Race-specific resistance loci, whether having qualitative or quantitative effects, present plant-breeding challenges for phenotypic selection and deciding which loci to select or stack with other resistance loci for improved durability. Previously, resistance to grapevine powdery mildew (GPM, caused by Erysiphe necator) was predicted to be conferred by at least three race-specific loci in the mapping family B37-28 × C56-11 segregating for GPM resistance from Vitis aestivalis. In this study, 9 years of vineyard GPM disease severity ratings plus a greenhouse and laboratory assays were genetically mapped, using a rhAmpSeq core genome marker platform with 2,000 local haplotype markers. A new qualitative resistance locus, named REN11, on the chromosome (Chr) 15 was found to be effective in nearly all (11 of 12) vineyard environments on leaves, rachis, berries, and most of the time (7 of 12) stems. REN11 was independently validated in a pseudo-testcross with the grandparent source of resistance, "Tamiami." Five other loci significantly predicted GPM severity on leaves in only one or two environments, which could indicate race-specific resistance or their roles in different timepoints in epidemic progress. Loci on Chr 8 and 9 reproducibly predicted disease severity on stems but not on other tissues and had additive effects with REN11 on the stems. The rhAmpSeq local haplotype sequences published in this study for REN11 and Chr 8 and 9 stem quantitative trait locus (QTL) can be used directly for marker-assisted selection or converted to SNP assays. In screening for REN11 in a diversity panel of 20,651 vines representing the diversity of Vitis, this rhAmpSeq haplotype had a false positive rate of 0.034% or less. The effects of the other foliar resistance loci detected in this study seem too unstable for genetic improvement regardless of quantitative effect size, whether due to race specificity or other environmental variables.

Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid and mitochondrial genome sequences. The cytoplasmic diversity identified was structured according to synthetic domestication groups (wine and raisin/table grape types) and interspecific-hybridization-driven groups with introgression from North American Vitis species, identifying five cytoplasmic groups and four major clusters. Fifty-two SNP markers were used to describe the diversity of the germplasm. Ten organelle genes showed distinct SNP annotations and effect predictions, of which six were chloroplast-derived and three were mitochondrial genes, in addition to one mitochondrial SNP affecting a nonannotated open reading frame. The results suggest that the application of GBS will aid in the study of cytoplasmic genomes in grapevine, which will enable further studies on the role of cytoplasmic genomes in grapevine germplasm, and then allow the exploitation of these sources of diversity in breeding.

Genotyping microarrays are widely used for genetic mapping, but in high-diversity organisms, the quality of SNP calls can be diminished by genetic variation near the assayed nucleotide. To address this limitation in grapevine, we developed a simple heuristic that uses hybridization intensity to genetically map phenotypes without the need to distinguish between polymorphic states. We applied this approach to the mapping of three previously mapped traits, each controlled by single major effect loci—color, flower sex, and powdery mildew resistance—and confirmed that intensity values outperform SNP calls in all cases. Further, because per sample cost is a major limitation to the adoption of genotyping microarrays in applied genetic research and plant breeding, we tested how many samples were required to map a Mendelian trait in an F1 grape population and found that we could identify the correct genomic region with as few as 12 samples. For high-diversity species for which genotyping arrays are available or under development, our findings suggest a powerful and cost-effective approach to identify large-effect QTL when faced with poor SNP quality.

A grapevine hybrid progeny was generated to track the inheritance of the Ren1 and the Run1 powdery mildew resistance alleles and the segregation of the powdery mildew resistance phenotype. Genotypic analysis was carried out using flanking microsatellite markers; phenotypic evaluations were done under in vitro and greenhouse conditions. Pairing the phenotypic and genotypic data demonstrated that Ren1 and Run1 acted as single dominant loci and assorted independently without considerable distortion of segregation. Chromosomal recombination events were detected in the Ren1 but not in the Run1 region, corroborating earlier observations that crossover between homologous chromosomes was suppressed around the Run1 locus. Taken together, the results confirmed that microsatellite marker-assisted selection is a reliable and expeditious method to combine multiple alleles that confer resistance to a pathogen.

Race-specific resistance against powdery mildews is well documented in small grains but, in other crops such as grapevine, controlled analysis of host-pathogen interactions on resistant plants is uncommon. In the current study, we attempted to confirm powdery mildew resistance phenotypes through vineyard, greenhouse, and in vitro inoculations for test cross-mapping populations for two resistance sources: (i) a complex hybrid breeding line, 'Bloodworth 81-107-11', of at least Vitis rotundifolia, V. vinifera, V. berlandieri, V. rupestris, V. labrusca, and V. aestivalis background; and (ii) Vitis hybrid 'Tamiami' of V. aestivalis and V. vinifera origin. Statistical analysis of vineyard resistance data suggested the segregation of two and three race-specific resistance genes from the two sources, respectively. However, in each population, some resistant progeny were susceptible in greenhouse or in vitro screens, which suggested the presence of Erysiphe necator isolates virulent on progeny segregating for one or more resistance genes. Controlled inoculation of resistant and susceptible progeny with a diverse set of E. necator isolates clearly demonstrated the presence of fungal races differentially interacting with race-specific resistance genes, providing proof of race specificity in the grape powdery mildew pathosystem. Consistent with known race-specific resistance mechanisms, both resistance sources were characterized by programmed cell death of host epidermal cells under appressoria, which arrested or slowed hyphal growth; this response was also accompanied by collapse of conidia, germ tubes, appressoria, and secondary hyphae. The observation of prevalent isolates virulent on progeny with multiple race-specific resistance genes before resistance gene deployment has implications for grape breeding strategies. We suggest that grape breeders should characterize the mechanisms of resistance and pyramid multiple resistance genes with different mechanisms for improved durability.

The single, dominant powdery mildew resistance locus Ren4 from Vitis romanetii prevents hyphal growth by Erysiphe necator. Previously, we showed that when introgressed into V. vinifera in the modified BC2 population 03-3004, Ren4 was linked with the simple sequence repeat marker VMC7f2 on chromosome 18—a marker that is associated with multiple disease resistance and seedlessness. However, in the current study, this marker was monomorphic in related breeding populations 05-3010 and 07-3553. To enhance marker-assisted selection at this locus, we developed multiplexed SNP markers using three approaches: conversion of bulked segregant analysis AFLP markers, sequencing of candidate genes and regions flanking known V. vinifera SNPs, and hybridization to the Vitis9KSNP genotyping array. The Vitis9KSNP array was more cost-efficient than all other approaches tested for marker discovery and genotyping, enabling the genotyping of 1317 informative SNPs within the span of 1 week and at a cost of 11 cents per SNP. From a total of 1,446 high quality, informative markers segregating in 03-3004, we developed a haplotype signature of 15 multiplexed SNP markers linked with Ren4 in 03-3004, 5 of which were linked in 05-3010, and 6 of which were linked in 07-3553. Two of these populations segregated for seedlessness, which was tightly linked with Ren4 in 03-3004 (2 cM) but not in 05-3010 (22 cM). Chromosomal rearrangements were detected among these three populations and the reference genome PN40024. Since this is the first application of the Vitis9KSNP array in a breeding program, some suggestions are provided for application of genotyping arrays. Our results provide novel markers for tracking and pyramiding this unique resistance gene and for further functional characterization of this region on chromosome 18 encoding multiple disease resistance and seedlessness.

In the present study we screened the progeny of Vitis vinifera x V romanetii populations segregating for resistance to powdery mildew and determined the presence of a single, dominant locus. Ren4, conferring rapid and extreme resistance to the grapevine powdery mildew fungus Erysiphe necator. In each of nine Ren4 pseudo-backcross 2 (pBC(2)) and pBC(3) populations (1,030 progeny), resistance fit a 1:1 segregation ratio and overall segregated as 543 resistant progeny to 487 susceptible. In fullsib progeny, microscopic observations revealed the reduction of penetration success rate (as indicated by the emergence of secondary hyphae) from 86% in susceptible progeny to below 10% in resistant progeny. Similarly, extreme differences were seen macroscopically. Ratings for Ren4 pBC(2) population 03-3004 screened using natural infection in a California vineyard and greenhouse and using artificial inoculation of an aggressive New York isolate were fully consistent among all three pathogen sources and environments. From 2006 to 2010, Ren4 pBC(2) and pBC3 vines were continuously screened in California and New York (in the center of diversity for E. necator), and no sporulating colonies were observed. For population 03-3004, severity ratings on leaves, shoots, berries, and rachises were highly correlated (R-2 = 0.875 to 0.996) in the vineyard. Together, these data document a powdery mildew resistance mechanism not previously described in the Vitaceae or elsewhere, in which a dominantly inherited resistance prevents hyphal emergence and is non-race-specific and tissue-independent. In addition to its role in breeding for durable resistance. Ren4 may provide mechanistic insights into the early events that enable powdery mildew infection.

In the present study we screened the progeny of Vitis vinifera × V. romanetii populations segregating for resistance to powdery mildew and determined the presence of a single, dominant locus, Ren4, conferring rapid and extreme resistance to the grapevine powdery mildew fungus Erysiphe necator. In each of nine Ren4 pseudo-backcross 2 (pBC(2)) and pBC(3) populations (1,030 progeny), resistance fit a 1:1 segregation ratio and overall segregated as 543 resistant progeny to 487 susceptible. In full-sib progeny, microscopic observations revealed the reduction of penetration success rate (as indicated by the emergence of secondary hyphae) from 86% in susceptible progeny to below 10% in resistant progeny. Similarly, extreme differences were seen macroscopically. Ratings for Ren4 pBC(2) population 03-3004 screened using natural infection in a California vineyard and greenhouse and using artificial inoculation of an aggressive New York isolate were fully consistent among all three pathogen sources and environments. From 2006 to 2010, Ren4 pBC(2) and pBC(3) vines were continuously screened in California and New York (in the center of diversity for E. necator), and no sporulating colonies were observed. For population 03-3004, severity ratings on leaves, shoots, berries, and rachises were highly correlated (R(2) = 0.875 to 0.996) in the vineyard. Together, these data document a powdery mildew resistance mechanism not previously described in the Vitaceae or elsewhere, in which a dominantly inherited resistance prevents hyphal emergence and is non-race-specific and tissue-independent. In addition to its role in breeding for durable resistance, Ren4 may provide mechanistic insights into the early events that enable powdery mildew infection.

Phylloxera has been an important pest in California since its 'discovery in 1880 within Sonoma and Napa counties. Phylloxera-resistant rootstocks and germplasm were selected from American grape species native to the eastern United States. Breeding programs to develop improved phylloxera-resistant rootstocks were started in the late nineteenth century. Resistance to phylloxera has been reported to be controlled by several genes. To focus on one aspect of resistance to phylloxera, a greenhouse screening method was used to observe absence/presence of root nodosities produced by phylloxera. Only one source of phylloxera biotype A from Fresno County was used to reduce the complication of various biotypes. Grape rootstocks with known field reaction to phylloxera were evaluated to test the reliability of the greenhouse test. A design II mating factorial cross was made between male and female rootstocks with a range of resistance to susceptibility. The reaction of their progeny to phylloxera was observed in the greenhouse. All populations segregated for resistance/susceptibility with a few exceptions. Dog Ridge crossed with two susceptible genotypes gave all susceptible offspring. Kober 5BB crossed with susceptible or resistant genotypes gave all resistant offspring. The segregation of resistance to nodosity development could be explained by two complementary dominant genes in most families.

Six raisin grape cultivars and 10 new raisin grape selections were analyzed for antioxidant activity (ABTS assay) and for total and individual phenolic compounds. Samples were freeze–dried and values are reported on a dry weight basis. Antioxidant activity across the 16 samples ranged from 7.7 to 60.9μmol Trolox/g DW, with A95-27 exhibiting the greatest activity. Total phenolic content, determined in gallic acid equivalents using the Folin–Ciocalteau assay, ranged from 316.3 to 1141.3mg gallic acid/100g DW and was strongly correlated (r=0.990) with antioxidant results. Concentrations of individual phenolics were determined by HPLC. trans-Caftaric acid was the predominant compound in all samples. A95-15 contained the lowest concentration (153.5μg/g DW) of caftaric acid, while Fiesta contained the highest concentration (598.7μg/g DW). Selections A56-66, A95-15, and A95-27 had much higher levels of catechin (86.5–209.1μg/g DW) and epicatechin (126.5–365.7μg/g DW) than the other samples.

Traditional production of raisins by hand harvesting and drying grapes on paper trays is labor intensive and at risk to inclement weather. Dried-on-vine (DOV) raisin production uses mechanical harvesters and the risk of rain damage is reduced. Earlier-ripening raisin cultivars have been developed and released that are suited for this new production system. Raisin breeders would also benefit by knowing if there are differences in drying rates among cultivars. If raisin cultivars were both early ripening and had rapid dry rates, then they would be well suited for DOV raisin production. In a study over three seasons from 2002 to 2004, results showed significant differences among cultivars for drying rates. Summer Muscat, Diamond Muscat, and Primus dried the fastest and Thompson Seedless consistently dried the slowest. DOVine and Selma Pete were intermediate. Water loss was affected more by berry size than by Brix. Drying rate increased more by removing the epicuticular wax by a chloroform dip than by rubbing. Summer Muscat dried faster than Thompson Seedless even when wax was removed by chloroform or rubbing. Results indicate that skin characteristics in addition to epicuticular wax might play a role in the differences in raisin cultivar drying rate. There were large differences among cultivars in the amount of cuticle as compared to epicuticular wax. These findings show that breeding advances are possible in the development of raisin grapes with high drying rates.

Pierce's disease (PD), caused by the bacterium Xylella fastidiosa, is an important disease of grapevines in California, across the southern United States, and into South America. In regions where disease pressure is high, the cultivation of Vitis vinifera cultivars is difficult or impossible. This study reports on the introgression of PD resistance into elite wine, table, and raisin grape genetic backgrounds and on the reliability of PCR-based marker-assisted selection (MAS) to accelerate the breeding of PD-resistant grapes. This work documents the introgression of PD resistance from a homozygous resistant form of V. arizonica, b43-17. A total of 4,321 seedlings from 83 different crosses of resistant selections and high-quality V. vinifera cultivars from the F1 and first and second modified backcross generations (mBC1 and mBC2) were screened with two to three flanking microsatellite markers (VVIP26, ctg1026876 and VMC2a5) in the early spring 2006 and 2007. The alleles linked to resistance were unique in size and were not shared by susceptible V. vinifera selections. Based on the presence of unique resistant alleles, 1,683 seedlings from wine, table, and raisin grape background were selected. The distinctiveness of these resistant alleles allows the use of MAS to optimize the breeding of PD-resistant grape cultivars.

The rootstock Freedom is the offspring of two open-pollinated parents (1613-59 and Dog Ridge 5), sources of root-knot nematode resistance. As phylloxera has increased in importance in vineyards, the risk of Vitis vinifera-derived phylloxera susceptibility from the unknown pollen donors is a concern. To clarify the pedigree of Freedom, genetic profiles of 31 potential progenitors were analyzed with 30 microsatellite markers. We confirm the reported parent (1613-59) and grandparent (1613C) of Freedom and identify 3306C (V. riparia x V. rupestris) as the pollen parent of 1613-59. We were unable to identify the pollen parent of Dog Ridge 5.

Additional index words.cultivar, fruit breeding, Vitis vinifera, Vitis labrusca, hybrid, table grape 'Thomcord' (Vitis vinifera L. • V. labrusca L.) is a midseason, blue-black seedless table grape (Fig. 1) that is suitable for farmers' markets and shipping to domestic markets.It has the aromatic flavor reminiscent of 'Concord' with firmer flesh and skin that adheres to the flesh.It is more suitable to the hot, dry growing conditions found in the San Joaquin Valley than 'Concord'.'Thomcord' was released to provide a 'Concord'-flavored, seedless grape adapted to the growing conditions of the San Joaquin Valley of California.

‘Diamond Muscat’, ‘DOVine’, ‘Fiesta’, and ‘Selma Pete’ grapevines ( Vitis vinifera ) were evaluated to determine their suitability for making dry-on-vine (DOV) raisins on an open-gable trellis. The experiment was a split-plot, with training system, head, bilateral, or quadrilateral cordons as the main plot, and grapevine cultivar (Diamond Muscat, DOVine, Fiesta, or Selma Pete) as the subplot. Yield components, fruit composition, and raisin yield and quality were evaluated annually. Vine training style did not affect fruit composition, or raisin yield or quality, but vines trained to quadrilateral cordons produced more clusters on renewal shoots than head-trained vines. ‘DOVine’, ‘Fiesta’, and ‘Selma Pete’ produced about 4.75 tons/acre of raisins, ≈10% more than ‘Diamond Muscat’. ‘Diamond Muscat’ vines produced the most clusters on renewal shoots, an undesirable trait, and the most clusters per vine. ‘Fiesta’ matured later than the other cultivars, therefore it had the lowest soluble solids, the poorest raisin grades, and the highest field moisture at harvest. ‘Selma Pete’ grapes matured as early, or earlier, than the grapes of other cultivars, they had among the highest soluble solids and raisin grades, and the raisins generally dried well. Thus, ‘Selma Pete’ grapevines had the best overall performance of the cultivars tested.

Nineteen peach [ Prunus persica (L.) Batsch] genotypes and 45 plum ( Prunus salicina Erhr. and hybrids) genotypes with different flesh and skin color were analyzed for their antioxidant content and activity. Anthocyanin content, phenolic content, and antioxidant activity were higher in red-flesh than in light-colored flesh peaches. Carotenoid content was higher in yellow-flesh peaches than in light-colored ones. Red-flesh plums generally had higher anthocyanin and phenolic contents than the other plums but not necessarily greater antioxidant capacity. The total phenolic content had the most consistent and highest correlation with antioxidant activity, indicating that it is more important in determining the antioxidant activity of peaches and plums than are the anthocyanin or carotenoid contents. In general, the wide range of phytochemical content and antioxidant activity found indicates that the genetic variability present can be used to develop cultivars with enhanced health benefits.