Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1

Promoter replication of grape MYB transcription factor is associated with a new red flesh phenotype

KEY MESSAGE

In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.

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.

Mechanisms for leaf color changes in Osmanthus fragrans 'Ziyan Gongzhu' using physiology, transcriptomics and metabolomics

BACKGROUND

Color-leaved O. fragrans is a variety of Osmanthus fragrans, which has both the fragrance of Osmanthus and the color of color-leaved plants. However, the molecular mechanism of color change of color-leaved O. fragrans is not clear. In this study, we analyzed the regulatory mechanism of four different color leaves of 'Ziyan Gongzhu' through physiological, transcriptome and metabolome levels.

RESULTS

Firstly, we measured the leaf pigments content and leaf chromatic parameters for correlation analysis, indicating a significant correlation between them. Overall, the content of chlorophyll a + b is low and the content of anthocyanin is high in T1 and T2 leaves, along with low expression of chlorophyll synthesis genes (HEMA, CHLG, and CAO, etc.) and high expression of anthocyanin synthesis genes (F3H, F3'H, DFR and ANS, etc.), resulting purple red and light purple in T1 and T2 leaves, respectively. It was also found that the pigment closely related to the color leaves of 'Ziyan Gongzhu' was cyanidin. The content anthocyanins, may be regulated by two putative MYB activators (OfMYB3 and OfMYB4) and two putative MYB repressors (OfMYB1 and OfMYB2). In contrast, the content of chlorophyll a + b is high and the content of anthocyanin is low in T3 and T4 leaves, along with high expression of chlorophyll synthesis genes and low expression of anthocyanin synthesis genes, resulting yellow green and dark green in T3 and T4 leaves, respectively. And abnormal chloroplast development affects chlorophyll content in T1, T2, and T3 leaves. Although the content of carotenoids first dropped in T2 leaves, it then rapidly accumulated in T4 leaves, in sync with the increase in the expression of genes related to carotenoid biosynthesis (ZDS, LHYB, and ZEP, for example). Analysis of photosynthetic, carbohydrate and hormone-related differentially abundant metabolites (DAMs) and DEGs found that they may participate in the regulation of leaf color change of 'Ziyan Gongzhu' by affecting pigment synthesis.

CONCLUSION

Our results pave the way for a comprehensive knowledge of the regulatory processes governing leaf color in 'Ziyan Gongzhu' and identify possible genes for application regarding molecular colored-leaf cultivar breeding.

Chimeras in Merlot grapevine revealed by phased assembly

Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.

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.

Integrated Approach from Sample-to-Answer for Grapevine Varietal Identification on a Portable Graphene Sensor Chip

Identifying grape varieties in wine, related products, and raw materials is of great interest for enology and to ensure its authenticity. However, these matrices' complexity and low DNA content make this analysis particularly challenging. Integrating DNA analysis with 2D materials, such as graphene, offers an advantageous pathway toward ultrasensitive DNA detection. Here, we show that monolayer graphene provides an optimal test bed for nucleic acid detection with single-base resolution. Graphene's ultrathinness creates a large surface area with quantum confinement in the perpendicular direction that, upon functionalization, provides multiple sites for DNA immobilization and efficient detection. Its highly conjugated electronic structure, high carrier mobility, zero-energy band gap with the associated gating effect, and chemical inertness explain graphene's superior performance. For the first time, we present a DNA-based analytic tool for grapevine varietal discrimination using an integrated portable biosensor based on a monolayer graphene field-effect transistor array. The system comprises a wafer-scale fabricated graphene chip operated under liquid gating and connected to a miniaturized electronic readout. The platform can distinguish closely related grapevine varieties, thanks to specific DNA probes immobilized on the sensor, demonstrating high specificity even for discriminating single-nucleotide polymorphisms, which is hard to achieve with a classical end-point polymerase chain reaction or quantitative polymerase chain reaction. The sensor was operated in ultralow DNA concentrations, with a dynamic range of 1 aM to 0.1 nM and an attomolar detection limit of ∼0.19 aM. The reported biosensor provides a promising way toward developing decentralized analytical tools for tracking wine authenticity at different points of the food value chain, enabling data transmission and contributing to the digitalization of the agro-food industry.

Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies

In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.

Comparative Study on Grape Berry Anthocyanins of Various Teinturier Varieties

The red-fleshed grape cultivars, called teinturier or dyer grapes, contain anthocyanins in both the skin and flesh. These phenolic compounds exhibit excellent coloring ability, and as antioxidants, they are important bioactive compounds in food crops. In this work, anthocyanin patterns of grape berries of fifteen teinturier varieties collected from the gene bank located at Pécs in the southwest of Hungary were compared. Anthocyanin profiles of numerous varieties originating from Hungary such as 'Bíborkadarka', 'Kármin', 'Kurucvér', and 'Turán' are reported for the first time. Anthocyanins extracted separately from the skin and juice were analyzed using high-performance liquid chromatography coupled with a photodiode array detector. For the identification of compounds, high-resolution orbitrap mass spectrometry was used. All in all, twenty-one anthocyanins were identified and quantified. We found that anthocyanin patterns differed significantly in the skin and juice for all investigated cultivars. For Vitis vinifera varieties, the predominant anthocyanin in the skin was malvidin-3-O-glucoside, while the main pigment in the juice was peonidin-3-O-glucoside. For the first time, a significant amount of diglucosides was detected in two Vitis Vinifera cultivars with a direct relationship. In general, the pigment composition of the skin was much more complex than that of the juice. The comparative study with presented patterns gives valuable and beneficial information from a chemotaxonomical point of view. Our results also help to choose the appropriate teinturier varieties with the desired anthocyanins for food coloring or winemaking purposes.

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.

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.

Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x 'Seyval blanc' cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera 'PN40024' genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.

Flavonoids - flowers, fruit, forage and the future

Flavonoids are plant-specific secondary metabolites that arose early during land-plant colonisation, most likely evolving for protection from UV-B and other abiotic stresses. As plants increased in complexity, so too did the diversity of flavonoid compounds produced and their physiological roles. The most conspicuous are the pigments, including yellow aurones and chalcones, and the red/purple/blue anthocyanins, which provide colours to flowers, fruits and foliage. Anthocyanins have been particularly well studied, prompted by the ease of identifying mutants of genes involved in biosynthesis or regulation, providing an important model system to study fundamental aspects of genetics, gene regulation and biochemistry. This has included identifying the first plant transcription factor, and later resolving how multiple classes of transcription factor coordinate in regulating the production of various flavonoid classes - each with different activities and produced at differing developmental stages. In addition, dietary flavonoids from fruits/vegetables and forage confer human- and animal-health benefits, respectively. This has prompted strong interest in generating new plant varieties with increased flavonoid content through both traditional breeding and plant biotechnology. Gene-editing technologies provide new opportunities to study how flavonoids are regulated and produced and to improve the flavonoid content of flowers, fruits, vegetables and forages.

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.

A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

Bilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi-C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker-trait association between these two species, as the loci involved in key characters are orthologous.

Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. 'Gamay' grapevines (Vitis vinifera L.)

White-fleshed grape cv. 'Gamay' and its two teinturier variants presented distinct spatial-temporal accumulation of anthocyanins, with uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. In most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while 'teinturier' cultivars also accumulate anthocyanins in the pulp. Here, we investigated the teinturier cvs. 'Gamay de Bouze' and 'Gamay Fréaux' (two somatic variants of the white-fleshed cv. 'Gamay') through metabolic and transcript analysis to clarify whether these two somatic variants have the same anthocyanin accumulation pattern in the skin and pulp, and whether primary metabolites are also affected. The skin of the three cultivars and the pulp of 'Gamay de Bouze' begun to accumulate anthocyanins at the onset of berry ripening. However, the pulp of 'Gamay Fréaux' exhibited a distinct anthocyanin accumulation pattern, starting as early as fruit set with very low level of sugars. The highest level of anthocyanins was found in 'Gamay Fréaux' skin, followed by 'Gamay de Bouze' and 'Gamay'. Consistently, the transcript abundance of genes involved in anthocyanin biosynthesis were in line with the anthocyanin levels in the three cultivars. Despite no evident differences in pulp sugar content, the concentration of glucose and fructose in the skin of 'Gamay Fréaux' was only half of those in the skin of 'Gamay' and 'Gamay de Bouze' throughout all berry ripening, suggesting an uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. The study provides a comprehensive view of metabolic consequences in grape somatic variants and the three almost isogenic genotypes can serve as ideal reagents to further uncover the mechanisms underlying the linkage between sugar and anthocyanin accumulation.

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.