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Prof. Anne Fennell
South Dakota State University

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0 Genomics
0 Grapevine
0 abiotic stress
0 Dormancy
0 perennial

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Dormancy
perennial

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Journal article
Published: 09 April 2021 in Proceedings of the National Academy of Sciences
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Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.

ACS Style

Cheng Zou; Mélanie Massonnet; Andrea Minio; Sagar Patel; Victor Llaca; Avinash Karn; Fred Gouker; Lance Cadle-Davidson; Bruce Reisch; Anne Fennell; Dario Cantu; Qi Sun; Jason P. Londo. Multiple independent recombinations led to hermaphroditism in grapevine. Proceedings of the National Academy of Sciences 2021, 118, 1 .

AMA Style

Cheng Zou, Mélanie Massonnet, Andrea Minio, Sagar Patel, Victor Llaca, Avinash Karn, Fred Gouker, Lance Cadle-Davidson, Bruce Reisch, Anne Fennell, Dario Cantu, Qi Sun, Jason P. Londo. Multiple independent recombinations led to hermaphroditism in grapevine. Proceedings of the National Academy of Sciences. 2021; 118 (15):1.

Chicago/Turabian Style

Cheng Zou; Mélanie Massonnet; Andrea Minio; Sagar Patel; Victor Llaca; Avinash Karn; Fred Gouker; Lance Cadle-Davidson; Bruce Reisch; Anne Fennell; Dario Cantu; Qi Sun; Jason P. Londo. 2021. "Multiple independent recombinations led to hermaphroditism in grapevine." Proceedings of the National Academy of Sciences 118, no. 15: 1.

Journal article
Published: 31 March 2021 in Plants
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Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD buds. Gene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.

ACS Style

Shuchi Smita; Michael Robben; Anup Deuja; Monica Accerbi; Pamela Green; Senthil Subramanian; Anne Fennell. Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine. Plants 2021, 10, 669 .

AMA Style

Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela Green, Senthil Subramanian, Anne Fennell. Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine. Plants. 2021; 10 (4):669.

Chicago/Turabian Style

Shuchi Smita; Michael Robben; Anup Deuja; Monica Accerbi; Pamela Green; Senthil Subramanian; Anne Fennell. 2021. "Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine." Plants 10, no. 4: 669.

Journal article
Published: 30 December 2020 in Horticulturae
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Grapevine sustainability is impacted by the timing of dormancy initiation and freezing tolerance in fall and winter and chilling fulfillment and bud break in the spring. These traits have genetic and local temperature contributing factors; therefore, this study was undertaken to develop an understanding of these characteristics in four recently developed cold climate cultivars. The cold hardiness and chilling fulfillment profiles were monitored in Brianna, Frontenac gris, La Crescent and Marquette using differential thermal analyses and bud break assays. Bud cold hardiness of all cultivars increased with the declining temperatures from November through February, after which the buds began to lose freezing tolerance. There were significant differences in cold hardiness and chilling fulfillment between cultivars during the endodormant and ecodormant period of winter. Marquette had the greatest freezing tolerance from early November through midwinter suggesting it has potential as a sentinel cultivar for comparisons of new cold climate selections. Brianna was slower to acclimate and deacclimated more rapidly than the other cultivars. Chilling fulfillment under natural field or constant 4 °C conditions showed no main effect differences for chilling accumulation condition; however, there were significant cultivar, condition, and time point interactions, indicating the cultivars differed in chilling fulfillment responses.

ACS Style

Turhan Yilmaz; Dilmini Alahakoon; Anne Fennell. Freezing Tolerance and Chilling Fulfillment Differences in Cold Climate Grape Cultivars. Horticulturae 2020, 7, 4 .

AMA Style

Turhan Yilmaz, Dilmini Alahakoon, Anne Fennell. Freezing Tolerance and Chilling Fulfillment Differences in Cold Climate Grape Cultivars. Horticulturae. 2020; 7 (1):4.

Chicago/Turabian Style

Turhan Yilmaz; Dilmini Alahakoon; Anne Fennell. 2020. "Freezing Tolerance and Chilling Fulfillment Differences in Cold Climate Grape Cultivars." Horticulturae 7, no. 1: 4.

Journal article
Published: 01 June 2020 in Horticulture Research
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Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research.

ACS Style

Sagar Patel; Michael Robben; Anne Fennell; Jason P. Londo; Dilmini Alahakoon; Roberto Villegas-Diaz; Padmapriya Swaminathan. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’. Horticulture Research 2020, 7, 92 .

AMA Style

Sagar Patel, Michael Robben, Anne Fennell, Jason P. Londo, Dilmini Alahakoon, Roberto Villegas-Diaz, Padmapriya Swaminathan. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’. Horticulture Research. 2020; 7 (1):92.

Chicago/Turabian Style

Sagar Patel; Michael Robben; Anne Fennell; Jason P. Londo; Dilmini Alahakoon; Roberto Villegas-Diaz; Padmapriya Swaminathan. 2020. "Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’." Horticulture Research 7, no. 1: 92.

Journal article
Published: 21 January 2020 in Nature Communications
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Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.

ACS Style

Cheng Zou; Avinash Karn; Bruce Reisch; Allen Nguyen; Yongming Sun; Yun Bao; Michael S. Campbell; Deanna Church; Stephen Williams; Xia Xu; Craig A. Ledbetter; Sagar Patel; Anne Fennell; Jeffrey C. Glaubitz; Matthew Clark; Doreen Ware; Jason Londo; Qi Sun; Lance Cadle-Davidson. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications 2020, 11, 1 -11.

AMA Style

Cheng Zou, Avinash Karn, Bruce Reisch, Allen Nguyen, Yongming Sun, Yun Bao, Michael S. Campbell, Deanna Church, Stephen Williams, Xia Xu, Craig A. Ledbetter, Sagar Patel, Anne Fennell, Jeffrey C. Glaubitz, Matthew Clark, Doreen Ware, Jason Londo, Qi Sun, Lance Cadle-Davidson. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications. 2020; 11 (1):1-11.

Chicago/Turabian Style

Cheng Zou; Avinash Karn; Bruce Reisch; Allen Nguyen; Yongming Sun; Yun Bao; Michael S. Campbell; Deanna Church; Stephen Williams; Xia Xu; Craig A. Ledbetter; Sagar Patel; Anne Fennell; Jeffrey C. Glaubitz; Matthew Clark; Doreen Ware; Jason Londo; Qi Sun; Lance Cadle-Davidson. 2020. "Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus." Nature Communications 11, no. 1: 1-11.

Journal article
Published: 09 January 2020 in Plants
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Tamarix spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of T. chinensis and T. ramosissima from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference Tamarix (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the Beta vulgaris subsp. vulgaris (Amaranthaceae, Carophyllales order) genome assembly. T. ramosissima took longer to show water stress symptoms than T. chinensis. There were 2068 and 669 differentially expressed genes (DEG) in T. chinensis and T. ramosissima, respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in T. chinensis, in contrast to one small molecular function network in T. ramosissima.

ACS Style

Padmapriya Swaminathan; Michelle Ohrtman; Abigail Carinder; Anup Deuja; Cankun Wang; John Gaskin; Anne Fennell; Sharon Clay. Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States. Plants 2020, 9, 86 .

AMA Style

Padmapriya Swaminathan, Michelle Ohrtman, Abigail Carinder, Anup Deuja, Cankun Wang, John Gaskin, Anne Fennell, Sharon Clay. Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States. Plants. 2020; 9 (1):86.

Chicago/Turabian Style

Padmapriya Swaminathan; Michelle Ohrtman; Abigail Carinder; Anup Deuja; Cankun Wang; John Gaskin; Anne Fennell; Sharon Clay. 2020. "Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States." Plants 9, no. 1: 86.

Journal article
Published: 08 November 2019 in Horticulture Research
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Grapevine (Vitis spp.) contains a wealth of phytochemicals that have received considerable attention due to health-promoting properties and biological activities as phytoalexins. To date, the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited. Here, metabolic quantitative trait locus (mQTL) mapping was conducted using grapevine stems of a segregating F2 population. Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry (LC-HRMS), resulting in the detection of 1317 ions/features. In total, 19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software, resulting in the identification of four mQTLs. Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18, accounting for phenotypic variances of 29.0% and 38.4%. Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18. This 2.8-Mbp region contains 48 genes with R-gene motifs, including variants of TIR, NBS, and LRR, that might potentially confer resistance to powdery mildew, downy mildew, or other pathogens. The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites, including phytoalexins. In addition, haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.

ACS Style

Soon L. Teh; Bety Rostandy; Mani Awale; James J. Luby; Anne Fennell; Adrian D. Hegeman. Genetic analysis of stilbenoid profiles in grapevine stems reveals a major mQTL hotspot on chromosome 18 associated with disease-resistance motifs. Horticulture Research 2019, 6, 1 -11.

AMA Style

Soon L. Teh, Bety Rostandy, Mani Awale, James J. Luby, Anne Fennell, Adrian D. Hegeman. Genetic analysis of stilbenoid profiles in grapevine stems reveals a major mQTL hotspot on chromosome 18 associated with disease-resistance motifs. Horticulture Research. 2019; 6 (1):1-11.

Chicago/Turabian Style

Soon L. Teh; Bety Rostandy; Mani Awale; James J. Luby; Anne Fennell; Adrian D. Hegeman. 2019. "Genetic analysis of stilbenoid profiles in grapevine stems reveals a major mQTL hotspot on chromosome 18 associated with disease-resistance motifs." Horticulture Research 6, no. 1: 1-11.

Journal article
Published: 01 May 2019 in Horticulture Research
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Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine ‘Chambourcin’ (Vitis L.) as a model to explore the rootstock–scion relationship. We examined leaf shape, ion concentrations, and gene expression in ‘Chambourcin’ grown ungrafted as well as grafted to three different rootstocks (‘SO4’, ‘1103P’ and ‘3309C’) across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on ‘Chambourcin’ leaf morphology, ionomics, and gene expression. Researchers in the US have uncovered how rootstocks affect scions following grafting, which will help to develop more resilient crops. A team led by Allison Miller of Saint Louis University grafted the ‘Chambourcin’ grape variety onto three different rootstocks and investigated the effect on leaf shape, ion concentration, and gene expression in the scion. They discovered that the rootstock influenced how leaf shape changed in response to different irrigation conditions. A similar irrigation-dependent effect of rootstock was found for the ion composition in the shoot. The team also identified roughly 100 genes with altered expression in each of the grafted vines, including five genes which were altered by all three graft combinations. These findings are a first step toward understanding the relationship between rootstocks and scions and modulating it to produce crops better adapted to challenging environments.

ACS Style

Zoë Migicovsky; Zachary N. Harris; Laura L. Klein; Mao Li; Adam McDermaid; Daniel H. Chitwood; Anne Fennell; Laszlo G. Kovacs; Misha Kwasniewski; Jason Londo; Qin Ma; Allison J. Miller. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research 2019, 6, 1 -13.

AMA Style

Zoë Migicovsky, Zachary N. Harris, Laura L. Klein, Mao Li, Adam McDermaid, Daniel H. Chitwood, Anne Fennell, Laszlo G. Kovacs, Misha Kwasniewski, Jason Londo, Qin Ma, Allison J. Miller. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. Horticulture Research. 2019; 6 (1):1-13.

Chicago/Turabian Style

Zoë Migicovsky; Zachary N. Harris; Laura L. Klein; Mao Li; Adam McDermaid; Daniel H. Chitwood; Anne Fennell; Laszlo G. Kovacs; Misha Kwasniewski; Jason Londo; Qin Ma; Allison J. Miller. 2019. "Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard." Horticulture Research 6, no. 1: 1-13.

Journal article
Published: 13 February 2019 in BMC Plant Biology
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Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot.

ACS Style

Vedbar Singh Khadka; Kimberley Vaughn; Juan Xie; Padmapriya Swaminathan; Qin Ma; Grant R. Cramer; Anne Y. Fennell. Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.). BMC Plant Biology 2019, 19, 1 -20.

AMA Style

Vedbar Singh Khadka, Kimberley Vaughn, Juan Xie, Padmapriya Swaminathan, Qin Ma, Grant R. Cramer, Anne Y. Fennell. Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.). BMC Plant Biology. 2019; 19 (1):1-20.

Chicago/Turabian Style

Vedbar Singh Khadka; Kimberley Vaughn; Juan Xie; Padmapriya Swaminathan; Qin Ma; Grant R. Cramer; Anne Y. Fennell. 2019. "Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)." BMC Plant Biology 19, no. 1: 1-20.

Communication
Published: 01 February 2019 in Molecules
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In this research, we propose a novel concept for a non-destructive evaluation of volatiles emitted from ripening grapes using solid-phase microextraction (SPME). This concept is novel to both the traditional vinifera grapes and the cold-hardy cultivars. Our sample models are cold-hardy varieties in the upper Midwest for which many of the basic multiyear grape flavor and wine style data is needed. Non-destructive sampling included a use of polyvinyl fluoride (PVF) chambers temporarily enclosing and concentrating volatiles emitted by a whole cluster of grapes on a vine and a modified 2 mL glass vial for a vacuum-assisted sampling of volatiles from a single grape berry. We used SPME for either sampling in the field or headspace of crushed grapes in the lab and followed with analyses on gas chromatography-mass spectrometry (GC-MS). We have shown that it is feasible to detect volatile organic compounds (VOCs) emitted in-vivo from single grape berries (39 compounds) and whole clusters (44 compounds). Over 110 VOCs were released to headspace from crushed berries. Spatial (vineyard location) and temporal variations in VOC profiles were observed for all four cultivars. However, these changes were not consistent by growing season, by location, within cultivars, or by ripening stage when analyzed by multivariate analyses such as principal component analysis (PCA) and hierarchical cluster analyses (HCA). Research into aroma compounds present in cold-hardy cultivars is essential to the continued growth of the wine industry in cold climates and diversification of agriculture in the upper Midwestern area of the U.S.

ACS Style

Somchai Rice; Devin L. Maurer; Anne Fennell; Murlidhar Dharmadhikari; Jacek A. Koziel. Evaluation of Volatile Metabolites Emitted In-Vivo from Cold-Hardy Grapes during Ripening Using SPME and GC-MS: A Proof-of-Concept. Molecules 2019, 24, 536 .

AMA Style

Somchai Rice, Devin L. Maurer, Anne Fennell, Murlidhar Dharmadhikari, Jacek A. Koziel. Evaluation of Volatile Metabolites Emitted In-Vivo from Cold-Hardy Grapes during Ripening Using SPME and GC-MS: A Proof-of-Concept. Molecules. 2019; 24 (3):536.

Chicago/Turabian Style

Somchai Rice; Devin L. Maurer; Anne Fennell; Murlidhar Dharmadhikari; Jacek A. Koziel. 2019. "Evaluation of Volatile Metabolites Emitted In-Vivo from Cold-Hardy Grapes during Ripening Using SPME and GC-MS: A Proof-of-Concept." Molecules 24, no. 3: 536.

Data descriptor
Published: 31 January 2019 in Data
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In this research dataset, we summarize for the first time volatile organic compounds (VOCs) emitted in vivo from ripening wine grapes. We studied four cold-hardy cultivars grown in the Midwestern U.S.: St. Croix, Frontenac, Marquette, and La Crescent. These cultivars have gained popularity among local growers and winemakers, but still very little is known about their performance compared with long-established V. vinifera grapes. Volatiles were collected using two novel approaches: biogenic emissions from grape clusters on a vine and single grape berries. A third approach was headspace collection of volatiles from crushed grapes. Solid-phase microextraction (SPME) was used to collect volatiles. Vacuum-assisted SPME was used in the case of single grape berry. Collected VOCs were analyzed using separation and identification on a gas chromatograph mass spectrometer (GC-MS). More than 120 VOCs were identified using mass spectral libraries. The dataset provides evidence that detecting biogenic emissions from growing grapes is feasible. The dataset provides a record of temporal and spatial variability of VOCs, many of which could potentially impart aroma and flavor in the wine. The number of VOCs detected followed the order from single berry (the least) to crushed berry (the most). Thus, more information for potential use in harvesting in order to obtain the desired flavor is found in data from crushed grapes.

ACS Style

Somchai Rice; Devin L. Maurer; Anne Fennell; Murlidhar Dharmadhikari; Jacek A. Koziel. Biogenic Volatiles Emitted from Four Cold-Hardy Grape Cultivars During Ripening. Data 2019, 4, 22 .

AMA Style

Somchai Rice, Devin L. Maurer, Anne Fennell, Murlidhar Dharmadhikari, Jacek A. Koziel. Biogenic Volatiles Emitted from Four Cold-Hardy Grape Cultivars During Ripening. Data. 2019; 4 (1):22.

Chicago/Turabian Style

Somchai Rice; Devin L. Maurer; Anne Fennell; Murlidhar Dharmadhikari; Jacek A. Koziel. 2019. "Biogenic Volatiles Emitted from Four Cold-Hardy Grape Cultivars During Ripening." Data 4, no. 1: 22.

Journal article
Published: 22 January 2019 in Plants
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Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of the Plant Kingdom. A Hidden Markov Model (HMM) profile of the MAPK genes utilized reference sequences from A. thaliana and G. max, yielding a total of 96 MPKs and 37 MKKs in the genomes of A. trichopoda, A. coerulea, C. reinhardtii, D. carota, H. annuus, S. lycopersicum, and S. fallax. Among them, 28 MPKs and eight MKKs were confirmed in H. annuus. Phylogenetic analyses revealed four clades within each subfamily. Transcriptomic analyses showed that at least 19 HaMPK and seven HaMKK genes were induced in response to salicylic acid (SA), sodium chloride (NaCl), and polyethylene glycol (Peg) in leaves and roots. Of the seven published sunflower microRNAs, five microRNA families are involved in targeting eight MPKs. Additionally, we discussed the need for using MAP Kinase nomenclature guidelines across plant species. Our identification and characterization of MAP Kinase genes would have implications in sunflower crop improvement, and in advancing our knowledge of the diversity and evolution of MAPK genes in the Plant Kingdom.

ACS Style

Surendra Neupane; Sarah E. Schweitzer; Achal Neupane; Ethan J. Andersen; Anne Fennell; Ruanbao Zhou; Madhav P. Nepal. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). Plants 2019, 8, 28 .

AMA Style

Surendra Neupane, Sarah E. Schweitzer, Achal Neupane, Ethan J. Andersen, Anne Fennell, Ruanbao Zhou, Madhav P. Nepal. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). Plants. 2019; 8 (2):28.

Chicago/Turabian Style

Surendra Neupane; Sarah E. Schweitzer; Achal Neupane; Ethan J. Andersen; Anne Fennell; Ruanbao Zhou; Madhav P. Nepal. 2019. "Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.)." Plants 8, no. 2: 28.

Journal article
Published: 16 January 2019 in Foods
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The Midwest wine industry has shown a marked increase in growers, hectares planted, wineries, and wine production. This growth coincides with the release of cold-hardy cultivars such as Brianna and Frontenac gris, in 2001 and 2003, respectively. These white grape varieties account for one-third of the total area grown in the state of Iowa. It is generally accepted that the wine aroma profile plays a crucial role in developing a local, sustainable brand. However, the identity of Brianna/Frontenac Gris-based wine aromas and their link to the grape berry chemistry at harvest is unknown. This study aims to preliminarily characterize key odor-active compounds that can influence the aroma profile in wines made from Brianna and Frontenac gris grapes harvested at different stages of ripening. Brianna and Frontenac gris grapes were harvested approximately 7 days apart, starting at 15.4 °Brix (3.09 pH) and 19.5 °Brix (3.00 pH), respectively. Small batch fermentations were made for each time point with all juices adjusted to the same °Brix prior to fermentation. Odor-active compounds were extracted from wine headspace using solid-phase microextraction (SPME) and analyzed by gas chromatography-mass spectrometry (GC-MS) and simultaneous olfactometry (O). Over 30 odor-active compounds were detected. Aromas in Brianna wines developed from “cotton candy” and “floral”, to “banana” and “butterscotch”, then finally to “honey”, “caramel” and an unknown neutral aroma. Frontenac gris wines changed from an unknown neutral aroma to “fruity” and “rose”. Results from the lay audiences’ flavor and aroma descriptors also indicate a shift with harvest date and associated °Brix. To date, this is the first report of wine aromas from Brianna and Frontenac gris by GC-MS-O. Findings from this research support the hypothesis that aroma profiles of Brianna and Frontenac gris wines can be influenced by harvesting the grapes at different stages of ripening.

ACS Style

Somchai Rice; Madina Tursumbayeva; Matthew Clark; David Greenlee; Murlidhar Dharmadhikari; Anne Fennell; Jacek A. Koziel. Effects of Harvest Time on the Aroma of White Wines Made from Cold-Hardy Brianna and Frontenac Gris Grapes Using Headspace Solid-Phase Microextraction and Gas Chromatography-Mass Spectrometry-Olfactometry. Foods 2019, 8, 29 .

AMA Style

Somchai Rice, Madina Tursumbayeva, Matthew Clark, David Greenlee, Murlidhar Dharmadhikari, Anne Fennell, Jacek A. Koziel. Effects of Harvest Time on the Aroma of White Wines Made from Cold-Hardy Brianna and Frontenac Gris Grapes Using Headspace Solid-Phase Microextraction and Gas Chromatography-Mass Spectrometry-Olfactometry. Foods. 2019; 8 (1):29.

Chicago/Turabian Style

Somchai Rice; Madina Tursumbayeva; Matthew Clark; David Greenlee; Murlidhar Dharmadhikari; Anne Fennell; Jacek A. Koziel. 2019. "Effects of Harvest Time on the Aroma of White Wines Made from Cold-Hardy Brianna and Frontenac Gris Grapes Using Headspace Solid-Phase Microextraction and Gas Chromatography-Mass Spectrometry-Olfactometry." Foods 8, no. 1: 29.

Preprint
Published: 03 December 2018
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Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we use the French-American hybrid grapevine ‘Chambourcin’ (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in ‘Chambourcin’ grown own-rooted as well as grafted to three different rootstocks (‘SO4’, ‘1103P’ and ‘3309C’) across two years and three different irrigation treatments. Results described here demonstrate that 1) the largest source of variation in leaf shape stems from the interaction of rootstock by irrigation; 2) leaf position, but also rootstock and rootstock by irrigation interaction, are the primary sources of variation in leaf ion concentrations; and 3) gene expression in scion leaves exhibited significantly different patterns of gene expression from ungrafted vines, and these expression patterns were rootstock-specific. Our work provides an initial description of the subtle and complex effect of grafting on ‘Chambourcin’ leaf morphology, ionomics and gene expression in grapevine scions. Further work across multiple years, environments and additional phenotypes is required in order to determine how the relationship between the rootstock and the scion can best be leveraged for adapting grapevines to a changing climate.

ACS Style

Zoe Migicovsky; Zachary N. Harris; Laura L. Klein; Mao Li; Adam McDermaid; Daniel H. Chitwood; Anne Fennell; Laszlo G. Kovacs; Misha Kwasniewski; Jason P. Londo; Qin Ma; Allison J. Miller. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. 2018, 484212 .

AMA Style

Zoe Migicovsky, Zachary N. Harris, Laura L. Klein, Mao Li, Adam McDermaid, Daniel H. Chitwood, Anne Fennell, Laszlo G. Kovacs, Misha Kwasniewski, Jason P. Londo, Qin Ma, Allison J. Miller. Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard. . 2018; ():484212.

Chicago/Turabian Style

Zoe Migicovsky; Zachary N. Harris; Laura L. Klein; Mao Li; Adam McDermaid; Daniel H. Chitwood; Anne Fennell; Laszlo G. Kovacs; Misha Kwasniewski; Jason P. Londo; Qin Ma; Allison J. Miller. 2018. "Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard." , no. : 484212.

Journal article
Published: 01 September 2018 in Journal of Proteomics
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Certain grapevine genotypes become dormant in response to decreasing photoperiod and others require low temperature or both environmental cues to induce dormancy. This study used a proteomic approach to gain an understanding of the underlying molecular events involved in bud dormancy commitment. Two F siblings (F2-110 and F2-040) with differences in photoperiod induced dormancy responsiveness were subjected to long day (LD, 15 h, paradormancy maintenance or dormancy inhibition) or short day (SD, 13 h, endodormancy commitment) treatment. Proteins were extracted at two time points (28 days and 42 days) of LD and SD photoperiod exposure, and label-free quantitative shotgun proteomic analysis was performed for three biological replicates of each treatment and time point. A total of 1577 non-redundant proteins were identified in the combined dataset of eight different conditions (2 genotypes, 2 photoperiods and 2 timepoints, available via ProteomeXchange with identifier PXD001627). Genotype specific patterns of budbreak and protein expression were detected in response to the differential photoperiod treatment at the two time points. Peroxidases, dehydrogenases and superoxide dismutases were more abundant at 42 SD than at 28 SD in the dormancy responsive F2-110, suggesting that oxidative stress response related proteins could be markers of endodormancy commitment in grapevine buds.

ACS Style

Iniga George; Anne Y. Fennell; Paul A. Haynes. Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine. Journal of Proteomics 2018, 187, 13 -24.

AMA Style

Iniga George, Anne Y. Fennell, Paul A. Haynes. Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine. Journal of Proteomics. 2018; 187 ():13-24.

Chicago/Turabian Style

Iniga George; Anne Y. Fennell; Paul A. Haynes. 2018. "Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine." Journal of Proteomics 187, no. : 13-24.

Journal article
Published: 19 March 2018 in Separations
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Understanding the aroma profile of wines made from cold climate grapes is needed to help winemakers produce quality aromatic wines. The current study aimed to add to the very limited knowledge of aroma-imparting compounds in wines made from the lesser-known Frontenac and Marquette cultivars. Headspace solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) with simultaneous olfactometry was used to identify and quantify selected, aroma-imparting volatile organic compounds (VOC) in wines made from grapes harvested at two sugar levels (22° Brix and 24° Brix). Aroma-imparting compounds were determined by aroma dilution analysis (ADA). Odor activity values (OAV) were also used to aid the selection of aroma-imparting compounds. Principal component analysis and hierarchical clustering analysis indicated that VOCs in wines produced from both sugar levels of Marquette grapes are similar to each other, and more similar to wines produced from Frontenac grapes harvested at 24° Brix. Selected key aroma compounds in Frontenac and Marquette wines were ethyl hexanoate, ethyl isobutyrate, ethyl octanoate, and ethyl butyrate. OAVs >1000 were reported for three aroma compounds that impart fruity aromas to the wines. This study provides evidence that aroma profiles in Frontenac wines can be influenced by timing of harvesting the berries at different Brix. Future research should focus on whether this is because of berry development or accumulation of aroma precursors and sugar due to late summer dehydration. Simultaneous chemical and sensory analyses can be useful for the understanding development of aroma profile perceptions for wines produced from cold-climate grapes.

ACS Style

Somchai Rice; Nanticha Lutt; Jacek A. Koziel; Murlidhar Dharmadhikari; Anne Fennell. Determination of Selected Aromas in Marquette and Frontenac Wine Using Headspace-SPME Coupled with GC-MS and Simultaneous Olfactometry. Separations 2018, 5, 20 .

AMA Style

Somchai Rice, Nanticha Lutt, Jacek A. Koziel, Murlidhar Dharmadhikari, Anne Fennell. Determination of Selected Aromas in Marquette and Frontenac Wine Using Headspace-SPME Coupled with GC-MS and Simultaneous Olfactometry. Separations. 2018; 5 (1):20.

Chicago/Turabian Style

Somchai Rice; Nanticha Lutt; Jacek A. Koziel; Murlidhar Dharmadhikari; Anne Fennell. 2018. "Determination of Selected Aromas in Marquette and Frontenac Wine Using Headspace-SPME Coupled with GC-MS and Simultaneous Olfactometry." Separations 5, no. 1: 20.

Preprint
Published: 16 March 2018
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MotivationNext-Generation Sequencing has made available much more large-scale genomic and transcriptomic data. Studies with RNA-sequencing (RNA-seq) data typically involve generation of gene expression profiles that can be further analyzed, many times involving differential gene expression (DGE). This process enables comparison across samples of two or more factor levels. A recurring issue with DGE analyses is the complicated nature of the comparisons to be made, in which a variety of factor combinations, pairwise comparisons, and main or blocked main effects need to be tested.ResultsHere we present a tool called IRIS-DGE, which is a server-based DGE analysis tool developed using Shiny. It provides a straightforward, user-friendly platform for performing comprehensive DGE analysis, and crucial analyses that help design hypotheses and to determine key genomic features. IRIS-DGE integrates the three most commonly used R-based DGE tools to determine differentially expressed genes (DEGs) and includes numerous methods for performing preliminary analysis on user-provided gene expression information. Additionally, this tool integrates a variety of visualizations, in a highly interactive manner, for improved interpretation of preliminary and DGE analyses.AvailabilityIRIS-DGE is freely available at http://bmbl.sdstate.edu/IRIS/[email protected] informationSupplementary data are available at Bioinformatics online.

ACS Style

Brandon Monier; Adam McDermaid; Jing Zhao; Anne Fennell; Qin Ma. IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression. 2018, 283341 .

AMA Style

Brandon Monier, Adam McDermaid, Jing Zhao, Anne Fennell, Qin Ma. IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression. . 2018; ():283341.

Chicago/Turabian Style

Brandon Monier; Adam McDermaid; Jing Zhao; Anne Fennell; Qin Ma. 2018. "IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression." , no. : 283341.

Review
Published: 27 February 2018 in Briefings in Bioinformatics
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Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes. However, there is still a considerable gap between biclustering methodology development and comprehensive data interpretation, mainly because of the lack of knowledge for the selection of appropriate biclustering tools and further supporting computational techniques in specific studies. Here, we first deliver a brief introduction to the existing biclustering algorithms and tools in public domain, and then systematically summarize the basic applications of biclustering for biological data and more advanced applications of biclustering for biomedical data. This review will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency.

ACS Style

Juan Xie; Anjun Ma; Anne Fennell; Qin Ma; Jing Zhao. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Briefings in Bioinformatics 2018, 20, 1450 -1465.

AMA Style

Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Briefings in Bioinformatics. 2018; 20 (4):1450-1465.

Chicago/Turabian Style

Juan Xie; Anjun Ma; Anne Fennell; Qin Ma; Jing Zhao. 2018. "It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data." Briefings in Bioinformatics 20, no. 4: 1450-1465.

Comparative study
Published: 17 January 2018 in BMC Genomics
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De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families. The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.

ACS Style

Sagar Patel; Zhixiu Lu; Xiaozhu Jin; Padmapriya Swaminathan; Erliang Zeng; Anne Y. Fennell. Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly. BMC Genomics 2018, 19, 57 .

AMA Style

Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y. Fennell. Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly. BMC Genomics. 2018; 19 (1):57.

Chicago/Turabian Style

Sagar Patel; Zhixiu Lu; Xiaozhu Jin; Padmapriya Swaminathan; Erliang Zeng; Anne Y. Fennell. 2018. "Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly." BMC Genomics 19, no. 1: 57.

Communication
Published: 18 September 2017 in Fermentation
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Cold-hardy grape cultivars have become popular in northern regions. Wines from these cultivars are low in tannins and lighter in color compared to Vitis vinifera. The northern regions are striving to enhance desired ″full body″ and red color qualities in the wine produced from cold-hardy grapes. The objective of this study was to compare tannin and pigment content in skins and seeds of three cold-hardy red grape cultivars, at two time points, from two locations, using the Adams-Harbertson (A-H) assay. The A-H assay is based on protein precipitation and spectrophotometry. Total tannin concentrations detected in Frontenac, Marquette, and St. Croix berries, ranged from 0.29 to 0.66 mg/berry catechin equivalents (CE). Bitter seed tannins were most abundant in Marquette berries (0.54 ± 0.66 mg/berry CE). Softer skin tannins were most abundant in St. Croix berries (0.24 ± 0.19 mg/berry CE). Monomeric anthocyanins contributed to over 60% of the total color at pH 4.9 and were highest in St. Croix skins (74.21% of the total color at pH 4.9). Varying amounts of short polymeric pigments and long polymeric pigments were present in grape skins, indicating that pigmented tannins had already formed by harvest. This is the first evaluation of tannins and pigments in Frontenac, Marquette, and St. Croix berries.

ACS Style

Somchai Rice; Jacek A. Koziel; Murlidhar Dharmadhikari; Anne Fennell. Evaluation of Tannins and Anthocyanins in Marquette, Frontenac, and St. Croix Cold-Hardy Grape Cultivars. Fermentation 2017, 3, 47 .

AMA Style

Somchai Rice, Jacek A. Koziel, Murlidhar Dharmadhikari, Anne Fennell. Evaluation of Tannins and Anthocyanins in Marquette, Frontenac, and St. Croix Cold-Hardy Grape Cultivars. Fermentation. 2017; 3 (3):47.

Chicago/Turabian Style

Somchai Rice; Jacek A. Koziel; Murlidhar Dharmadhikari; Anne Fennell. 2017. "Evaluation of Tannins and Anthocyanins in Marquette, Frontenac, and St. Croix Cold-Hardy Grape Cultivars." Fermentation 3, no. 3: 47.