Genome-wide association study of berry-related traits in grape [Vitis vinifera L.] based on genotyping-by-sequencing markers

Characterization of Bunch Compactness in a Diverse Collection of Vitis vinifera L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number

Bunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a genetically diverse collection of 116 Vitis vinifera L. cultivars and lines enriched for table grapes over two seasons. For this, 3D scanning-based morphological data were combined with ground measurements of 14 BC-related traits, observing high correlations among both approaches (R2 > 0.90-0.97). The multivariate analysis suggests that the attributes 'berries per bunch', 'berry weight and width', and 'bunch weight and length' could be considered as the main descriptors for BC, optimizing evaluation times. Then, GWASs based on a set of 70,335 SNPs revealed that GBS analysis in this same population enabled the detection of several SNPs associated with different sub-traits, with a locus for 'berries per bunch' in chromosome (chr) 18 being the most prominent. Enrichment analysis of significant and frequent SNPs found simultaneously in several traits and seasons revealed the over-representation of discrete functions such as alpha-linolenic acid metabolism and glycan degradation. In summary, the utility of 3D automated phenotyping was validated for table grape backgrounds, and new SNPs and candidate genes associated with the BC trait were detected. The latter could eventually become a selection tool for grapevine breeding programs.

Comprehensive insights on association mapping in perennial fruit crops breeding - Its implications, current status and future perspectives

In order to provide food and nutritional security for the world's rapidly expanding population, fruit crop researchers have identified two critical priorities: increasing production and preserving fruit quality during the pre- and post-harvest periods. The genetic basis of these complex, commercially important fruit traits which are uniquely regulated by polygenes or multi-allelic genes that interact with one another and the environment can be analyzed with the aid of trait mapping tools. The most interesting trait mapping approach that offers the genetic level investigation for marker-trait associations (MTAs) for these complex fruit traits, without the development of mapping population, is association mapping. This approach was used during the genetic improvement program, emphasizing the obstacles (breeding strategies adopted, generation interval, and their genomic status) pertaining to perennial fruit crops. This method of studying population diversity and linkage disequilibrium in perennial fruit crops has been made possible by recent developments in genotyping, phenotyping, and statistical analysis. Thus, the purpose of this review is to provide an overview of different trait mapping techniques, with a focus on association mapping (method, essential components, viability, constraints, and future perspective) and its advantages, disadvantages, and possibilities for breeding perennial fruit crops.

Genome-Wide Association Study of Grape Texture Based on Puncture

Grapes are grown extensively around the world and play a crucial role in overall fruit production globally. The quality of the grape is largely determined by the texture of the flesh, making it a key focus for grape breeders. Our study was conducted on 437 grape accessions using a puncture method to analyze berry texture characteristics. The results reveal strong correlations among the five texture parameters of grape accessions. Following the GWAS analysis using 2,124,668 population SNPs, 369 significant SNP locations linked to the grape berry texture were discovered. Through the process of gene annotation and expression analysis in the localization regions, several genes potentially linked to berry texture were identified, including E13A, FIS1A, CML35, AGL2, and AGL62. E13A, FIS1A, and CML35 were identified as potentially more relevant to grape berry texture based on gene expression analysis. Further investigation through transient transformation demonstrated that overexpressing E13A and CML35 resulted in notable changes in grape pulp texture. During this study, the berry textures of 437 grape accessions were comprehensively evaluated, and several important candidate genes were screened based on GWAS and analysis of gene function. This discovery paves the way for future research and breeding initiatives related to grape berry texture.

Grapevine pangenome facilitates trait genetics and genomic breeding

Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.

Single nucleotide polymorphism (SNP) analysis reveals ancestry and genetic diversity of cultivated and wild grapevines in Croatia

BACKGROUND

Croatia is a geographically small country with a remarkable diversity of cultivated and spontaneous grapevines. Local germplasm has been characterised by microsatellite markers, but a detailed analysis based on single nucleotide polymorphisms (SNPs) is still lacking. Here we characterize the genetic diversity of 149 accessions from three germplasm repositories and four natural sites using 516,101 SNPs to identify complete parent-offspring trios and their relations with spontaneous populations, offering a proof-of-concept for the use of reduced-representation genome sequencing in population genetics and genome-wide association studies (GWAS).

RESULTS

Principal component analysis revealed a clear discontinuity between cultivated (V. vinifera subsp. sativa) and spontaneous grapevines, supporting the notion that the latter represent local populations of the wild progenitor (V. vinifera subsp. sylvestris). ADMIXTURE identified three ancestry components. Two sativa components are alternatively predominant in cultivars grown either in northern Adriatic Croatia and Continental Croatia or in Dalmatia (i.e. central and southern Adriatic Croatia). A sylvestris component, which is predominant in accessions from spontaneous populations, is a minor ancestry component in cultivated accessions. TREEMIX provided evidence of unidirectional migration from the vineyards to natural sites, suggesting that gene flow has gone preferentially from the introduced domesticated germplasm into local wild populations rather than vice versa. Identity-by-descent analysis indicated an extensive kinship network, including 14 complete parent-offspring trios, involving only cultivated accessions, six full-sibling relationships and invalidated a presumed pedigree of one of the most important varieties in Croatia, 'Plavac Mali'. Despite this strong population structure, significant association was found between 143 SNPs and berry skin colour and between 2 SNPs and leaf hairiness, across two previously known genomic regions.

CONCLUSIONS

The clear genetic separation between Croatian cultivars and sylvestris ruled out the hypothesis that those cultivars originated from local domestication events. On the other hand, the evidence of a crop-to-wild gene flow signals the need for an urgent adoption of conservation strategies that preserve the residual genetic integrity of wild relatives. The use of this reduced-representation genome sequencing protocol in grapevine enables an accurate pedigree reconstruction and can be recommended for GWAS experiments.

Genotyping-by-sequencing-based high-resolution mapping reveals a single candidate gene for the grapevine veraison locus Ver1

Veraison marks the transition from berry growth to berry ripening and is a crucial phenological stage in grapevine (Vitis vinifera): the berries become soft and begin to accumulate sugars, aromatic substances, and, in red cultivars, anthocyanins for pigmentation, while the organic acid levels begin to decrease. These changes determine the potential quality of wine. However, rising global temperatures lead to earlier flowering and ripening, which strongly influence wine quality. Here, we combined genotyping-by-sequencing with a bioinformatics pipeline on ∼150 F1 genotypes derived from a cross between the early ripening variety "Calardis Musqué" and the late-ripening variety "Villard Blanc". Starting from 20,410 haplotype-based markers, we generated a high-density genetic map and performed a quantitative trait locus analysis based on phenotypic datasets evaluated over 20 yrs. Through locus-specific marker enrichment and recombinant screening of ∼1,000 additional genotypes, we refined the originally postulated 5-mb veraison locus, Ver1, on chromosome 16 to only 112 kb, allowing us to pinpoint the ethylene response factor VviERF027 (VCost.v3 gene ID: Vitvi16g00942, CRIBIv1 gene ID: VIT_16s0100g00400) as veraison candidate gene. Furthermore, the early veraison allele could be traced back to a clonal "Pinot" variant first mentioned in the seventeenth century. "Pinot Precoce Noir" passed this allele over "Madeleine Royale" to the maternal grandparent "Bacchus Weiss" and, ultimately, to the maternal parent "Calardis Musqué". Our findings are crucial for ripening time control, thereby improving wine quality, and for breeding grapevines adjusted to climate change scenarios that have a major impact on agro-ecosystems in altering crop plant phenology.

Comprehensive genetic diversity and genome-wide association studies revealed the genetic basis of avocado fruit quality traits

Introduction

Avocado (Persea americana) is a highly nutritious fruit gaining worldwide popularity. However, its cultivation is currently reliant on a limited number of cultivars with restricted genetic diversity. This study aims to investigate the genetic diversity and population structure of avocado germplasm and identify genetic loci associated with key fruit quality traits that influence customer preference.

Methods

A diversity panel of 110 avocado accessions was analyzed using 4,706 high-quality single nucleotide polymorphisms (SNPs). Genetic diversity and population structure were analyzed using pairwise FST, AMOVA, admixture analysis, and phylogenetic analysis. Genome-wide association studies (GWAS) were conducted targeting nine fruit quality traits using two models: General Linear Model (GLM) with Principal Component Analysis (PCA) and Mixed Linear Model (MLM) with PCA and kinship (PCA + K).

Results

The analysis revealed three distinct populations corresponding to the three avocado ecotypes: Guatemalan, West Indian, and Mexican. Phylogenetic analysis indicated a closer relationship between the Guatemalan and West Indian races compared to the Mexican race in our Florida germplasm collection. GWAS led to identification of 12 markers within 11 genomic regions significantly associated with fruit quality traits such as fruit color, shape, taste, and skin texture. These markers explained between 14.84% to 43.96% of the phenotypic variance, with an average of 24.63%. Annotation of these genomic regions unveiled candidate genes potentially responsible for controlling these traits.

Discussion

The findings enhance our understanding of genetic diversity and population structure in avocado germplasm. The identified genetic loci provide valuable insights into the genetic basis of fruit quality traits, aiding breeding programs in developing improved avocado cultivars. Marker-assisted selection can accelerate the development of new varieties, promoting a more diverse and resilient avocado market.

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Biography of Vitis genomics: recent advances and prospective

The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.

Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

Metabolite and transcriptome analyses reveal the effects of salinity stress on the biosynthesis of proanthocyanidins and anthocyanins in grape suspension cells

Proanthocyanidins (PAs) and anthocyanins are flavonoids that contribute to the quality and health benefits of grapes and wine. Salinity affects their biosynthesis, but the underlying mechanism is still unclear. We studied the effects of NaCl stress on PA and anthocyanin biosynthesis in grape suspension cells derived from berry skins of Vitis vinifera L. Cabernet Sauvignon using metabolite profiling and transcriptome analysis. We treated the cells with low (75 mM NaCl) and high (150 mM NaCl) salinity for 4 and 7 days. High salinity inhibited cell growth and enhanced PA and anthocyanin accumulation more than low salinity. The salinity-induced PAs and anthocyanins lacked C5'-hydroxylation modification, suggesting the biological significance of delphinidin- and epigallocatechin-derivatives in coping with stress. The genes up-regulated by salinity stress indicated that the anthocyanin pathway was more sensitive to salt concentration than the PA pathway, and WGCNA analysis revealed the coordination between flavonoid biosynthesis and cell wall metabolism under salinity stress. We identified transcription factors potentially involved in regulating NaCl dose- and time-dependent PA and anthocyanin accumulation, showing the dynamic remodeling of flavonoid regulation network under different salinity levels and durations. Our study provides new insights into regulator candidates for tailoring flavonoid composition and molecular indicators of salt stress in grape cells.

T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality

Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies

Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.

Favorable Loci Identified for Stripe Rust Resistance in Chinese Winter Wheat Accessions via Genome-Wide Association Study

Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Currently, the utilization of resistant cultivars is the most viable way to reduce yield losses. In this study, a panel of 188 wheat accessions from China was evaluated for stripe rust resistance, and genome-wide association studies were performed using high-quality Diversity Arrays Technology markers. According to the phenotype and genotype data, a total of 26 significant marker-trait associations were identified, representing 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3A, 3B, 5A, 5B, 6B, 7B, and 7D. Of the 18 QTLs, almost all were associated with adult plant resistance (APR) except QYr.nwsuaf-6B.2, which was associated with all-stage resistance (also known as seedling resistance). Three of the 18 QTLs were mapped far from previously identified Pst resistance genes and QTLs and were considered potentially new loci. The other 15 QTLs were mapped close to known resistance genes and QTLs. Subsequent haplotype analysis for QYr.nwsuaf-2A and QYr.nwsuaf-7B.3 revealed the degrees of resistance of the panel in the APR stage. In summary, the favorable alleles identified in this study may be useful in breeding for disease resistance to stripe rust.

Berry texture QTL and candidate gene analysis in grape (Vitis vinifera L.)

Berry texture is a noteworthy economic trait for grape; however, the genetic bases and the complex gene expression and regulatory mechanism for the diverse changes in berry texture are still poorly understood. In this study, the results suggest that it is difficult to obtain high-mesocarp firmness (MesF) and high-pericarp puncture hardness (PPH) grape cultivars with high pericarp brittleness (PerB). The high-density linkage map was constructed using whole-genome resequencing based on 151 F1 individuals originating from intraspecific hybridization between the firm-flesh cultivar 'Red Globe' and soft-flesh cultivar 'Muscat Hamburg'. The total length of the consensus map was 1613.17 cM, with a mean genetic distance between adjacent bin markers of 0.59 cM. Twenty-seven quantitative trait loci (QTLs) for berry MesF, PPH, and PerB were identified in linkage groups (LGs) 1, 3, 4, 6, 8, 9, 10, 11, 14, 16, and 17, including twelve QTLs that were firstly detected in LGs 6, 11, and 14. Fourteen promising candidate genes were identified from the stable QTL regions in LGs 10, 11, 14, and 17. In particular, VvWARK2 and VvWARK8 refer to chromosome 17 and are two promising candidate genes for MesF and PPH, as the VvWARK8 gene may increase pectin residue binding with WARK for high berry firmness maintenance and the allele for VvWARK2 carrying the 'CC' and 'GA' genotypes at Chr17:1836764 and Chr17:1836770 may be associated with non-hard texture grape cultivars. In addition, real-time quantitative polymerase chain reaction (RT-qPCR) verification revealed that the promising candidate transcription factor genes VvMYB4-like, VvERF113, VvWRKY31, VvWRKY1, and VvNAC83 may regulate cell wall metabolism candidate gene expression for grape berry texture changes.

Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding

In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.

Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

BACKGROUND

The myeloblastosis (MYB) superfamily is the largest transcription factor family in plants that play diverse roles during stress responses. However, the biotic stress-responsive MYB transcription factors of the grapevine have not been systematically studied. In China, grapevine berries are often infected with the grapevine berry inner necrosis virus (GINV), which eventually reduces the nutritional quality and commodity value.

RESULTS

The present study identified and characterized 265 VvMYB or VvMYB-related genes of the "Crimson seedless" grapevine. Based on DNA-binding domain analysis, these VvMYB proteins were classified into four subfamilies, including MYB-related, 2R-MYB, 3R-MYB, and 4R-MYB. Phylogenetic analysis divided the MYB transcription factors into 26 subgroups. Overexpression of VvMYB58 suppressed GINV abundance in the grapevine. Further qPCR indicated that among 41 randomly selected VvMYB genes, 12 were induced during GINV infection, while 28 were downregulated. These findings suggest that VvMYB genes actively regulate defense response in the grapevine.

CONCLUSION

A deeper understanding of the MYB TFs engaged in GINV defense response will help devise better management strategies. The present study also provides a foundation for further research on the functions of the MYB transcription factors.

Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r² was between 0.45 and 0.2 and became flat when r² was 0.05. The average LD decay for the entire genome was 30 kb when r^2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

Large-scale population structure and genetic architecture of agronomic traits of garlic

Garlic, an asexually propagated crop, is the second important bulb crop after the onion and is used as a vegetable and medicinal plant. Abundant and diverse garlic resources have been formed over thousands of years of cultivation. However, genome variation, population structure and genetic architecture of garlic agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing in 606 garlic accessions collected from 43 countries. Population structure, principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations. Twenty agronomic traits, including above-ground growth traits, bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study. In total, 542 SNPs were associated with these agronomic traits, among which 188 SNPs were repeatedly associated with more than two traits. One SNP (chr6: 1896135972) was repeatedly associated with ten traits. These associated SNPs were located within or near 858 genes, 56 of which were transcription factors. Interestingly, one non-synonymous SNP (Chr4: 166524085) in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits. Additionally, gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in 'vegetative to reproductive phase transition of meristem', 'shoot system development', 'reproductive process', etc. These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.

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.

Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape

Pearl of Csaba (PC) is a valuable backbone parent for early-ripening grapevine (Vitis vinifera) breeding, from which many excellent early ripening varieties have been bred. However, the genetic basis of the stable inheritance of its early ripening trait remains largely unknown. Here, the pedigree, consisting of 40 varieties derived from PC, was re-sequenced for an average depth of ∼30×. Combined with the resequencing data of 24 other late-ripening varieties, 5,795,881 high-quality single nucleotide polymorphisms (SNPs) were identified following a strict filtering pipeline. The population genetic analysis showed that these varieties could be distinguished clearly, and the pedigree was characterized by lower nucleotide diversity and stronger linkage disequilibrium than the non-pedigree varieties. The conserved haplotypes (CHs) transmitted in the pedigree were obtained via identity-by-descent analysis. Subsequently, the key genomic segments were identified based on the combination analysis of haplotypes, selective signatures, known ripening-related quantitative trait loci (QTLs), and transcriptomic data. The results demonstrated that varieties with a superior haplotype, H1, significantly (one-way ANOVA, P < 0.001) exhibited early grapevine berry development. Further analyses indicated that H1 encompassed VIT_16s0039g00720 encoding a folate/biopterin transporter protein (VvFBT) with a missense mutation. VvFBT was specifically and highly expressed during grapevine berry development, particularly at veraison. Exogenous folate treatment advanced the veraison of "Kyoho". This work uncovered core haplotypes and genomic segments related to the early ripening trait of PC and provided an important reference for the molecular breeding of early-ripening grapevine varieties.

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.

Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

Perspectives and recent progress of genome-wide association studies (GWAS) in fruits

BACKGROUND

Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. OVERVIEW AND PROGRESS: Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops.

AIMS AND PROSPECTS

This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.

Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics

Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.

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.

Genome-wide association analysis provides molecular insights into the natural variation of watermelon seed size

Seed-consumption watermelon tend to have larger-sized seeds, while flesh-consumed watermelon often require relatively smaller seed. Therefore, the seed size of watermelon has received extensive attention from consumers and breeders. However, the study on the natural variation and genetic mechanism of watermelon seed size is not clear enough. In the present study, 100 seed weight, seed hilum length, seed length, seed width, and seed thickness in 197 watermelon accessions were examined. Furthermore, association analysis was conducted between seed size traits and high-quality SNP data. The results revealed that there was a strong correlation between the five seed traits. And seed enlargement was an important feature during watermelon seed size domestication. Meanwhile, the seed consumption biological species C. mucosospermu and C. lanatus edible seed watermelon had a significantly bigger seed size than other species's. Eleven non-repeating significant SNPs above the threshold line were obtained by GWAS analysis. Four of them on chromosome 5 were considered to be closely associated with seed size traits, i.e. S5: 32250307, S5: 32250454, S5: 32256177, S5: 32260870, which could be used as potential molecular markers for the breeding of watermelon cultivars with target seed size. In addition, combined with gene annotation information and previous reports, five genes near the four significant SNPs may regulate seed size. And qRT-PCR analysis showed that two genes Cla97C05G104360 and Cla97C05G104380, which may be involved in abscisic acid metabolism, may play an important role in regulating the seed size of watermelon. Our findings provide molecular insights into natural variation in watermelon seed size, and gives valuable information of molecular marker-assisted breeding.

Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits

Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of Muscadinia rotundifolia cv. Noble. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26 394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.

Pip shape echoes grapevine domestication history

The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.

High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait

Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F5 population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP markers were utilized for the construction of genetic linkage map and QTL analysis. Overall read mapping percentage of 87.29% was achieved in this study with the total length of mapped region ranging from 2,956,730 to 25,537,525 bp. A total of 41,111 polymorphic SNPs were identified, and a final of 1,841 SNPs were filtered for the construction of a linkage map. A total of 12 linkage groups were constructed corresponding to each chromosome with 1,308 SNP markers with the map length of 2506.8 cM. Further, two QTLs such as Pm-2.1 and Pm-5.1 were identified in chromosomes 2 and 5, respectively, for the PM resistance. Overall, the outcomes of the present endeavor can be utilized for the marker-assisted selection of pepper with powdery mildew-resistant trait.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

BACKGROUND

Understanding the complexity of the vine plant's response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an 'ad hoc' association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit.

RESULTS

In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance.

CONCLUSIONS

Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

Single Nucleotide Polymorphism Detection for Peach Gummosis Disease Resistance by Genome-Wide Association Study

Peach gummosis is one of the most widespread and destructive diseases. It causes growth stunting, yield loss, branch, trunk, and tree death, and is becoming a restrictive factor in healthy and sustainable development of peach production. Although a locus has been identified based on bi-parental quantitative trait locus (QTL) mapping, selection of gummosis-resistant cultivars remains challenging due to the lack of resistant parents and of the complexity of an inducing factor. In this study, an integrated approach of genome-wide association study (GWAS) and comparative transcriptome was used to elucidate the genetic architecture associated with the disease using 195 accessions and 145,456 genome-wide single nucleotide polymorphisms (SNPs). The broad-sense and narrow-sense heritabilities were estimated using 2-year phenotypic data and genotypic data, which gave high values of 70 and 73%, respectively. Evaluation of population structure by neighbor-joining and principal components analysis (PCA) clustered all accessions into three major groups and six subgroups, mainly according to fruit shape, hairy vs. glabrous fruit skin, pedigree, geographic origin, and domestication history. Five SNPs were found to be significantly associated with gummosis disease resistance, of which SNPrs285957, located on chromosome6 across 28 Mb, was detected by both the BLINK and the FarmCPU model. Six candidate genes flanked by or harboring the significant SNPs, previously implicated in biotic stress tolerance, were significantly associated with this resistance. Two highly resistant accessions were identified with low disease severity, which could be potential sources of resistance genes for breeding. Our results provide a fresh insight into the genetic control of peach gummosis disease.

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.

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment

Background

In a previous study, the early ripening of Kyoho grape following H₂O₂ treatment was explored at the physiological level, but the mechanism by which H₂O₂ promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H₂O₂.

Results

In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing.

Conclusions

The RNA-sequencing analysis indicated that H₂O₂ treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07180-y.

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

BACKGROUND

Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits.

RESULTS

In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape.

CONCLUSIONS

A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.

Transcriptome analysis of table grapes (Vitis vinifera L.) identified a gene network module associated with berry firmness

Berry firmness is one of the main selection criteria for table grape breeding. However, the underlying genetic determinants and mechanisms involved in gene expression during berry development are still poorly understood. In this study, eighteen libraries sampled from Vitis vinifera L. cv. ‘Red Globe’ and ‘Muscat Hamburg’ at three developmental stages (preveraison, veraison and maturation) were analyzed by RNA sequencing (RNA-Seq). The firmness of ‘Red Globe’ was significantly higher than that of ‘Muscat Hamburg’ at the three developmental stages. In total, a set of 4,559 differentially expressed genes (DEGs) was identified between ‘Red Globe’ and ‘Muscat Hamburg’ in the preveraison (2,259), veraison (2030) and maturation stages (2682), including 302 transcription factors (TFs). Weighted gene coexpression network analysis (WGCNA) showed that 23 TFs were predicted to be highly correlated with fruit firmness and propectin content. In addition, the differential expression of the PE, PL, PG, β-GAL, GATL, WAK, XTH and EXP genes might be the reason for the differences in firmness between ‘Red Globe’ and ‘Muscat Hamburg’. The results will provide new information for analysis of grape berry firmness and softening.

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

BACKGROUND

Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds.

RESULTS

Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed.

CONCLUSIONS

We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing

Background

Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map.

Results

We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected.

Conclusions

High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding.

Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers

Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of individuals belonging to Vitis species not commonly used in the breeding programs, was genotyped using the 18k SNP genotyping array. SNP results were compared to the established SSR (Simple Sequence Repeat) markers in terms of heterozygosity and genetic structure of the core collection. Genotyping array has proved to be a valuable tool for genotyping of grapevine rootstocks, with more than 90% of SNPs successfully amplified. Structure analysis detected a high degree of admixed genotypes, supported by the complex genetic background of non-vinifera germplasm. Moreover, SNPs clearly differentiated non-vinifera and vinifera germplasm. These results represent a first step in studying the genetic diversity of non-conventional breeding material that will be used to select rootstocks with high tolerance to limiting environmental conditions.

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.

Molecular cloning and characterization of a grapevine (Vitis vinifera L.) serotonin N-acetyltransferase (VvSNAT2) gene involved in plant defense

Background

Melatonin is a ubiquitous molecule and exists across kingdoms. Studies on melatonin in plants have mainly focused on its physiological influence on growth and development, and on its biosynthesis. A number of studies have been conducted on the melatonin content and exogenous melatonin treatment of grapevine (Vitis vinifera L.). However, key genes or enzymes of the melatonin biosynthetic pathway remain unclear.

Results

In this study, we cloned and identified the gene encoding serotonin N-acetyltransferase (SNAT) in grapevine (VvSNAT2). The VvSNAT2 protein was identified from a collection of 30 members of the grapevine GCN5-related N-acetyltransferase (GNAT) superfamily. Phylogenetic and protein sublocalization analyses showed that the candidate gene VvGNAT16 is VvSNAT2. Characterization of VvSNAT2 showed that its enzymatic activity is highest at a pH of 8.8 and a temperature of 45 °C. Analysis of enzyme kinetics showed the values of K_m and V_max of VvSNAT2 using serotonin were 392.5 μM and 836 pmol/min/mg protein, respectively. The expression of VvSNAT2 was induced by melatonin treatment and pathogen inoculation. Overexpression of VvSNAT2 in Arabidopsis resulted in greater accumulation of melatonin and chlorophyll and enhanced resistance to powdery mildew in the transgenic plants compared with the wild type (WT). Additionally, our data showed that the marker genes in the salicylic acid (SA) signaling pathway were expressed to higher levels in the transgenic plants compared with the WT.

Conclusions

The VvSNAT2 gene was cloned and identified in grapevine for the first time. Our results indicate that VvSNAT2 overexpression activates the SA and JA signaling pathways; however, the SA pathway plays a central role in VvSNAT2-mediated plant defense.

The grapevine R2R3-type MYB transcription factor VdMYB1 positively regulates defense responses by activating the stilbene synthase gene 2 (VdSTS2)

BACKGROUND

Resveratrol is a naturally occurring plant stilbene that exhibits a wide range of valuable biological and pharmacological properties. Although the beneficial effects of trans-resveratrol to human health and plant protection against fungal pathogens and abiotic stresses are well-established, yet little is known about the molecular mechanisms regulating stilbene biosynthesis in plant defense progress.

RESULTS

Here, we cloned and identified the Chinese wild grape (Vitis davidii) R2R3-MYB transcription factor VdMYB1, which activates defense responses against invading pathogen. VdMYB1 transcripts were significantly upregulated after inoculation with the grapevine powdery mildew fungus Erysiphe necator (Schw.) Burr. Transient expression analysis using onion epidermal cells and Arabidopsis thaliana protoplasts showed that VdMYB1 was localized in the nucleus. Yeast one-hybrid assays revealed that VdMYB1 acts as a transcriptional activator. Grapevine leaves transiently overexpressing VdMYB1 showed a lower number of fungal conidiophores compared with wild-type leaves. Overexpression of VdMYB1 in grapevine leaves did not alter the expression of genes in salicylic acid- and jasmonate-dependent pathways, but affected the expression of stilbene synthase (STS) genes, key regulators of flavonoid metabolism. Results of electrophoretic mobility shift assays and in vivo transcriptional activation assays showed that VdMYB1 binds to the MYB binding site (MYBBS) in the STS2 gene promoter, thus activating STS2 transcription. In heterologous expression assays using tobacco leaves, VdMYB1 activated STS2 gene expression and increased the accumulation of resveratrol.

CONCLUSIONS

Our study showed that VdMYB1 activates STS2 gene expression to positively regulate defense responses, and increases the content of resveratrol in leaves.

Dissection of loci conferring resistance to stripe rust in Chinese wheat landraces from the middle and lower reaches of the Yangtze River via genome-wide association study

Stripe rust (Yr), caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a devastating foliar disease of wheat in China. Chinese wheat landraces originating from the middle and lower reaches of the Yangtze River are potential stripe-rust resistance resources. To identify APR genes for stripe-rust resistance, a panel of 188 accessions derived from the middle and lower reaches of the Yangtze River were inoculated with a mixture of Chinese P. striiformis f. sp. tritici races and resistance evaluated under field conditions in five environments at adult-plant stages. Seventy-three accessions showed degrees of stable resistance. Combining phenotypic datasets from multiple field experiments with high-quality Diversity Arrays Technology and simple sequence repeat markers, we detected 21 marker-trait associations spanning 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6B, and 6D, respectively. Single QTLs explained 9.67% to 16.14% of the observed phenotypic variation. Nine QTLs co-localized with previously reported Yr genes or genomic regions. The remaining QTLs were potential novel loci associated with adult-stage stripe-rust resistance. Two novel QTLs, QYr.sicau-3B.2 and QYr.sicau-5B.3, located on chromosomes 3B and 5B significantly explained 16.14% and 11.16% of the phenotypic variation, respectively. Haplotype analysis revealed that accessions carrying APR variants or their combinations showed enhanced degrees of resistance. The potentially novel loci or genomic regions associated with adult-stage resistance may be useful to improve stripe-rust resistance in current wheat cultivars and for future isolation of stripe-rust resistance genes.

Genome-Wide Identification and Expression Analysis of GA2ox, GA3ox, and GA20ox Are Related to Gibberellin Oxidase Genes in Grape (Vitis Vinifera L.)

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (VvGA2oxs, VvGA3oxs, and VvGA20oxs) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis GA2oxs, GA3oxs, and GA20oxs genes already reported, the VvGA2oxs, VvGA3oxs, and VvGA20oxs genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of VvGA2oxs, VvGA3oxs, and VvGA20oxs gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 GAoxs genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of VvGAox genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of VvGA2oxs and VvGA20oxs in different tissues at different developmental stages of grapes were relatively higher than that of VvGA3oxs. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the GAoxs gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some VvGA2oxs was upregulated under GA3 treatment. Simultaneously, some VvGA3oxs and VvGA20oxs were upregulated under uniconazole treatment. In a nutshell, the GA2ox gene mainly functions to inactivate biologically active GAs, while GA20ox mainly degrades C20 gibberellins, and GA3ox is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of VvGAoxs would provide a basis for understanding the evolution and function of the VvGAox gene family in a grape plant.

Functional Characterization of Resistance to Powdery Mildew of VvTIFY9 from Vitis vinifera

Powdery mildew is a disease caused by fungal pathogens that harms grape leaves and fruits. The TIFY gene family is a plant-specific super-family involved in the process of plants’ development and their biotic and abiotic stress responses. This study aimed to learn the function of the VvTIFY9 gene to investigate molecular mechanisms of grape resistance to powdery mildew. A VvTIFY9 protein encoding a conserved motif (TIF[F/Y]XG) was characterized in grape (Vitis vinifera). Sequence analysis confirmed that VvTIFY9 contained this conserved motif (TIF[F/Y]XG). Quantitative PCR analysis of VvTIFY9 in various grape tissues demonstrated that the expression of VvTIFY9 was higher in grape leaves. VvTIFY9 was induced by salicylic acid (SA) and methyl jasmonate (MeJA) and it also quickly responded to infection with Erysiphe necator in grape. Analysis of the subcellular localization and transcriptional activation activity of VvTIFY9 showed that VvTIFY9 located to the nucleus and had transcriptional activity. Arabidopsis that overexpressed VvTIFY9 were more resistant to Golovinomyces cichoracearum, and quantitative PCR revealed that two defense-related genes, AtPR1 and AtPDF1.2, were up-regulated in the overexpressing lines. These results indicate that VvTIFY9 is intimately involved in SA-mediated resistance to grape powdery mildew. This study provides the basis for exploring the molecular mechanism of grape resistance to disease resistance and candidate genes for transgenic disease resistance breeding of grape plants.

A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population

A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.