development in Dendrocalamus latiflorus

The mechanism of floral transition in bamboo remains unclear. Dendrocalamus latiflorus (Bambusease, Bambusoideae, Poaceae) is an economically and ecologically important clumping bamboo in tropical and subtropical areas. We evaluated morphological characteristics and gene expression profiling to study floral induction and early flower development in D. latiflorus. The detailed morphological studies on vegetative buds and floral organography were completed using paraffin sectioning and scanning electron microscopy. The 3 mm floral buds commence the development of stamen primordia and pistil primordium. Furthermore, homologs of floral transition-related genes, including AP1, TFL1, RFL, PpMADS1, PpMADS2, SPL9, FT, ID1, FCA, and EMF2, were detected and quantified by reverse transcriptase PCR and real-time PCR in vegetative and floral buds, respectively. Distinct expression profiles of ten putative floral initiation homologues that corresponded to the developmental stages defined by bud length were obtained and genes were characterized. Six of the genes (including DlTFL1, DlRFL, DlMADS2, DlID1, DlFCA, DlEMF2) showed statistically significant changes in expression during floral transition. DlAP1 demonstrated a sustained downward trend and could serve as a good molecular marker during floral transition in D. latiflorus. The combined analysis provided key candidate markers to track the transition from the vegetative to reproductive phase.

Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant

Exocarp color of sand pear is an important trait for the fruit production and has caused our concern for a long time. Our previous study explored the different expression genes between the two genotypes contrasting for exocarp color, which indicated the different suberin, cutin, wax and lignin biosynthesis between the russet- and green-exocarp. In this study, we carried out microscopic observation and Fourier transform infrared spectroscopy analysis to detect the differences of tissue structure and biochemical composition between the russet- and green-exocarp of sand pear. The green exocarp was covered with epidermis and cuticle which was replaced by a cork layer on the surface of russet exocarp, and the chemicals of the russet exocarp were characterized by lignin, cellulose and hemicellulose. We explored differential gene expression between the russet exocarp of 'Niitaka' and its green exocarp mutant cv. 'Suisho' using Illumina RNA-sequencing. A total of 559 unigenes showed different expression between the two types of exocarp, and 123 of them were common to the previous study. The quantitative real time-PCR analysis supports the RNA-seq-derived gene with different expression between the two types of exocarp and revealed the preferential expression of these genes in exocarp than in mesocarp and fruit core. Gene ontology enrichment analysis revealed divorced expression of lipid metabolic process genes, transport genes, stress responsive genes and other biological process genes in the two types of exocarp. Expression changes in lignin metabolism-related genes were consistent with the different pigmentation of russet and green exocarp. Increased transcripts of putative genes involved the suberin, cutin and wax biosynthesis in 'Suisho' exocarp could facilitate deposition of the chemicals and take a role in the mutant trait responsible for the green exocarp. In addition, the divorced expression of ATP-binding cassette transporters involved in the trans-membrane transport of lignin, cutin, and suberin precursors suggests that the transport process could also affect the composition of exocarp and take a role in the regulation of exocarp pigmentation. Results from this study provide a base for the analysis of the molecular mechanism underlying sand pear russet/green exocarp mutation, and presents a comprehensive list of candidate genes that could be used to further investigate the trait mutation at the molecular level.