Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1

Unearthing Grape Heritage: Morphological Relationships between Late Bronze-Iron Age Grape Pips and Modern Cultivars

The grapevine was one of the earliest domesticated fruit crops and has been cultivated since ancient times. It is considered one of the most important fruit crops worldwide for wine and table grape production. The current grape varieties are the outcome of prolonged selection initiated during the domestication process of their wild relative. Recent genetic studies have shed light on the origins of the modern domestic grapevine in western Europe, suggesting that its origin stems from the introgression between eastern domestic grapes and western wild grapes. However, the origin of ancient grapevines remains largely unexplored. In this study, we conducted an extensive analysis of 2228 well-preserved waterlogged archaeological grape pips from two sites in Sardinia (Italy), dated to the Late Bronze Age (ca. 1300-1100 BC) and the Iron Age (4th and 3rd centuries BC). Using morphometrics and linear discriminant analyses, we compared the archaeological grape pips with modern reference collections to differentiate between wild and domestic grape types and to investigate similarities with 330 modern cultivars. Grape pips from the Late Bronze Age displayed a high percentage of similarity with domesticated grapevines, with a small percentage assigned to wild ones, while the majority of grape pips from the Iron Age were classified as domestic. Discriminant analyses revealed that both white and red grape varieties were cultivated during the Late Bronze and Iron Ages, suggesting a high level of diversification in grape cultivation. Furthermore, a high percentage of archaeological grape pips from both periods showed strong similarities with modern cultivars from the Caucasus and Balkans. This suggests that the great diversity of grapevines present in Sardinia could result from interbreeding between western Asian cultivars and local grapevines that began in the Late Bronze Age. Additionally, a substantial proportion of archaeological grape pips exhibited similar morphometric characteristics to two important Mediterranean grape cultivars: "Muscat à petits grains blancs" and "Garnacha".

The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar 'Yan73' was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi)， Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in 'Cabernet Sauvignon' and 'Yan73' were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of 'Yan73' were higher than those of 'Cabernet Sauvignon'. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of 'Yan73' haplotype 2 genome. The 'Yan73' T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.

Genetic changes in the genus Vitis and the domestication of vine

The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.

Review: Status and prospects of association mapping in grapevine

Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.

Anthocyanin accumulation in grape berry flesh is associated with an alternative splicing variant of VvMYBA1

Anthocyanins are flavonoids that contribute to the color of grape berries and are an essential component of grape berry and wine quality. Anthocyanin accumulation in grape berries is dependent on the coordinated expression of genes encoding enzymes in the anthocyanin pathway that are principally regulated at the transcriptional level, with VvMYBA1 as the main transcriptional regulator in grapes. Alternative splicing (AS) events in VvMYBA1, however, have not been examined. In the present study, VvMYBA1-L, an AS variant of VvMYBA1, was identified in 'ZhongShan-Hong' (ZS-H) and its offspring. The AS variant is characterized by a deletion in the third exon of the open reading frame (ORF) of VvMYBA1-L, resulting in the early termination of the encoded protein. Overexpression of VvMYBA1-L in grape berries resulted in delayed flesh coloration and ectopic overexpression of VvMYBA1-L in tobacco inhibited the coloration of petals. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed that VvMYBA1-L interacts with VvMYBA1. Dual luciferase assays indicated that co-infiltration of VvMYC1 and VvMYBA1 significantly activated the promoter regulated expression of VvCHS3, VvDFR, VvUFGT, and VvF3H. In the presence of VvMYBA1-L, however, the induction effect of VvMYBA1 on the indicated promoters was significantly inhibited. Our findings provide insight into the essential role of VvMYBA1 and its variant, VvMYBA1-L, in regulating anthocyanin accumulation in grape berry flesh.

Strategy to minimize phenotyping in the selection of new table grape varieties

Morphological evaluation of large progenies is a problem in plant breeding programs, because of the need for skilled labor capable of characterizing various descriptors in a large number of individuals ripening simultaneously. In addition, the maintenance of progenies in the field for evaluation involves an unsustainable consumption of resources that could be reduced. Marker-assisted selection (MAS) offers the possibility of accelerating the process with the consequent saving of resources. The aim of this work is to propose a methodology that minimizes the phenotyping work for thousands of individuals of these breeding programs. The methodology consists of analyzing the complete progeny with a limited number of markers (27 SSR (Simple Sequence Repeat)) and a reduced description of morphological characters on a so-called training collection (27 individuals) obtained with Mstrat software. With this strategy, it was possible to estimate traits such as berry skin color or seedlessness in a progeny of more than 2000 individuals with a probability of 90%, and to discard 50% of individuals without muscat linked alleles.

Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes

LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification of these elements remains a challenge today. Moreover, current software can be relatively slow (from hours to days), sometimes involve a lot of manual work and do not reach satisfactory levels in terms of precision and sensitivity. Here we present Inpactor2, an accurate and fast application that creates LTR-retrotransposon reference libraries in a very short time. Inpactor2 takes an assembled genome as input and follows a hybrid approach (deep learning and structure-based) to detect elements, filter partial sequences and finally classify intact sequences into superfamilies and, as very few tools do, into lineages. This tool takes advantage of multi-core and GPU architectures to decrease execution times. Using the rice genome, Inpactor2 showed a run time of 5 minutes (faster than other tools) and has the best accuracy and F1-Score of the tools tested here, also having the second best accuracy and specificity only surpassed by EDTA, but achieving 28% higher sensitivity. For large genomes, Inpactor2 is up to seven times faster than other available bioinformatics tools.

First investigation on polyphenols and glycosidic aroma precursors in a spontaneous colour mutant of 'Glera', the principal grape variety of Prosecco sparkling wine

BACKGROUND

Somatic mutations in Vitis spp. are relatively frequent and can generate new agronomically interesting phenotypes. We report the discovery, genetic and chemical characterization of 'Glera rosa', a mutant for the berry skin colour of 'Glera', the main white cultivar used to produce Prosecco wine.

RESULTS

We ascertained the relationship between the skin colour of 'Glera rosa' and the polymorphisms in the Myb-gene transcription factors involved in polyphenol biosynthesis. We established that VvMybA1 was homozygous (VvMybA1a/VvMybA1a) in 'Glera' but heterozygous (VvmybA1a/VvmybA1b) in the 'Glera rosa' mutant. We verified that the VvMybA1a non-functional allele contained Grapevine Retrotransposon 1 (Gret1), while in the VvmybA1b allele Gret1 was missing, and the gene function was partially restored. The effects of mutation on 'Glera rosa' grape metabolites were studied by high-resolution mass spectrometry and gas chromatography/mass spectrometry analysis. Fifteen anthocyanins and five unique flavonols were found in the 'Glera rosa' mutant. The mutation also increased the contents of trans-resveratrol and its derivatives (i.e., piceatannol, E-ε-viniferin, cis- and trans-piceid) and of some flavonols in grape. Finally, the mutation did not significantly affect the typical aroma precursors of Glera grape such as glycosidic monoterpenes, norisoprenoids and benzenoids.

CONCLUSION

'Glera rosa' could be an interesting genetic source for the wine industry to produce Prosecco DOC rosé typology (made by adding up to 15% of 'Pinot Noir'), which was introduced to the market in 2020 with a worldwide massive success. © 2022 Society of Chemical Industry.

Molecular and physiologic mechanisms of advanced ripening by trunk girdling at early veraison of 'Summer Black' grape

Although the effects of girdling on grape berry development have been widely studied, the underlying mechanisms are poorly understood, especially at the molecular level. This study investigated the effect of trunk girdling on grape (Vitis L.) berry maturation. Girdling was performed on 5-year-old 'Summer Black' grapevines at early veraison, and transcriptional and physiologic analyses were performed. Trunk girdling promoted sugar accumulation and color development in berries and accelerated berry ripening by 25 days. Genes related to sucrose cleavage and polysaccharide degradation were upregulated at the transcriptional level, which was associated with increased monosaccharide accumulation and berry softening. Anthocyanin biosynthesis and accumulation were also enhanced by trunk girdling through the upregulation of anthocyanin biosynthesis genes including phenylalanine ammonia-lyase and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT). The increased expression of two VvUFGT genes was accompanied by the upregulation of VvMYBA2 under girdling. The upregulation of genes involved in ethylene biosynthesis and hormone (abscisic acid and brassinosteroid) responses and downregulation of genes involved in indoleacetic acid biosynthesis and response may have also promoted berry ripening in the girdling group. A total of 120 differentially expressed transcription factor genes from 29 gene families including MYB, ERF, and MYB-related were identified in the girdling group, which may participate in the regulation of berry development and ripening. These results provide molecular-level insight into the positive effects of trunk girdling on berry development in grapes.

A recessive mutation in muscadine grapes causes berry color-loss without influencing anthocyanin pathway

Anthocyanins, a major class of flavonoids, are important pigments of grape berries. Despite the recent discovery of the genetic cause underlying the loss of color, the metabolomic and molecular responses are unknown. Anthocyanin quantification among diverse berry color muscadines suggests that all genotypes could produce adequate anthocyanin quantities, irrespective of berry color. Transcriptome profiling of contrasting color muscadine genotypes proposes a potential deficiency that occurs within the anthocyanin transport and/or degradation mechanisms and might cause unpigmented berries. Genome-wide association studies highlighted a region on chromosome-4, comprising several genes encoding glutathione S-transferases involved in anthocyanin transport. Sequence comparison among genotypes reveals the presence of two GST4b alleles that differ by substituting the conserved amino acid residue Pro₁₇₁-to-Leu. Molecular dynamics simulations demonstrate that GST4b2–Leu₁₇₁ encodes an inactive protein due to modifications within the H-binding site. Population genotyping suggests the recessive inheritance of the unpigmented trait with a GST4b2/2 homozygous. A model defining colorless muscadines’ response to the mutation stimulus, avoiding the impact of trapped anthocyanins within the cytoplasm is established.

Transcriptome profiling and mutational analysis suggest a potential deficiency in anthocyanin transport by glutathione S-transferases and/or degradation mechanisms that might cause unpigmented berries.

Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves

BACKGROUND AND AIMS

Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree.

METHODS

Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before 'véraison', freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry.

KEY RESULTS AND CONCLUSIONS

The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.

Removal of a 10-kb Gret1 transposon from VvMybA1 of Vitis vinifera cv. Chardonnay

Many white grape cultivars have a nonfunctional VvMybA1 gene due to the presence of a 10-kb Gret1 transposon in its promoter. In this study, we successfully demonstrated removal of the 10-kb Gret1 transposon and functional restoration of a VvMybA1 allele in Vitis vinifera cv. Chardonnay through transgenic expression of Cas9 and two gRNAs simultaneously targeting two junction sequences between Gret1 LTRs and VvMybA1. We generated 67 and 24 Cas9-positive vines via Agrobacterium-mediated and biolistic bombardment transformation, respectively. While the editing efficiencies were as high as 17% for the 5' target site and 65% for the 3' target site, simultaneous editing of both 5' and 3' target sites resulting in the removal of Gret1 transposon from the VvMybA1 promoter was 0.5% or less in most transgenic calli, suggesting that these calli had very limited numbers of cells with the Gret1 removed. Nevertheless, two bombardment-transformed vines, which shared the same unique editing features and were likely derived from a singly edited event, were found to have the Gret1 successfully edited out from one of their two VvMybA1 alleles. The edited allele was functionally restored based on the detection of its expression and a positive coloring assay result in leaves. Precise removal of more than a 10-kb DNA fragment from a gene locus in grape broadens the possibilities of using gene editing technologies to modify various trait genes in grapes and other plants.

Demethylation of the 3' LTR region of retrotransposon in VvMYBA1BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in 'Brazil' grape

Black-skinned and red-fleshed grape 'Brazil' is a bud sport of rosy-skinned 'Benitaka'. 'Brazil' has a much higher anthocyanin content in the skin than that of 'Benitaka' and is characterized by the accumulation of anthocyanins in the flesh. Our genomic analysis of the VvMYBA loci, which regulate anthocyanin biosynthesis, suggested that the difference in skin and flesh color between 'Brazil' and 'Benitaka' cannot be explained by genomic alteration at the loci. Expression levels of VvMYBA1 and anthocyanin biosynthesis-related genes in skin and flesh were significantly higher in 'Brazil' than in 'Benitaka' throughout berry development. DNA methylation levels in the 3' long terminal repeat (LTR) of a retrotransposon in the upstream region of VvMYBA1^BEN allele were clearly higher in the skin and flesh of 'Benitaka' than in those of 'Brazil' throughout berry development. These findings suggest that a dramatic decrease in DNA methylation level in the 3' LTR of the retrotransposon in the VvMYBA1^BEN allele in 'Brazil' increases the expression levels of VvMYBA1 and anthocyanin accumulation in skin and flesh. Our findings also suggest that skin and flesh colors are inherited together and vary depending on the presence or absence of the VvMYBA1^BEN allele.

Transcriptional profiling of two muscadine grape cultivars "Carlos" and "Noble" to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening

In commercial fruit production, synchronized ripening and stable shelf life are important properties. The loosely clustered or non-bunching muscadine grape has unrealized potential as a disease-resistant cash crop, but requires repeated hand harvesting due to its unsynchronized or long or heterogeneous maturation period. Genomic research can be used to identify the developmental and environmental factors that control fruit ripening and postharvest quality. This study coupled the morphological, biochemical, and genetic variations between "Carlos" and "Noble" muscadine grape cultivars with RNA-sequencing analysis during berry maturation. The levels of antioxidants, anthocyanins, and titratable acids varied between the two cultivars during the ripening process. We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. These findings may help develop a large-scale database of the genetic factors of muscadine grape ripening and postharvest profiles and allow the discovery of the factors underlying the ripeness heterogeneity at harvest. These genetic resources may allow us to combine applied and basic research methods in breeding to improve table and wine grape ripening uniformity, quality, stress tolerance, and postharvest handling and storage.

Grapevine Leafroll-Associated Virus 3 Genotype Influences Foliar Symptom Development in New Zealand Vineyards

Grapevine leafroll disease (GLD) constrains wine production worldwide. In New Zealand, the main causal agent of GLD is grapevine leafroll-associated virus 3 (GLRaV-3). To control GLD, an integrated management program is used and includes removing (roguing) GLRaV-3-infected vines from the vineyard. The classical foliar symptoms from virus-infected red-berry cultivars are leaves with dark red intervein, green veins, and downward rolling of margins. Growers use these phenotypic cues to undertake visual symptom identification (VSI) for GLD. However, the influence of the known large genetic variation among GLRaV-3 isolates on the foliar symptoms from different grapevine cultivars remains undescribed, especially in cool-climate growing environments, such as New Zealand. Over three vintages (2015, 2016, and 2017), VSI for GLD was undertaken at three field sites in New Zealand (Auckland, Hawke’s Bay, and Marlborough), each including four cultivars (Merlot, Pinot noir, Sauvignon blanc, and Pinot gris) infected with three GLRaV-3 genotypes (Groups I, VI, and X) or GLRaV-3-uninfected control plants. Throughout this study, no visual symptoms were observed on white-berry cultivars infected with GLRaV-3. For red-berry cultivars, the greatest variability in observed foliar symptoms among regional study sites, cultivars, and GLRaV-3 genotypes was observed early in the growing season. In particular, Group X had significantly delayed symptom expression across all three sites compared with Groups I and VI. As the newly infected, young vines matured in years 2 and 3, the GLRaV-3 genotype, cultivar, region, and environmental conditions had minimal influence on the accuracy of VSI, with consistently high (>95%) within-vintage identification by the end of each vintage. The results from this study strongly support the use of VSI for the GLD management of red-berry cultivar grapevines, Merlot and Pinot noir, as a reliable and cost-effective tool against GLD.

Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia)

Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine glutathione S-transferase4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 126 breeding selections, 76 cultivars, and 359 progeny from 3 mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action. VrGST4 was expressed in skins of both black and bronze muscadines at similar levels. While nonsynonymous polymorphisms between black and bronze muscadines were discovered in VrGSTF12, another Type I GST-coding gene in the muscadine color locus, this gene was ruled out as a possible candidate for berry color because RNA sequencing indicated it is not expressed in berry skins at véraison from black or bronze genotypes. These results suggest that the bronze phenotype in muscadines is regulated by a mechanism distinct from the MybA gene cluster responsible for berry color variation in Vitis vinifera.

A 69 kbp Deletion at the Berry Color Locus Is Responsible for Berry Color Recovery in Vitis vinifera L. Cultivar 'Riesling Rot'

‘Riesling Weiss’ is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is ‘Riesling Rot’, a red-berried variant of ‘Riesling Weiss’ that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of ‘Riesling Rot’ revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR. The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of ‘Riesling Weiss’, ‘Riesling Rot’, and the ancestor ‘Heunisch Weiss’ along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of ‘Riesling Weiss’ was inherited from the white-berried parent variety ‘Heunisch Weiss’. Since no color mutants of ‘Heunisch Weiss’ are described that could have served as allele donors, we concluded that, in contrast to the public opinion, ‘Riesling Rot’ resulted from a mutational event in ‘Riesling Weiss’ and not vice versa.

Methylation of MYBA1 is Associated with the Coloration in "Manicure Finger" Grape Skin

The "Manicure Finger" grape is notable for its fingerlike berries with a bright red top and yellow base; however, the mechanism underlying this color difference remains unknown. This study showed that the anthocyanin concentration and the expression levels of anthocyanin-related genes in the top skin were notably higher than those in the basal skin. The expression levels of DFR, UFGT, and GST were significantly correlated with the anthocyanin content. The promoters of the two VvUFGT alleles can be activated by VvMYBA1, which was verified by the yeast one-hybrid assay, the dual-luciferase reporter gene assay, and the electrophoretic mobility shift assay. Moreover, the methylation level of the VvMYBA1 promoter (-1488 to -1083 bp) in the top skin was significantly lower than that in the basal skin and was positively correlated with the anthocyanin content. Our data suggest that methylation levels of the VvMYBA1 promoter play a crucial role in regulating grape skin coloration.

Integrative Analyses of Metabolomes and Transcriptomes Provide Insights into Flavonoid Variation in Grape Berries

Flavonoids in grapes contribute the quality of the berry, but the flavonoid diversity and the regulatory networks underlying the variation require a further investigation. In this study, we integrated multi-omics data to systematically explore the global metabolic and transcriptional profiles in the skins and pulps of three grape cultivars. The results revealed large-scale differences involved in the flavonoid metabolic pathway. A total of 133 flavonoids, including flavone and flavone C-glycosides, were identified. Beyond the visible differences of anthocyanins, there was large variation in other sub-branched flavonoids, most of which were positively correlated with anthocyanins in grapes. The expressions of most flavonoid biosynthetic genes and the major regulators MYBA1 were strongly consistent with the changes in flavonoids. Integrative analysis identified two novel transcription factors (MYB24 and MADS5) and two ubiquitin proteins (RHA2) as promising regulatory candidates for flavonoid biosynthesis in grapes. Further verification in various grape accessions indicated that five major genes including flavonol 3'5'-hydroxylase (F3'5'H), UDP-glucose:flavonoid 3-O-glycosyl-transferase, anthocyanin O-methyltransferase, acyltransferase (3AT), and glutathione S-transferase (GST4) controlled flavonoid variation in grape berries. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in grape berries and the further development of grape health products.

The role of VvMYBA2r and VvMYBA2w alleles of the MYBA2 locus in the regulation of anthocyanin biosynthesis for molecular breeding of grape (Vitis spp.) skin coloration

In grape, MYBA1 and MYBA2 at the colour locus are the major genetic determinants of grape skin colour, and the mutation of two functional genes (VvMYBA1 and VvMYBA2) from these loci leads to white skin colour. This study aimed to elucidate the regulation of grape berry coloration by isolating and characterizing VvMYBA2w and VvMYBA2r alleles. The overexpression of VvMYBA2r up-regulated the expression of anthocyanin biosynthetic genes and resulted in higher anthocyanin accumulation in transgenic tobacco than wild-type (WT) plants, especially in flowers. However, the ectopic expression of VvMYBA2w inactivated the expression of anthocyanin biosynthetic genes and could not cause obvious phenotypic modulation in transgenic tobacco. Unlike in VvMYBA2r, CA dinucleotide deletion shortened the C-terminal transactivation region and disrupted the transcriptional activation activity of VvMYBA2w. The results indicated that VvMYBA2r positively regulated anthocyanin biosynthesis by forming the VvMYBA2r-VvMYCA1-VvWDR1 complex, and VvWDR1 enhanced anthocyanin accumulation by interacting with the VvMYBA2r-VvMYCA1 complex; however, R⁴⁴ L substitution abolished the interaction of VvMYBA2w with VvMYCA1. Meanwhile, both R⁴⁴ L substitution and CA dinucleotide deletion seriously affected the efficacy of VvMYBA2w to regulate anthocyanin biosynthesis, and the two non-synonymous mutations were additive in their effects. Investigation of the colour density and MYB haplotypes of 213 grape germplasms revealed that dark-skinned varieties tended to contain HapC-N and HapE2, whereas red-skinned varieties contained high frequencies of HapB and HapC-Rs. Regarding ploidy, the higher the number of functional alleles present in a variety, the darker was the skin colour. In summary, this study provides insight into the roles of VvMYBA2r and VvMYBA2w alleles and lays the foundation for the molecular breeding of grape varieties with different skin colour.

Domestication of Crop Metabolomes: Desired and Unintended Consequences

The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.

Towards Sensor-Based Phenotyping of Physical Barriers of Grapes to Improve Resilience to Botrytis Bunch Rot

Botrytis bunch rot is one of the economically most important fungal diseases in viticulture (aside from powdery mildew and downy mildew). So far, no active defense mechanisms and resistance loci against the necrotrophic pathogen are known. Since long, breeders are mostly selecting phenotypically for loose grape bunches, which is recently the most evident trait to decrease the infection risk of Botrytis bunch rot. This study focused on plant phenomics of multiple traits by applying fast sensor technologies to measure berry impedance (Z _REL ), berry texture, and 3D bunch architecture. As references, microscopic determined cuticle thickness (MS _CT ) and infestation of grapes with Botrytis bunch rot were used. Z _REL hereby is correlated to grape bunch density OIV204 (r = -0.6), cuticle thickness of berries (r = 0.61), mean berry diameter (r = -0.63), and Botrytis bunch rot (r = -0.7). However, no correlation between Z _REL and berry maturity or berry texture was observed. In comparison to the category of traditional varieties (mostly susceptible), elite breeding lines show an impressive increased Z _REL value (+317) and a 1-μm thicker berry cuticle. Quantitative trait loci (QTLs) on LGs 2, 6, 11, 15, and 16 were identified for Z _REL and berry texture explaining a phenotypic variance of between 3 and 10.9%. These QTLs providing a starting point for the development of molecular markers. Modeling of Z _REL and berry texture to predict Botrytis bunch rot resilience revealed McFadden R ² = 0.99. Taken together, this study shows that in addition to loose grape bunch architecture, berry diameter, Z _REL , and berry texture values are probably additional parameters that could be used to identify and select Botrytis-resilient wine grape varieties. Furthermore, grapevine breeding will benefit from these reliable methodologies permitting high-throughput screening for additional resilience traits of mechanical and physical barriers to Botrytis bunch rot. The findings might also be applicable to table grapes and other fruit crops like tomato or blueberry.

Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.

The proanthocyanin-related transcription factors MYBC1 and WRKY44 regulate branch points in the kiwifruit anthocyanin pathway

The groups of plant flavonoid metabolites termed anthocyanins and proanthocyanins (PA) are responsible for pigmentation in seeds, flowers and fruits. Anthocyanins and PAs are produced by a pathway of enzymes which are transcriptionally regulated by transcription factors (TFs) that form the MYB-bHLH-WD40 (MBW) complex. In this study, transcriptomic analysis of purple-pigmented kiwifruit skin and flesh tissues identified MYBC1, from subgroup 5 of the R2R3 MYB family, and WRKY44 (highly similar to Arabidopsis TTG2) as candidate activators of the anthocyanin pathway. Transient over-expression of MYBC1 and WRKY44 induced anthocyanin accumulation in tobacco leaves. Dual luciferase promoter activation assays revealed that both MYBC1 and WRKY44 were able to strongly activate the promoters of the kiwifruit F3'H and F3'5'H genes. These enzymes are branch points of the pathway which specifies the type of anthocyanin accumulated. Stable over-expression of MYBC1 and WRKY44 in kiwifruit calli activated the expression of F3'5'H and PA-related biosynthetic genes as well as increasing levels of PAs. These results suggest that while previously characterised anthocyanin activator MYBs regulate the overall anthocyanin biosynthesis pathway, the PA-related TFs, MYBC1 and WRKY44, more specifically regulate key branch points. This adds a layer of regulatory control that potentially balances anthocyanin and PA levels.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

BACKGROUND

The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers.

METHODS

In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms.

RESULTS

Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported.

CONCLUSION

This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

Single berry reconstitution prior to RNA-sequencing reveals novel insights into transcriptomic remodeling by leafroll virus infections in grapevines

Leafroll viruses are among the most devastating pathogens in viticulture and are responsible for major economic losses in the wine industry. However, the molecular interactions underlying the effects on fruit quality deterioration are not well understood. The few molecular studies conducted on berries from infected vines, associated quality decreases with the repression of key genes in sugar transport and anthocyanin biosynthesis. Sampling protocols in these studies did however not account for berry heterogeneity and potential virus induced phenological shifts, which could have biased the molecular information. In the present study, we adopted an innovative individual berry sampling protocol to produce homogeneous batches for RNA extraction, thereby circumventing berry heterogeneity and compensating for virus induced phenological shifts. This way a characterization of the transcriptomic modulation by viral infections was possible and explain why our results differ significantly from previously reported repression of anthocyanin biosynthesis and sugar metabolism. The present study provides new insights into the berry transcriptome modulation by leafroll infection, highlighting the virus induced upregulation of plant innate immunity as well as an increased responsiveness of the early ripening berry to biotic stressors. The study furthermore emphasizes the importance of sampling protocols in physiological studies on grapevine berry metabolism.

New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

BACKGROUND

Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes.

RESULTS

A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs.

CONCLUSION

These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.

Identification of Selective Sweeps in the Domesticated Table and Wine Grape (Vitis vinifera L.)

Grapevine (Vitis vinifera) is one of the most important fruit species in the Classical Mediterranean world. It is thought to have been domesticated 6,000-8,000 years ago in the Near East. However, the domestication of its wild relative into wine grapes or table grapes remains largely unknown. In this study, we analyzed 30 table grapes, 30 wine grapes, 30 dual-purpose grape accessions, as well as 30 wild relatives (Vitis vinifera ssp. sylvestris). The phenotypic comparison showed striking differences in berry weight, acidity and the content of aroma. Based on a total of 7,522,958 single-nucleotide polymorphisms, we identified several significant selective sweep regions for table and wine grapes. Besides the well-known sex-determination locus on chromosome 2, the other four highest signals shared by table and wine grapes could not be linked to the known QTLs. The identification of these genomic regions under selection sweep may reveal agronomically important traits that have been selected during grape domestication. This information not only sheds light on the mechanisms of adaptions and diversification, but also guide the genetic improvement in breeding programs.

Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. 'Moscatel Galego')

BACKGROUND

Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most well studied somatic variation in this species is the one affecting fruit pigmentation, leading to a plethora of different berry skin colors. Color depletion and reversion are often observed in the field. In this study we analyzed the origin of a novel white-to-red skin color reversion and studied its possible metabolic and transcriptomic consequences on cv. 'Muscat à Petits Grains Blancs' (synonym cv. 'Moscatel Galego Branco'), a member of the large family of Muscats.

RESULTS

The mild red-skinned variant (cv. 'Muscat à Petits Grains Rouge', synonym cv. 'Moscatel Galego Roxo'), characterized by a preferential accumulation of di-hydroxylated anthocyanins, showed in heterozygosis a partially-excised Gret1 retrotransposon in the promoter region of the MYBA1 anthocyanin regulator, while MYBA2 was still in homozygosis for its non-functional allele. Through metabolic (anthocyanin, resveratrol and piceid quantifications) and transcriptomic (RNA-Seq) analyses, we show that within a near-isogenic background, the transcriptomic consequences of color reversion are largely associated to diminished light/UV-B responses probably as a consequence of the augment of metabolic sunscreens (i.e. anthocyanins).

CONCLUSIONS

We propose that the reduced activity of the flavonoid tri-hydroxylated sub-branch and decreased anthocyanin synthesis and modification (e.g. methylation and acylation) are the potential causes for the mild red-skinned coloration in the pigmented revertant. The observed positive relation between anthocyanins and stilbenes could be attributable to an increased influx of phenylpropanoid intermediaries due to the replenished activity of MYBA1, an effect yet to be demonstrated in other somatic variants.

High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia)

Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color. The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F₁ populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the 'Black Beauty' × 'Nesbitt' and 'Supreme' × 'Nesbitt' populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64-5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09-11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.

Functional MYB transcription factor encoding gene AN2 is associated with anthocyanin biosynthesis in Lycium ruthenicum Murray

BACKGROUND

Lycium ruthenicum Murray is an important economic plant in China and contains higher levels of anthocyanins in its fruits than other Lyciums. However, the genetic mechanism of anthocyanin production in this plant is unknown.

RESULTS

Based on previous transcriptome analysis, LrAN2 and LbAN2, encoding MYB transcription factors, were isolated from L. ruthenicum and L. barbarum, respectively. Both genes contained two introns, encoded 257 amino acids with two-Aa difference, and carried the unabridged HTH-MYB, MYB-like DNA-binding, and SANT domains. In the phylogenetic trees, LrAN2 and LbAN2 were found to be closely related to NtAN2, which regulates anthocyanin biosynthesis in tobacco. Overexpression of LrAN2 and LbAN2 induced anthocyanin biosynthesis in all tissues of tobacco. The anthocyanin content in the leaves of transgenic lines with LbAN2 was lower than LrAN2. It indicated that the function of LbAN2 was weaker than LrAN2. The AN2 transcript could be detected only in the fruits of L. ruthenicum and increased during fruit development, accompanied by anthocyanin accumulation. In natural population, the alleles LrAN2 and LrAN2 were associated strictly with L. ruthenicum and L. barbarum, respectively. Moreover, an AN2 genetic diversity study suggested that Lyciums with yellow, white, purple, and jujube red fruits were derived from L. ruthenicum.

CONCLUSIONS

Two AN2 alleles, from L. ruthenicum and L. barbarum, were functional MYB transcriptor regulating anthocyanin biosynthesis. The functional diversity and high expression level of LrAN2 could be the reason for high anthocyanin content in the fruit of L. ruthenicum. Lyciums with yellow, white, purple, and jujube red fruits were derived from L. ruthenicum based on AN2 sequence diversity. The results may be advantageous in identifying new varieties and breeding new cultivars.

Molecular characterization of berry color locus on the portuguese cv. ‘Fernão Pires’ and cv. ‘Verdelho’ and their red-berried somatic variant cultivars

Genotyping studies are increasing the knowledge on grapevine biodiversity, particularly regarding grape berry skin color somatic variants, supporting the research on the color trait. This study aimed to evaluate the effect of the berry color locus, and its surrounding genomic region, on the color variation of the Portuguese white-skinned cultivars ‘Fernão Pires’ and ‘Verdelho’ and its derived red-berried somatic variants cv. ‘Fernão Pires Rosado’ and cv. ‘Verdelho Roxo’, respectively.

The analysis of Gret1 insertion within the VvMYBA1 gene revealed no polymorphism responsible for white-to-red shift of the red-skinned cv. ‘Fernão Pires Rosado’ and cv. ‘Verdelho Roxo’. Moreover, VvMYBA2 showed an important role regarding the phenotypic variation of cv. ‘Fernão Pires’, through the recovery of the functional allele G on cv. ‘Fernão Pires Rosado’. Regarding the data obtained for cv. ‘Verdelho’ and cv. ‘Verdelho Roxo’, both cultivars showed Gret1 insertion on VvMYBA1 and non-functional T allele on VvMYBA2 in homozygosity for both cell layers of shoot apical meristem, suggesting the occurrence of other mutational events responsible for the color gain.

Coloring biology in grape skin: a prospective strategy for molecular farming

Grapevine is one of the earliest domesticated fruit crops that has been widely prized and cultivated for its fruit and wine. Grapes exhibit a wide range of colors, ranging from the green/yellow to the dark blue tones according to the amount and composition of anthocyanin. During the last decades, many studies regarding the genetic control of the grape color in European, American and Asian cultivars have been well documented. DNA binding genes for several transcription factors, such as MYBA1 and MYBA2 haplotype compositions at the color locus are the key determinant of anthocyanin diversity and grape skin color development. Retrotransposon in the MYBA1 promoter region and mutation in MYBA2 coding sequence resulted in a white-skinned grape. The MYB haplotypes affect the ratio of tri/di-hydroxylated anthocyanins and methylated/non-methylated anthocyanins through the regulation of several structural genes involved in the anthocyanin biosynthesis, resulting in diverse colored tones. The present review provides an overview of the current state of the molecular mechanisms underlying the genetic regulations of the anthocyanin accumulation and diversification in grapes. The hypothesized models described in this review is a step forward to potentially predict the color diversification in different grape cultivars, which translate the advances in fundamental plant biology toward the application of grape molecular breeding.

Berry color variation in grapevine as a source of diversity

Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.

Roles of R2R3-MYB transcription factors in transcriptional regulation of anthocyanin biosynthesis in horticultural plants

This review contains functional roles of MYB transcription factors in the transcriptional regulation of anthocyanin biosynthesis in horticultural plants. This review describes potential uses of MYB TFs as tools for metabolic engineering for anthocyanin production. Anthocyanins (ranging from red to blue) are controlled by specific branches of the anthocyanin biosynthetic pathway and are mostly visible in ornamentals, fruits, and vegetables. In the present review, we describe which R2R3-MYB transcription factors (TFs) control the transcriptional regulation of anthocyanin structural genes involved in the specific branches of the anthocyanin biosynthetic pathway in various horticultural plants (e.g., ornamentals, fruits, and vegetables). In addition, some MYBs responsible for anthocyanin accumulation in specific tissues are described. Moreover, we highlight the phylogenetic relationships of the MYBs that suppress or promote anthocyanin synthesis in horticultural crops. Enhancement of anthocyanin synthesis via metabolic genetic engineering of anthocyanin MYBs, which is described in the review, is indicative of the potential use of the mentioned anthocyanin-related MYBs as tools for anthocyanin production. Therefore, the MYBs would be suitable for metabolic genetic engineering for improvement of flower colors, fruit quality, and vegetable nutrients.

Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology

A bud sport is a lateral shoot, inflorescence or single flower/fruit with a visibly different phenotype from the rest of the plant. The new phenotype is often caused by a stable somatic mutation in a single cell that is passed on to its clonal descendants and eventually populates part or all of a meristem. In many cases, a bud sport can be vegetatively propagated, thereby preserving the novel phenotype without sexual reproduction. Bud sports provide new characteristics while retaining the desirable qualities of the parent plant, which is why many bud sports have been developed into popular cultivars. We present an overview of the history of bud sports, the causes and methods of detecting somaclonal variation, and the types of mutant phenotypes that have arisen spontaneously. We focus on examples where the molecular or cytological changes causing the phenotype have been identified. Analysis of these sports has provided valuable insight into developmental processes, gene function and regulation, and in some cases has revealed new information about layer-specific roles of some genes. Examination of the molecular changes causing a phenotype and in some cases reversion back to the original state has contributed to our understanding of the mechanisms that drive genomic evolution.

The heterologous expression of Arabidopsis PAP2 induces anthocyanin accumulation and inhibits plant growth in tomato

Anthocyanins are naturally occurring secondary metabolites, responsible for the color of many plants. The Arabidopsis thaliana MYB90/PAP2 (production of anthocyanin pigment 2) was introduced into tomato to study its effect on anthocyanin accumulation. The transgenic tomato displayed much greater anthocyanin accumulation than wild type in all plant organs, but the organs were not fully purple in color except for the stamen. The expression of anthocyanin biosynthetic genes and an anthocyanin-related basic helix-loop-helix (bHLH) gene SlAN1 was significantly increased in the transgenic line, suggesting that ectopic expression of AtPAP2 increases the expression of anthocyanin-related structural and regulatory genes to enhance anthocyanin content. Yeast two-hybrid assays revealed that the endogenous MYB protein SlAN2 interacted with two putative bHLH partners, SlAN1 and SlJAF13, while AtPAP2 only interacted with SlJAF13, which may be why AtPAP2 transgenic plants showed limited anthocyanin accumulation in fruits. In addition to anthocyanin accumulation, the transgenic tomato plants were significantly smaller in size, and the length of primary roots and number of lateral roots were obviously decreased. The expression of lignin biosynthetic genes was downregulated in transgenic tomato plants, which may be the reason for the inhibited growth. The lateral organ boundaries-domain (LBD) genes, which regulate lateral root organogenesis in the auxin signaling pathway, were downregulated in transgenic tomato roots, which may partly account for the disturbed lateral root formation in the transformants. Taken together, the results demonstrate that heterologous expression of transcription factor AtPAP2 not only resulted in anthocyanin accumulation but also inhibited plant growth in tomato.

Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication

We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.

A group of grapevine MYBA transcription factors located in chromosome 14 control anthocyanin synthesis in vegetative organs with different specificities compared with the berry color locus

Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phenotypes; however, the red pigmentation found in vegetative organs suggests the presence of additional regulators. This work describes a genomic region of chromosome 14 containing three closely related R2R3-MYB genes, named MYBA5, MYBA6 and MYBA7. Ectopic expression of the latter two genes in grapevine hairy roots promoted anthocyanin accumulation without affecting other phenylpropanoids. Transcriptomic profiling of hairy roots expressing MYBA1, MYBA6 and MYBA7 showed that these regulators share the activation of late biosynthetic and modification/transport-related genes, but differ in the activation of the FLAVONOID-3'5'-HYDROXYLASE (F3'5'H) family. An alternatively spliced MYBA6 variant was incapable of activating anthocyanin synthesis, however, because of the lack of an MYC1 interaction domain. MYBA1, MYBA6.1 and MYBA7 activated the promoters of UDP-GLUCOSE:FLAVONOID 3-O-GLUCOSYLTRANSFERASE (UFGT) and ANTHOCYANIN 3-O-GLUCOSIDE-6″-O-ACYLTRANSFERASE (3AT), but only MYBA1 induced F3'5'H in concordance with the low proportion of tri-hydroxylated anthocyanins found in MYBA6-A7 hairy roots. This putative new color locus is related to the red/cyanidic pigmentation of vegetative organs in black- and white-skinned cultivars, and forms part of the UV-B radiation response pathway orchestrated by ELONGATED HYPOCOTYL 5 (HY5). These results demonstrate the involvement of additional anthocyanin regulators in grapevine and suggest an evolutionary divergence between the two grape color loci for controlling additional targets of the flavonoid pathway.

Differences in Vvufgt and VvmybA1 Gene Expression Levels and Phenolic Composition in Table Grape (Vitis vinifera L.) 'Red Globe' and Its Somaclonal Variant 'Pink Globe'

A novel 'Red Globe' (RG)-derived grape variety, 'Pink Globe' (PG), was described and registered as a new genotype, with earlier ripening and sweeter taste than those of RG. Microsatellite analysis revealed that PG and RG are undifferentiable; however, the PG VvmybA1c contains six single-nucleotide polymorphisms within the coding and noncoding region, possibly related to the reduced VvmybA1 expression levels. Conversely, HPLC-DAD-ESI-MS/MS analysis showed significantly lower anthocyanin content in PG skin than in RG skin, and PG had no detectable trihydroxylated anthocyanins. Total flavonols did not differ between the variants, although some quercetin derivate concentrations were lower in PG. HPLC-FLD analysis revealed slightly higher concentrations of epicatechin and a procyanidin dimer in PG seeds, although the antioxidant capacity of crude extracts from either variety did not differ significantly. These differences, particularly in monomeric anthocyanin content, can be attributed to altered activity of a MYB-type transcription factor, reducing Vvufgt expression.

Novel R2R3-MYB transcription factors from Prunus americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus

The level of anthocyanins in plants vary widely among cultivars, developmental stages and environmental stimuli. Previous studies have reported that the expression of various MYBs regulate anthocyanin pigmentation during growth and development. Here we examine the activity of 3 novel R2R3-MYB transcription factor (TF) genes, PamMybA.1, PamMybA.3 and PamMybA.5 from Prunus americana. The anthocyanin accumulation patterns mediated by CaMV double35S promoter (db35Sp) controlled expression of the TFs in transgenic tobacco were compared with citrus-MoroMybA, Arabidopsis-AtMybA1 and grapevine-VvMybA1 transgenics during their entire growth cycles. The db35Sp-PamMybA.1 and db35Sp-PamMybA.5 constructs induced high levels of anthocyanin accumulation in both transformed tobacco calli and the regenerated plants. The red/purple color pigmentation induced in the PamMybA.1 and PamMybA.5 lines was not uniformly distributed, but appeared as patches in the leaves, whereas the flowers showed intense uniform pigmentation similar to the VvMybA1 expressing lines. MoroMybA and AtMybA1 showed more uniform pink coloration in both vegetative and reproductive tissues. Plant morphology, anthocyanin content, seed viability, and transgene inheritance were examined for the PamMybA.5 transgenic plants and compared with the controls. We conclude that these TFs alone are sufficient for activating anthocyanin production in plants and may be used as visible reporter genes for plant transformation. Evaluating these TFs in a heterologous crop species such as citrus further validated that these genes can be useful for the metabolic engineering of anthocyanin production and cultivar enhancement.

RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development

Grapevine berry development is a complex and genetically controlled process, with many morphological, biochemical and physiological changes occurring during the maturation process. Research carried out on grapevine berry development has been mainly concerned with wine grape, while barely focusing on table grape. 'Fujiminori' is an important table grapevine cultivar, which is cultivated in most provinces of China. In order to uncover the dynamic networks involved in anthocyanin biosynthesis, cell wall development, lipid metabolism and starch-sugar metabolism in 'Fujiminori' fruit, we employed RNA-sequencing (RNA-seq) and analyzed the whole transcriptome of grape berry during development at the expanding period (40 days after full bloom, 40DAF), véraison period (65DAF), and mature period (90DAF). The sequencing depth in each sample was greater than 12×, and the expression level of nearly half of the expressed genes were greater than 1. Moreover, greater than 64% of the clean reads were aligned to the Vitis vinifera reference genome, and 5,620, 3,381, and 5,196 differentially expressed genes (DEGs) were identified between different fruit stages, respectively. Results of the analysis of DEGs showed that the most significant changes in various processes occurred from the expanding stage to the véraison stage. The expression patterns of F3'H and F3'5'H were crucial in determining red or blue color of the fruit skin. The dynamic networks of cell wall development, lipid metabolism and starch-sugar metabolism were also constructed. A total of 4,934 SSR loci were also identified from 4,337 grapevine genes, which may be helpful for the development of phylogenetic analysis in grapevine and other fruit trees. Our work provides the foundation for developmental research of grapevine fruit as well as other non-climacteric fruits.

Allelic Variation and Transcriptional Isoforms of Wheat TaMYC1 Gene Regulating Anthocyanin Synthesis in Pericarp

Recently the TaMYC1 gene encoding bHLH transcription factor has been isolated from the bread wheat (Triticum aestivum L.) genome and shown to co-locate with the Pp3 gene conferring purple pericarp color. As a functional evidence of TaMYC1 and Pp3 being the same, higher transcriptional activity of the TaMYC1 gene in colored pericarp compared to uncolored one has been demonstrated. In the current study, we present additional strong evidences of TaMYC1 to be a synonym of Pp3. Furthermore, we have found differences between dominant and recessive Pp3(TaMyc1) alleles. Light enhancement of TaMYC1 transcription was paralleled with increased AP accumulation only in purple-grain wheat. Coexpression of TaMYC1 and the maize MYB TF gene ZmC1 induced AP accumulation in the coleoptile of white-grain wheat. Suppression of TaMYC1 significantly reduced AP content in purple grains. Two distinct TaMYC1 alleles (TaMYC1p and TaMYC1w) were isolated from purple- and white-grained wheat, respectively. A unique, compound cis-acting regulatory element had six copies in the promoter of TaMYC1p, but was present only once in TaMYC1w. Analysis of recombinant inbred lines showed that TaMYC1p was necessary but not sufficient for AP accumulation in the pericarp tissues. Examination of larger sets of germplasm lines indicated that the evolution of purple pericarp in tetraploid wheat was accompanied by the presence of TaMYC1p. Our findings may promote more systematic basic and applied studies of anthocyanins in common wheat and related Triticeae crops.

Patterns of genomic and phenomic diversity in wine and table grapes

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.

Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)

Background

The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii, in order to find some key genes that are related to anthocyanins accumulation in V. davidii.

Results

The results of anthocyanins detection revealed that 3,5-O-diglucoside anthocyanins is the predominant anthocyanins in V. davidii. It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii. After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii. The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR).

Conclusions

The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in V. davidi at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in V. davidii.

Electronic supplementary material

The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.