Progress 05/01/24 to 04/30/25
Outputs
Target Audience:This research has led to the development of the first genetic linkage map for the 'Norton' grape incorporating both SSR and rhAmpSeq haplotype markers. The integration of these markers has significantly enhanced marker density and provided a strong foundation for future grape breeding efforts. Research findings have been presented at several professional events, including the 2024 American Society for Enology and Viticulture - Eastern Section Annual Conference, the 2025 VitisGen3 Annual Advisory Meeting, the 2025 Show Me State Grape and Wine Symposium, the 31stFrank Einhellig Graduate Interdisciplinary Forum, and the Missouri Wine and Grape Research Board meeting. Beyond professional conferences, the results have also been shared at grower meetings in collaboration with viticulture and enology advisors to help educate growers on the value of marker-assisted selection andthe benefits of improving 'Norton'.Additionally, Missouri State University maintains an online blog through MSFES, where new insights and knowledge from this study have been disseminated to the general public. Changes/Problems:None What opportunities for training and professional development has the project provided?Linking the educational, research and extension resources with the V. aestivalis-derived 'Norton' grape breeding program within the College of Agriculture (COAG) at Missouri State University (MSU), Grape and Wine Institute (GWI) at University of Missouri (MU) and VitisGen3 program at Cornell University and University of Minnesota, this proposed work includes interdisciplinary training opportunities for students in plant breeding, genetics, genomics and metabolomics with a specific focus on grapevine rooting ability traits. The following are the core competencies that have been provided. Build Research CapacityMapping population maintenance Haplotype marker development via rhAmpSeq technology Linkage map construction using both SSR and Haplotype markers Conduction of a segregation analysis for root ability related traits Quantitative Trait Loci (QTLs) identification via R package Utilization of molecular markers to be applied for future marker-assisted selection Build Educational Capacity Comprehension of the basics and application of various molecular marker techniques Acquaintance with grapevine rooting ability assessments Familiarity with SSR and haplotype markers applications in grapevine breeding Implementation of marker-assisted selection into teaching materials for students to understand the plant molecular breeding concept Ability to make public presentations and write reports and manuscripts for publication Build Experiential Extension and Viticulture Capacity While advanced degrees often focus on narrow research questions, Dr. Volenberg provides graduate students with broader learning opportunities through viticulture and Extension engagement. Specifically, extension allows students to build professional relationships with grape growers, vineyard managers and other professionals. These relationships begin with simple introductions and grow through consistent interaction and trust. Students come to see that Extension is not just about solving viticulture problems--it's also about understanding the people behind the vineyards and connecting with their individual goals and challenges. Over time, vineyards become more than just places; they become part of a shared community. Students learn the value of listening, teamwork, and admitting when they don't have all the answers. As a graduate student advisor, it is inspiring to witness a student confidently admit they don't know the answer but commit to consulting others and following up with the grower. These real-world experiences offer lessons that go far beyond the classroom. Undergraduates: Students were invited to attend a viticulture and enology conference conducted through the University of Missouri Grape and Wine Institute on March 5-7, 202. 5 Graduate Students: Jacob Schneider (August 2020 - Present): Genetic Study of Grapevine Rooting Ability from Dormant Hardwood Cuttings Achyut Duwadi (August 2022 - May 2024): GeneticCharacterization of Botrytis Bunch Rot Resistance in Viitis aestivalis-derived 'Norton'-based Populatiion Tabinda Shahid:(August 2022 - May 2024): Cold Hardiness in Vitis Interspecific Hybrid 'Chambourcin'-based Population Qiuni Yang (August 2023 - Present): Berry Quality in Vitis Interspecific Hybrid 'Chambourcin'-based Population How have the results been disseminated to communities of interest?Chin-Feng Hwang, Li-Ling Chen, Achyut Duwadi, Surya Sapkota, Cheng Zou and Lance Cadle-Davidson, "Discovery of a Novel Locus Associated with Grapevine Powdery Mildew Susceptibility", 2025 Show Me State Symposium, Columbia, Missouri, March 05, 2025 - An Oral Presentation. Qiuni Yang, Li-Ling Chen and Chin-Feng Hwang, "Identification of a Stable QTL for Juice Color in a Vitis Interspecific Hybrid 'Chambourcin'-based Population", 2025 Show Me State Symposium, Columbia, Missouri, March 05, 2025 - An Oral Presentation. Jacob Schneider, Li-Ling Chen and Chin-Feng Hwang, "Genetic study of Dormant Rooting in a Vitis aestivalis-based population", VitisGen3 Annual Meeting, San Diego, California, January 09, 2025 - An Oral Presentation. Qiuni Yang, Li-Ling Chen and Chin-Feng Hwang, "Identification of a Juice Color QTL from a 'Chambourcin'-derived Population", VitisGen3 Annual Meeting, San Diego, California, January 09, 2025 - An Oral Presentation. Jacob Schneider, Li-Ling Chen and Chin-Feng Hwang, "Marker Discovery for Adventitious Rooting in Dormant Hardwood Cuttings of Grapevine," 48th American Society for Enology and Viticulture-Eastern Section, American Society for Enology and Viticulture, Cleveland, OH, July 10, 2024 - An Oral Presentation. Chin-Feng Hwang, Li-Ling Chen and Achyut Duwadi, "Optimizing 'Chambourcin' Grape Breeding Using Molecular Genetic Approaches," 48th American Society for Enology and Viticulture-Eastern Section, American Society for Enology and Viticulture, Cleveland, OH, July 10, 2024 - An Oral Presentation. Dean Volenberg, Viticulture updates: focus on evaluating cold damage. Missouri Grape Growers Association Annual Viticulture Field Day. Lake of the Ozarks. June 11, 2024 Dean Volenberg, Grape growing: The science and art. Thescience and art. Missouri Vocational Agriculture Teachers Association. July 24, 2024. Springfield, MO Dean Volenberg, Wine faults and off-flavors. Missouri Vocational Agriculture Teachers Association. July 24, 2024. Springfield, MO Dean Volenberg, Grapes of the South Midwest. The First Midwest Sommelier Festival. August 18, 2024. Hermann, MO Dean Volenberg, and Stephan Sommer. 2024. Missouri Annual Report to NE2220: Multi-state Coordinated Evaluation of Grape Cultivars and Clones. October 22-25, Ames, IA Dean Volenberg, Introduction to viticulture. Missouri State University, AGP 575/675 Plant Breeding and Genetics course. February 6, 2025 Melanie Carrahher, Jim Schoelz, and Dean Volenberg, 2025. Prevalence of Grapevine Vein Clearing Virus in Missouri vineyards. Show Me Grape and Wine Conference and Symposium. March 5, 2025. Columbia, MO Dean Volenberg, 2025. Viticulture updates: Focus on powdery mildew. Show Me Grape and Wine Conference and Symposium. March 6, 2025. Columbia, MO Dean Volenberg, 2025. Markets and cost of establishment. Beginner Grape School. March 7, 2025. Columbia, MO Dean Volenberg, Site selection and successful vineyard establishment. Beginner Grape School. March 7, 2025. Columbia, MO Dean Volenberg, Grape insect pests and management. Beginner Grape School. March 7, 2025. Columbia, MO What do you plan to do during the next reporting period to accomplish the goals?Submit the final report by July 2025
Impacts
What was accomplished under these goals?
Objective 1 - Build Research Capacity for Grapevine Improvement at MSU and MU 1.1. Construct a Norton linkage map using both SSR and rhAmpSeq-based SNP markers A mapping population consisting of 273 F1 genotypes was developed from a cross between 'Norton' and 'Cabernet Sauvignon.' This population was utilized to construct an improved high-resolution consensus map in LepMAP3. The map incorporates 356 simple sequence repeats (SSRs) and 1,522 RNase H2-dependent amplicon sequencing (rhAmpSeq) markers. A total of 1,918 markers were clustered into 19 linkage groups, spanning a genetic distance of 1,663.05 centimorgan (cM) with an average inter-marker distance of 0.87 cM. 1.2. Conduct a two-year segregation analysis of the entire F1 mapping population for rooting ability from the hardwood dormant cuttings Measured traits include the average root number, longest main root, rooting percentage, total surface area, and morphological rank of overall rooting percentage (0-4). All traits segregated. Statistical analysis of the phenotypes showed some weak positive correlations with each other, for instance root number with total root length. There were none to small correlations between phenotypes and the cane parameters, such as node number, cane weight or length and diameter. Each trait analyzed segregated in non-Mendelian fashion, as a complex quantitative trait and was used for further QTL analyses. 1.3. Identify DNA markers associated with the rooting ability for future marker-assisted selection The linkage map was further developed using LepMAP3, and four phenotypes (average root number, longest main root, rooting percentage and surface area) were analyzed using R/QTL. Results from four years showed potential marker-trait associations on the linkage groups shown below, along with the respective LODs and associated markers. Note that three QTL were stable across two years: average root number in 2018 and 2022, surface area in 2022 and 2023, and percent rooting in 2021 and 2022. No other traits showed up across years. Many LG's showed similar regions of interest for the other phenotypes, such as 4, 5, 9, 18, and 19. Average Root Number: LG-18 ('18); POS 9.83; LOD 3.736; Marker- rh_chr18_2813601 Average Root Number: LG-18 ('22); POS 12.95; LOD 5.459; Marker- rh_chr18_3488083 Average Root Number: LG 13 ('22); POS 70.63; LOD 4.564; Marker - SC8_0071_075 Longest Main Root: LG 9 ('22); POS 25.68; LOD 4.61; Marker- rh_chr9_6523189 Longest Main Root: LG 18 ('23); POS 1.78; LOD 6.26; Marker- rh_chr18_227536 % Rooting: LG 19 ('21, '22*); POS 34.70; LOD 3.900; Marker- rh_chr19_3429612 % Rooting: LG 9 ('21*, '22); POS 25.70; LOD; 4.080; Marker- rh_chr9_6523189 % Rooting: LG 8 ('23); POS 43.90; LOD 4.710; Marker- rh_chr8_13104592 Surface Area: LG 4 ('22); POS 8.05; LOD 4.09; Marker- rh_chr4_130509 Surface Area: LG 4 ('23); POS 27.5; LOD 4.22; Marker- BM438035 *Borderline significance warrants further analysis. Objective 2 - Build Educational Capacity of MSU and MU 2.1. Incorporate rooting ability phenotyping concept in the "Plant Breeding and Genetics" course Dr. Hwang continues to teach the Plant Breeding and Genetics course, which provides a comprehensive introduction to the principles of classical breeding and biotechnology. In Spring 2025, five students (4 undergraduates and 1 graduate) enrolled in the course. The curriculum emphasizes lectures on the development of SSR and SNP markers in grapevine, marker-assisted selection for F1 hybrid identification, rooting ability phenotyping using WinRHIZO software and linkage mapping. Student feedback highlights that understanding advanced molecular breeding technologies is crucial for enhancing their competitiveness in the job market. 2.2. Offer hands-on experience on grapevine interspecific hybrid identification using DNA markers in the "Plant Breeding and Genetics Lab" course Dr. Hwang and Li-Ling Chen, Clinical Instructor, continue to offer the 576/AGP 676 laboratory hands-on course in Spring 2025. This course focuses on teaching general techniques including 1) isolation of DNA from grape leaves, 2) determination of the concentration of isolated DNA using a NanoDrop, 3) performance of PCR, 4) visualization of DNA via electrophoresis and 5) running a DNA fragment analysis via capillary electrophoresis. These procedures are utilized to verify the true hybrids at the seedling stage by using SSR markers. A total of 22 students (21 undergraduates and 1 graduate student) will complete the course in May 2025. Of the undergraduate students, 17 are from Southwest University in Chongqing, China. They are enrolled in a 3+1 dual degree program, which started in 2019, between Missouri State University and Southwest University, with an emphasis on plant breeding and biotechnology. 2.3. Provide two graduate assistantships to work on grape molecular breeding program Three graduate students, Achyut Duwadi and Tabinda Shahid (starting August 2022 and completed MS degree May 2024) as well as Qiuni Yang (starting August 2023) were recruited into the Plant Science graduate program under the support of this project. The key skills they have learned include emasculation of grapevine flowers, pollination, seed germination, propagation of cuttings, assessment of disease index and vineyard management; laboratory skills include DNA extraction, PCR, analysis of SSRs via capillary electrophoresis, analysis of rhAmpSeq markers via TASSEL software, construction of the linkage map using LepMap software, mapping of quantitative trait loci (QTLs) via R package and phenotyping data collection. The anticipated graduation date for Qiuni Yang is scheduled for May 9th, 2025. Objective 3 - Build Experiential Extension and Viticulture Capacity at MSU and MU 3.1. Provide graduate students experiential Extension opportunities with grape growers, workshops and conferences Graduate and undergraduate students attended the Missouri Grape Growers Association Field Day on June 11, 2024. Among them were entomology graduate students whose research on insect diversity in vineyards overlapped with viticulture. They sought to better understand common insect pests and their management strategies. Their interest highlights how educators can offer hands-on, interdisciplinary experiences in areas like host-plant insect interactions. Graduate students involved in research in viticulture or enology were invited to participate in the Show Me Grape and Wine Symposium on March 5, 2025. Students were informed about the demographics of their audience, allowing them to craft messages that resonate with their target audience. Students were also encouraged to clearly explain how their research findings can be applied and provide attendees with relevant examples. Providing graduate students with the opportunity to interact with end-users of their research fosters the expansion of critical thinking regarding their work. 3.2. Provide graduate students experiential viticulture opportunities in commercial vineyards and MSU and MU vineyards Graduate students were exposed to the signs and symptomology of the five major diseases in Missouri vineyards, along with pest identification, environmental factors influencing disease, and host-plant responses. They also learned how weather conditions impact disease incidence and studied grapevine-virus interactions through plant responses. After training in the vineyard, students visited commercial vineyards to identify pest problems and engage with growers. The process of solving vineyard issues demonstrates the need to examine affected vines, understand vineyard management practices, and sometimes conduct petiole analysis to diagnose nutrient deficiencies. These outings highlighted the collaborative process between extension, research, and growers, providing students with both technical knowledge and hands-on experience in addressing vineyard challenges.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
Dustin G. Wilkerson, Cheng Zou, Qi Sun, Qandeela Nigar, Manon Paineau, Dario Cantu, Chin-Feng Hwang, and Lance Cadle-Davidson. "Comparative Genomics of Rpv3, a Multiallelic Downy Mildew Resistance Locus in Grapevine (Vitis sp.)"
- Type:
Peer Reviewed Journal Articles
Status:
Awaiting Publication
Year Published:
2025
Citation:
Achyut Duwadi, Surya Sapkota, Cheng Zou, Li-Ling Chen, Lance Cadle-Davidson and Chin-Feng Hwang. "A Novel Susceptibility Locus to Erysiphe necator (SEN2) Identified by Genetic Mapping of Automated Microscopy Computer Vision Data in Grapevines"
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2024
Citation:
Achyut Duwadi. Construction of a Linkage Map Using Novel DNA Markers and QTL Detection of Grapevine Powdery Mildew Resistance in 'Chambourcin'-based Hybrids
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2024
Citation:
Tabinda Shahid. Cold Hardiness in Vitis Interspecific Hybrid 'Chambourcin'-based Population
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Progress 05/01/23 to 04/30/24
Outputs
Target Audience:This research has led to the construction of the first genetic linkage map with both SSR andrhAmpSeq-derived haplotype markers for the 'Norton' grape.The integration of both SSR andrhAmpSeq-derived haplotype markers to construct a high-resolution 'Norton' linkage map has greatly assisted in improving marker-density and served as a foundation for future grape breeding.Research results have been presented at the VitisGen3 Annual Advisory meeting, 2023 American Society for Enology and Viticulture - Eastern Section Annual Conference, 2023 North American Grape Breeders Conference, 2024 Show Me State Grape and Wine Symposium, 30thFrank Einhellig Graduate Interdisciplinary Forum and Missouri Wine and Grape Research Board meeting.In addition to the professional conferences, the results have also been presented at grower meetings in conjunction with viticulture/enology advisors to better educate growers on the value of molecular breeding and the benefits of improving 'Norton'.In addition, MSU maintains an on-line Blog at MSFES; the new knowledge produced from this study has been disseminated to the general public through it. Changes/Problems:None What opportunities for training and professional development has the project provided?Linking the educational, research and extension resources with theV. aestivalis-derived 'Norton' grape breeding program within the College of Agriculture (COAG) at Missouri State University (MSU), Grape and Wine Institute (GWI) at University of Missouri (MU) and VitisGen3 program at Cornell University and University of Minnesota, this proposed work includes interdisciplinary training opportunities for students in plant breeding, genetics, genomics and metabolomics with a specific focus on grapevine rooting ability traits.The following are the core competencies that have been provided. Build Research Capacity 1.Mapping population maintenance 2. Haplotype marker development via rhAmpSeq technology 3. Linkage map construction using both SSR and rhAmpSeq-derived haplotype markers 4. Conduction of a segregation analysis for root ability related traits 5. Quantitative Trait Loci (QTLs) identification via R package 6. Utilization of molecular markers to be applied for future marker-assisted selection Build Educational Capacity 1. Comprehension of the basics and application of various molecular marker techniques 2. Acquaintance with grapevine rooting ability assessments 3. Familiarity with SSR and rhAmpSeq-derived haplotype markerapplications in grapevine breeding 4. Implementation of marker-assisted selection into teaching materials for students to understand the plant molecular breeding concept 5. Ability to make public presentations and write reports and manuscripts for publication Build Experiential Extension and Viticulture Capacity Advanced degrees tend to narrow learning to a specific question or two.Dr. Volenberg has provided graduate students the opportunity to expand learning both in Viticulture and Extension engagement.Specifically, Extension has provided students the opportunity to explore the development of establishing professional relationships with grape growers, vineyard managers and other vineyard professionals.Like most relationships, they start with an introduction of people and progress with building trust.Also, students realize that meeting with clientele involves not only solving viticulture-related problems but engaging with clients about their particular interests.Building a connection beyond what initially brought people together.Students saw first-hand and experienced the building of community.Over time, students begin to associate a particular vineyard with a grape grower or vineyard manager.The vineyard is no longer just a place.Graduate students look forward to working with growers and understand that listening to growers provides them an opportunity to learn.As students venture alone into the vineyards and work with growers, they soon realize the importance of how teamwork can help solve a problem.Yet not naïve, many students quickly realize that they do not have an answer for growers all the time.As a graduate student advisor, observing a student say that they do not know to a grower but will talk with others and communicate back to the grower is aspiring. Observing these lessons beyond the classroom only comes by providing students withexperiences. Student Training Opportunities Provided Undergraduates: Students were invited to attend a viticulture and enology conference conducted through the University of Missouri Grape and Wine Institute on March 13-15, 2024. Graduate Students: Jacob Schneider (August 2020 - Present): Genetic Study of Grapevine Rooting Ability from Dormant Hardwood Cuttings AchyutDuwadi(August 2022 - Present): Characterization of Penicillium chrysogenum resistance in 'Norton'-based Hybrids Tabinda Shahid (August 2022- Present): Cold Hardiness in Vitiis Interspecific Hybrid 'Chambourcin'-based Population Qiuni Yang (August 2023 - Present): Berry Quality inVitisInterspecific Hybrid 'Chambourcin'-based Population? How have the results been disseminated to communities of interest?Achyut Duwadi, Li-Ling Chen, and Chin-Feng, Hwang,Genetic Study of Powdery Mildew Resistance in a Vitis Interspecific Hybrid 'Chambourcin'-based Population, Annual Frank Einhellig Graduate Interdisciplinary Forum, April 27, 2024-A Poster Presentation. Tabinda Shahid, Li-Ling Chen and Chin-Feng Hwang,Cold Hardiness inVitisInterspecific Hybrid "Chambourcin"-based Population, Annual Frank Einhellig Graduate Interdisciplinary Forum, April 27, 2024 -A Poster Presentation. Qiuni Yang, Li-Ling Chen and Chin-Feng Hwang,Optimization of PCR Conditions for the Linkage Map Construction from a 'Jaeger 70' Grape-based Population, Annual Frank Einhellig Graduate Interdisciplinary Forum, April 27, 2024 -A Poster Presentation. Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding via Marker-assisted Selection, 2024 Show Me State Symposium, Columbia, Missouri, March 13, 2024-A Oral Presentation. Chin-Feng Hwangand Li-Ling Chen, Optimizing Grape Breeding Using Molecular Genetic Approaches, VitisGen3 Annual Meeting, San Diego, California, January 11, 2024 -An Oral Presentation. Jacob Schneider, Li-Ling Chen and Chin-Feng Hwang,Genetic Study of Dormant Rooting in Grapes, 2023North American Grape Breeders Conference, Fayetteville, Arkansas, October 3, 2023 -An Oral Presentation. Achyut Duwadi, Li-Ling Chen and Chin-Feng Hwang,Discovery of a QTL fromVitisaestivalis-derived 'Norton' for Postharvest Berry Rot Resistance, 2023North American Grape Breeders Conference, Fayetteville, Arkansas, October 3-4, 2023 -A Poster Presentation. Tabinda Shahid, Li-Ling Chen and Chin-Feng Hwang,Cold Hardiness in 'Chambourcin'-based Hybrids, 2023North American Grape Breeders Conference, Fayetteville, Arkansas, October 3-4, 2023 -A Poster Presentation. In additional to being the keynote speaker at the "2ndSymposium of Grape Genetics and Breeding" in Qingdao, China; Dr. Hwang delivered 5 seminars at 5 different University in 5 days. Please see the list below for details Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding Using Molecular Genetic Approaches, 2ndSymposium of Grape Genetics and Breeding, Qingdao, Shandong, China, August 26, 2023-An Oral Presentation. Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding via Marker-assisted Selection, Shandong Agricultural University, Taian, Shandong, China, August 25, 2023-An Oral Presentation. Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding Using Molecular Genetic Approaches, Zhengzhou Fruit Research Institute, Zhengzhou, Henan, China, August 24, 2023-An Oral Presentation. Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding via Marker-assisted Selection, Northwest A&F University, Yangling, Shaanxi, China, August 23, 2023,-An Oral Presentation. Chin-Feng Hwangand Li-Ling Chen,Optimizing Grape Breeding Using Molecular Genetic Approaches, Nanjing Agricultural University, Nanjing, Jangsu, China, August 22, 2023,-An Oral Presentation. Tabinda Shahid, Li-Ling Chen and Chin-Feng Hwang,Cold Hardiness in Chambourcin-based Hybrids, 47th American Society for Enology and Viticulture - Eastern Section Conference,Austin, Texas, June 8, 2023-An Oral Presentation. Achyut Duwadi, Li-Ling Chen, and Chin-Feng Hwang,Genetic Study of Postharvest Berry Rot Resistance in aVitis aestivalis-derived 'Norton'-based Population, 47thAmerican Society for Enology and Viticulture-Eastern Section, Austin, Texas, June 8-9, 2023-A Poster Presentation. (Best Poster Winer in Viticulture) Dean Volenberg, C. R. Adams, H. F. LaFond, Z. D. Fang, C. Spinka and J. E. Schoelz. 2023. Virus infections impact on berry juice quality in the interspecific cultivar Norton" ASEV-ES, June 7-9, 2023, Austin TX Dean Volenberg, Weather extremes in 2022 and 2023: What they mean for grapevines. Missouri Grape Growers Association Field Day, June 13, 2023. Augusta, MO Dean Volenberg, Growing grapes in the home garden. Discovery Garden Club, July 10, 2023, Columbia, MO Dean Volenberg, S. Sommer and L. Morton. Uncoupling Norton and Cynthiana with deep genomic sequencing. North American Grape Breeders Conference and Vitis-Muscadinia Alliance Conference, October 3-5, 2023, Fayettville, AR Dean Volenbergand S. Sommer. Wines and Vines of Missouri. American Wine Society annual meeting. November 10, 2023. St. Louis, MO. Dean Volenberg, Introduction to viticulture. Missouri State University, AGP 575/675 Plant Breeding and Genetics course. February 8, 2024. Jim Schoelz and Dean Volenberg, Grapevine vein clearing virus: Determining the incidence of GVCV during the year of establishment. Show Me Grape and Wine Conference and Symposium. March 13, 2024. Columbia, MO. Dean Volenberg,Norton and Cynthiana: history, lineage, genetic relationship and of course the wine. Show Me Grape and Wine Conference and Symposium. March 14, 2024. Columbia, MO. Dean Volenberg, Markets and cost of establishment. Beginner Grape School. March 15, 2024. Columbia, MO. Dean Volenberg, Site selection and successful vineyard establishment. Beginner Grape School. March 15, 2024. Columbia, MO. Dean Volenberg, Grape insect pests and management. Beginner Grape School. March 15, 2024. Columbia, MO. Dean Volenberg, Grape diseases and management. Beginner Grape School. March 15, 2024. Columbia, MO. Dean Volenberg, Managing non-bearing grapevines. Beginner Grape School. March 15, 2024. Columbia, MO. Dean Volenberg, Managing bearing grapevines. Beginner Grape School. March 15, 2024. What do you plan to do during the next reporting period to accomplish the goals?1. Maintain the existing mapping populations of Norton xCabernet Sauvignon at MSFES. 2. Analyze the rooting ability phenotyping data using WinZHIZO software 3. Localize the QTLs for rooting ability related traits. 4. Continue to teach "Plant Breeding and Genetics" and "Plant Breeding and Genetics Lab"courses with input from students and advisory committee. 5. Implement rhAmpSeq-derived haplotype makertechnology and rooting ability phenotyping protocols into VESTA online courses 6. Submit annual report in April 2025 and final report in July 2025, respectively
Impacts
What was accomplished under these goals?
Objective 1 - Build Research Capacity for Grapevine Improvement at MSU and MU 1.1. Construct a Norton linkage map using both SSR and rhAmpSeq-based SNP markers A mapping population with 273 F1genotypes was developed from a cross between 'Norton' and 'Cabernet Sauvignon' from which ahigh-resolutionconsensus map was constructed via356 simple sequence repeats (SSRs) and 1,368 RNase H2-dependent amplicon sequencing (rhAmpSeq)-derived haplotype markers.A total of 1,724 markers were clustered into 19 linkage groups, spanning a genetic distance of 1,360 centimorgan (cM). 1.2. Conduct a two-year segregation analysis of the entire F1mapping population for rooting ability from the hardwood dormant cuttings Measured traits include the longest main root, lateral root length, total root length, root number, and morphological rank of overall rooting ability (0-4).All traits segregated. Statistical analysis of the phenotypes showed some weak positive correlations with each other, for instance root number with total root length. There were none to small correlations between phenotypes and the cane parameters, such as node number, cane weight or length and diameter. Each trait will be further analyzed for its potential use as a quantitative phenotype for trait-genotype association, i.e. QTL. 1.3. Identify DNA markers associated with the rooting ability for future marker-assisted selection The first year was analyzed during the second year. During the third year, the second-year data was analyzed.Additionally, the linkage map was further developed using LepMAP3, and two phenotypes (Longest main root and Root number) were analyzed using R/QTL.Preliminary results of year two showed potential marker-trait associations on the linkage groups shown below, with the respective LODs and flanking markers. Root number: 13 (4.5) with flanking markers rh_chr13_15736455 and rh_chr13_16320948 Longest main root: 5 (6.1) with flanking markers rh_chr5_4744451 and rh_chr5_196931 Objective 2 - Build Educational Capacity of MSU and MU 2.1. Incorporate rooting ability phenotyping concept in the "Plant Breeding and Genetics" course Dr. Hwang continues to offer the Plant Breeding and Genetics course, which serves as a general introduction to the principles of classical breeding and biotechnology.Nine (6 undergraduate and 3 graduate) students registered for this course in Spring 2024.Lectures on the development of SSR and SNP marker in grapevine, marker-assisted selection for F1hybrid identification, rooting ability phenotyping using WinZHIZO software and linkage mapping are emphasized.The feedback from students indicates that knowledge of the cutting-edge molecular breeding technology is integral for their competitiveness in the job market. 2.2. Offer hands-on experience on grapevine interspecific hybrid identification using DNA markers in the"Plant Breeding and Genetics Lab" course Dr. Hwang and Li-Ling Chen, Clinical Instructor, continue to offer the 576/AGP 676 laboratory hands-on course in Spring 2024 to teach the general technique including 1) isolation of DNA from grape leaves, 2) determination of the concentration of isolated DNA using a NanoDrop, 3) performance of PCR, 4) visualization of DNA via electrophoresis and 5) running a DNA fragment analysis via capillary electrophoresis.These procedures are used to verify the true hybrids at the seedling stage by using SSR markers.Twenty (18 undergraduate and 2 graduate) students will complete the course in May 2024.Thirteen of undergraduate students participated in this course are from Southwest University, Chongqing, China.They arein a 3+1 dual degree program started in 2019 between Missouri State University and Southwest University with an emphasis on plant breeding and biotechnology. 2.3. Providetwograduate assistantships to work on grape molecular breeding program Three graduate students, Achyut Duwadi andTabinda Shahid (starting August 2022) as well as Qiuni Yang (starting August 2023)were recruited into the Plant Science graduate program under the support of this project.Thekey skillsthey havelearned include emasculation of grapevine flowers, pollination, seed germination, propagation of cuttings, assessment of disease index and vineyard management; laboratory skills include DNA extraction, PCR, analysis of SSRs via capillary electrophoresis, analysis ofrhAmpSeq-derived haplotype markers via TASSEL software, construction of the linkage map using LepMap software, mapping of quantitative trait loci (QTLs) via R packageandphenotyping data collection.The anticipated graduation date for Achyut and Tabinda is scheduled for May 10th, 2024. Jacob Schneider, a fourth-year collaborative Ph.D. student with Texas A&M University, continues the identification of the rooting ability related QTLs described in Objective 1.2 above. Objective 3 - Build Experiential Extension and Viticulture Capacity at MSU and MU 3.1. Provide graduate students experiential Extension opportunities with grape growers, workshops and conferences Graduate and undergraduate students participated in the Missouri Grape Growers Association Field Day on June 13, 2023.Students were exposed to robotic self-propelled vineyard sprayers as well as drone sprayers.These demonstrations expose students to the newest and evolving technologies entering the viticulture market.Moreover, the event provided the opportunity for students to engage with both grape growers and viticulture industry suppliers. Graduate students that are involved in research in viticulture or enology were invited to participate in the Show Me Grape and Wine Symposium on March 13, 2024.Participants in the symposium were from Missouri State University, St. Loius University, University of Missouri andUSDA-ARS Biological Control of Insects Research Laboratory, Columbia, MO.The symposium structure puts graduate students face-to-face with attendees that are the end users of the graduate students' research.These grape growers and winemakers are interested in how the research being presented can be applied to solve problems.Graduate students can address applied applications and address audience members questions at the conclusion of their presentations.Providing graduate students, the opportunity to interact with end-users of their research leads to the expansion of critical thinking of their research.In essence from academic research to applied research.Further, the participation opens the door for graduate students to build collaborations with the members of the grape and wine industry. 3.2. Provide graduate students experiential viticulture opportunities in commercial vineyards and MSU and MU vineyards Previously students and grape growers had the opportunity to learn the key factors in vineyard establishment at the replicated cultivar trial located in Columbia, MO.In 2023, participants were provided the opportunity to learn about managing bearing grapevines.Students and grape growers learned about establishing cordons, managing fruit set in young grapevines and pest management.Pest management changes drastically in bearing grapevines compared to non-bearing grapevines.Prior to these meetings, I engage with graduate students about conducting public meetings.Directing them to focus on the presenter and how the presenter guides the discussion and engages with the participants.Always stressing that learning is a two-way street, that includes both the participants and the presenter.These meetings also provide the opportunity for students to develop professional relationships with industry members.Often these professional relationships provide future internships or job opportunities for students.
Publications
- Type:
Theses/Dissertations
Status:
Under Review
Year Published:
2024
Citation:
Achyut Duwadi. Construction of a Linkage Map Using Novel DNA Markers and QTL Detection of Grapevine Powdery Mildew Resistance in 'Chambourcin'-based Hybrids
- Type:
Theses/Dissertations
Status:
Under Review
Year Published:
2024
Citation:
Cold Hardiness in Vitis Interspecific Hybrid 'Chambourcin'-based Population
- Type:
Journal Articles
Status:
Under Review
Year Published:
2024
Citation:
Achy Diwali, Surya Sapkota, Cheng Zou, Li-Ling Chen, Lance Cable-Davidson and Chin-Feng Hwang (2024). Construction of a linkage map and detection of a new grapevine powdery mildew resistance locus in Chambourcin-based hybrids
|
Progress 05/01/22 to 04/30/23
Outputs
Target Audience:This research has led to the construction of the first genetic linkage map with both SSR and SNP markers for the 'Norton' grape. The integration of both SSR and SNP markers to construct a high-resolution 'Norton' linkage map has greatly assisted in improving marker-density and served as a foundation for future grape breeding. Research results have been presented at the VitisGen3 Annual Advisory meeting, 2023 Show Me State Grape and Wine Symposium, 30th Frank Einhellig Graduate Interdisciplinary Forum and Missouri Wine and Grape Research Board meeting. In addition to the professional conferences, the results have also been presented at grower meetings in conjunction with viticulture/enology advisors to better educate growers on the value of molecular breeding and the benefits of improving 'Norton'. In addition, MSU maintains an on-line Blog at MSFES; the new knowledge produced from this study has been disseminated to the general public through it. Changes/Problems:None What opportunities for training and professional development has the project provided?Linking the educational, research and extension resources with the V. aestivalis-derived 'Norton' grape breeding program within the College of Agriculture (COAG) at Missouri State University (MSU), Grape and Wine Institute (GWI) at University of Missouri (MU) and VitisGen2&3 program at Cornell University and University of Minnesota, this proposed work includes interdisciplinary training opportunities for students in plant breeding, genetics, genomics and metabolomics with a specific focus on grapevine rooting ability traits. The following are the core competencies that have been provided. Build Research Capacity 1. Mapping population maintenance 2. SNP marker development via rhAmpSeq technology 3. Linkage map construction using both SSR and SNP markers 4. Conduction of a segregation analysis for root ability related traits 5. Utilization of molecular markers to be applied for future marker-assisted selection Build Educational Capacity 1. Comprehension of the basics and application of various molecular marker techniques 2. Acquaintance with grapevine rooting ability assessments 3. Familiarity with SSR and SNP markers applications in grapevine breeding 4. Implementation of marker-assisted selection into teaching materials for students to understand the plant molecular breeding concept 5. Ability to make public presentations and write reports and manuscripts for publication Build Experiential Extension and Viticulture Capacity Advanced degrees tend to narrow learning to a specific question or two. Dr. Volenberg has provided graduate students the opportunity to expand learning both in Viticulture and Extension engagement. Specifically, Extension has provided students the opportunity to explore the development of establishing professional relationships with grape growers, vineyard managers and other vineyard professionals. Like most relationships they start with an introduction of people and progress over time building trust. Over time, students realize that meeting with clientele involves not only solving viticulture-related problems but engaging with clients about their particular interests. Building a connection beyond what initially brought people together. Students saw first-hand and experienced the building of community. Over time, students begin to associate a particular vineyard with a grape grower or vineyard manager. The vineyard is no longer just a place. Graduate students look forward to working with growers and understand that listening to growers provides them an opportunity to learn. As students venture alone into the vineyards and work with growers they soon realize the importance of how teamwork can help solve a problem. Yet not naïve, many students quickly realize that they do not have an answer for growers all the time. As a graduate student advisor, observing a student say that they do not know to a grower but will talk with others and communicate back to the grower is aspiring. Observing these lessons beyond the classroom only comes by providing students with experiences. Student Training Opportunities Provided Undergraduates: 15 students were invited to attend a viticulture and enology conference conducted through the University of Missouri Grape and Wine Institute on March 1-3, 2023. Graduate Students: Jacob Schneider (August 2020 - Present): Genetic Study of Grapevine Rooting Ability from Dormant Hardwood Cuttings Achyut Duwadi (August 2022 - Present): Genetic Characterization of PostharvestBerry rot Resistance in Vitis aestivalis-deried 'Norton'-based population Tabinda Shahid (August 2022 - Present): Cold Hardiness in Vitis Interspecific Hybrid 'Chambourcin'-based Population How have the results been disseminated to communities of interest?Achyut Duwadi,Li-Ling Chen, and Chin-Feng, Hwang, Genetic Study of Postharvest Berry Rot Resistance in a Vitis aestivalis - derived 'Norton'-based Population, AnnualFrank Einhellig Graduate Interdisciplinary Virtual Forum, April 29, 2023 - A Poster Presentation Tabinda Shahid,Li-Ling Chen and Chin-Feng Hwang, Cold Hardiness in 'Chambourcin' X 'Cabernet Sauvignon' grapevine population, Annual Frank Einhellig Graduate Interdisciplinary Virtual Forum, April 29, 2023 - A Poster Presentation Jacob Schneider,Li-Ling Chen and Chin-Feng Hwang, Marker Discovery for Adventitious Rooting Ability in Dormant Hardwood Cuttings of Grapevine, 2023 Show Me Grape and Wine Symposium, March 1, 2023 - An Oral Presentation Achyut Duwadi,Li-Ling Chen, and Chin-Feng Hwang, Genetic Study of Botrytis Bunch Rot Resistance in a Vitis aestivalis-derived 'Norton'-based Population, 2023 Show Me Grape and Wine Symposium, March 1, 2023 - An Oral Presentation Tabinda Shahid, Li-Ling Chen and Chin-Feng Hwang, Cold Hardiness in Chambourcin-based Hybrids, 2023 Show Me Grape and Wine Symposium, March 1, 2023 - An Oral Presentation What do you plan to do during the next reporting period to accomplish the goals?1. Maintain the existing mapping populations of Norton x Cabernet Sauvignon at MSFES. 2. Construct a high-resolution Norton linkage map with rhAmpSeq-based SNP markers. 3. Analyze the rooting ability phenotyping data using WinZHIZO software 4. Localize the QTLs for rooting ability related traits. 5. Continue to teach "Plant Breeding and Genetics" and "Plant Breeding and Genetics Lab" courses with input from students and advisory committee. 6. Implement SNP technology and rooting ability phenotyping protocols into VESTA online courses 7. Submit annual report in April 2024 and final report in July 2024, respectively
Impacts
What was accomplished under these goals?
Objective 1 - Build Research Capacity for Grapevine Improvement at MSU and MU 1.1. Construct a Norton linkage map using both SSR and rhAmpSeq-based SNP markers Based on a set of ubiquitous 2,000 RNase H2-dependent amplicon sequencing (rhAmpSeq) markers of the Vitis genome, the mapping population of 'Norton' x 'Cabernet Sauvignon' with 273 progeny, plus parents were genotyped. The haplotype variants were analyzed using a custom analyze_amplicon.pl Perl scrip. The four most frequency haplotype alleles for each marker were obtained and converted to a variant call format (VCF) file using a custom Perl script, haplotype_to_VCF.pl. The VCF file was further imported into Trait Analysis by a SSociation Evolution and Linkage (TASSEL) for genotype imputation. Out of 2000 rhAmpSeq marker panel, a total of 1,981 makers were identified and saved as a VCF file. These identified rhAmpSeq markers were going through a post-imputation, a genotype with > 90% and markers with > 10% missing data across each individual were excluded. We have integrated 1,368 rhAmpSeq-SNPs and 356 SSRs markers to construct a high-resolution consensus map with a total of 1,724 markers. 1.2. Conduct a two-year segregation analysis of the entire F1 mapping population for rooting ability from the hardwood dormant cuttings Dormant cuttings of uniform size (14.5 g average) with >3 nodes were taken from ~199 hybrids of Vitis aestivalis-derived 'Norton' x V. vinifera 'Cabernet Sauvignon' by Jacob Schneider, on January of 2022 and 2023 from the Missouri State Fruit Experiment Station (MSFES) vineyard at Mountain Grove. Five cuttings were taken from each F1 individual as well as parents. The canes were left in a cool dark room (approximately 40 °F) for one month to ensure dormancy, then planted on early February of 2022 and 2023. Four rooting beds were filled with commercial growing mix (Fafard growing mix, Agawam, MA) composed of 50-55% composted pine bark, Canadian Sphagnum peat, perlite, vermiculite, and dolomitic limestone. The cuttings were treated with a low concentration (0.2%) of Indole-3 butyric acid (IBA), bundled in groups of 5and stuck 4-6 inches deep into 10-inch-deep rooting beds. Each rooting bed was bottom- heated to promote root development. The heating coils were set at 80 °F, placed in sand and covered with a weed barrier. The rooting beds are in a dark, unheated room to keep the upper portion of cuttings cool and unexposed to light so to avoid early bud break. The 4' x 4' rooting beds were supplied with 3.5 gallons of water per bed per week. Harvesting of the roots was completed during March of 2022 and 2023. Multiple traits were recorded and measured both on-sight and using WinRhizo imaging software. Measured traits include the longest main root, lateral root length, total root length, root number, and morphological rank of overall rooting ability (0-4). Each trait will be analyzed for its potential use as a quantitative phenotype for trait-genotype interaction/correlation. 1.3. Identify DNA markers associated with the rooting ability for future marker-assisted selection During the second year, first-year phenotypes (root number, longest main root, total root length, fine root length, and percent fine rooting) were analyzed (TASSEL) according to the linkage map described above. Preliminary results (pending the second-year data and confirmation using R/QTL) showed potential marker-trait associations on the following linkage groups with the respective LODs: Root number: 3 (3.219), 13 (3.575), 19 (3.736) Longest main root: 7 (5.286), 4 (3.838), 9 (4.514) Fine root length: 8 (5.191), 14 (3.512), 19 (3.737) Percent fine root: 1(4.113) Total root length: 4 (3.078), 8 (4.088) Objective 2 - Build Educational Capacity of MSU and MU 2.1. Incorporate rooting ability phenotyping concept in the "Plant Breeding and Genetics" course Dr. Hwang continues to offer the Plant Breeding and Genetics course, which serves as a general introduction to the principles of classical breeding and biotechnology. Nine (6 undergraduate and 3 graduate) students registered for this course in Spring 2023. Lectures on the development of SSR and SNP marker in grapevine, marker-assisted selection for F1 hybrid identification, rooting ability phenotyping using WinZHIZO software and linkage mapping are emphasized. The feedback from students indicates that knowledge of the cutting-edge molecular breeding technology is integral for their competitiveness in the job market. 2.2. Offer hands-on experience on grapevine interspecific hybrid identification using DNA markers in the "Plant Breeding and Genetics Lab" course Dr. Hwang and Li-Ling Chen, Clinical Instructor, continue to offer the 576/AGP 676 laboratory hands-on course in Spring 2023 to teach the general technique including 1) isolation of DNA from grape leaves, 2) determination of the concentration of isolated DNA using a NanoDrop, 3) performance of PCR, 4) visualization of DNA via electrophoresis and 5) running a DNA fragment analysis via capillary electrophoresis. These procedures are used to verify the true hybrids at the seedling stage by using SSR markers. Eight (5 undergraduate and 3 graduate) students will complete the course. 2.3. Provide two graduate assistantships to work on grape molecular breeding program Two new graduate students, Achyut Duwadi and Tabinda Shahid, were recruited into the Plant Science graduate program starting August 2022 under the support of this project. In the past 8 months, the key skills they have learned include emasculation of grapevine flowers, pollination, seed germination, propagation of cuttings, assessment of disease index and vineyard management; laboratory skills include DNA extraction, PCR, analysis of SSRs via capillary electrophoresis, analysis of SNPs via TASSEL software and phenotyping data collection Their anticipated graduation date will be May 2024. Jacob Schneider, a third-year collaborative Ph.D. student with Texas A&M University, continues the second-year rooting ability experiment described in Objective1.2 and 1.3 above. Objective 3 - Build Experiential Extension and Viticulture Capacity at MSU and MU 3.1. Provide graduate students experiential Extension opportunities with grape growers, workshops and conferences Graduate students participated in the Show Me Grape and Wine Symposium on March 1, 2023. The graduate students represented three Missouri Universities with five students from MSU, and one student from MU and St. Louis University. The students provided 12 to 15-minute presentations followed by 5-minutes of Q & A. Often many students present research results to an academic community and focus results on the initial research question or hypothesis. In comparison, grape growers and winemakers engage students in the applied aspects of their research. For example, how will a student's research results make growing grapes easier, grapes more productive or improve grape quality. The Conference and Symposium provides students the opportunity to interact with grape growers. Further students learn to think critically about the application of their research. 3.2. Provide graduate students experiential viticulture opportunities in commercial vineyards and MSU and MU vineyards A replicated cultivar trial located in Columbia, MO established in 2021 provided students and grape growers the opportunity to learn about vineyard establishment including prior year preparation of the site before planting, pruning one-year vines, drip irrigation installation, weed management in non-bearing vineyards, grow tube placement and timing and deer abatement. These relatively informal meetings provided students the opportunity to observe first-hand how an Extension Specialist conducts a group and answers questions. Additionally, students got a hands-on opportunity to ask questions and interact with grape growers.
Publications
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2023
Citation:
Jacob Schneider, Li-Ling Chen and Chin-Feng Hwang, Marker Discovery for Adventitious Rooting Ability in Dormant Hardwood Cuttings of Grapevine
|
Progress 05/01/21 to 04/30/22
Outputs
Target Audience:This research will lead to the construction of the first genetic linkage map with both SSR and SNP markers for the 'Norton' grape. The integration of both SSR and SNP markers to construct a high-resolution 'Norton' linkage map will greatly assist in improving marker-density and serve as a foundation for future grape breeding. Research results have been presented at the VitisGen2 Annual Advisory meeting, 45th American Society for Enology and Viticulture-Eastern Section Annual Conference, 2022 Show Me State Grape and Wine Conference and Missouri Wine and Grape Research Board meeting. In addition to the professional conferences, the results have also been presented at grower meetings in conjunction with viticulture/enology advisors to better educate growers on the value of molecular breeding and the benefits of improving 'Norton'. In addition, MSU maintains an on-line Blog at MSFES; the new knowledge produced from this study has been disseminated to the general public through it. Changes/Problems:None What opportunities for training and professional development has the project provided?Linking the educational, research and extension resources with the V. aestivalis-derived 'Norton' grape breeding program within the College of Agriculture (COAG) at Missouri State University (MSU), Grape and Wine Institute (GWI) at University of Missouri (MU) and VitisGen2 program at Cornell University, this proposed work includes interdisciplinary training opportunities for students in plant breeding, genetics, genomics and metabolomics with a specific focus on grapevine rooting ability traits. The following are the core competencies that have been provided. Build Research Capacity 1. Mapping population maintenance 2. SNP marker development via rhAmpSeq technology 3. Linkage map construction using both SSR and SNP markers 4. Conduction of a segregation analysis for root ability related traits 5. Utilization of molecular markers to be applied for future marker-assisted selection Build Educational Capacity 1. Comprehension of the basics and application of various molecular marker techniques 2. Acquaintance with grapevine rooting ability assessments 3. Familiarity with SSR and SNP markers applications in grapevine breeding 4. Implementation of marker-assisted selection into teaching materials for students to understand the plant molecular breeding concept 5. Ability to make public presentations and write reports and manuscripts for publication Build Experiential Extension and Viticulture Capacity Dr. Volenberg has had the opportunity to work with two outstanding graduate students in the past 12-monthes. His research is most always focused within commercial vineyards. This necessitates the formal introduction of students to growers, vineyard managers, as well as other various vineyard personnel. Although, many may overlook this as a formality, Dr. Volenberg explains to students that this is the beginning of Extension work and often the most difficult. This formal introduction and ensuing conversation is explained as the beginning of building trust with your clientele. Over time as Dr. Volenberg let graduate students grow and travel into vineyards alone, they acquire the skills to make personal phone calls to vineyard managers to determine if entry to vineyards is possible based on pesticide REI's. Once again, another opportunity to build trust with the clientele. As a graduate student advisor, it always is reassuring to see students learn and grow in a position. More striking, is to see students grow through experience when removed from the traditional classroom or computer screen. Student Training Opportunities Provided Undergraduates: Sydney Moore - Assisted in phenotyping of the rooting ability related traits Brogan Eyre - Developed in-vivo assay to assess the efficacy of selected fungicides for Pestalotiopsis spp. Students were invited to attend a viticulture and enology conference conducted through the University of Missouri Grape and Wine Institute on March 9-11, 2022. Graduate Students: Karlene Negus (June 2019 - August 2021): Genetic Characterization of Acidity in Vitis aestivalis-derived 'Norton'-based Population Kavya Tummala (January 2020 - August 2021):Rpv-3 Mediated Downy Mildew Resistance in Vitis Interspecific Hybrid 'Chambourcin'-based Population How have the results been disseminated to communities of interest?Karlene L. Negus, Li-Ling Chen, and Chin-Feng, Hwang, Genetic Characterization of Malic Acid in a Vitis aestivalis-derived 'Norton' population, Annual Frank Einhellig Graduate Interdisciplinary Virtual Forum, May 2, 2021 - An Oral Presentation Kavya Tummala, Li-Ling Chen and Chin-Feng Hwang, Marker-Assisted Selection to determine the introgression of Rpv-3 mediated downy mildew resistance in 'Chambourcin' X 'Cabernet Sauvignon' grapevine population, Annual Frank Einhellig Graduate Interdisciplinary Virtual Forum, May 2, 2021 - A Poster Karlene L. Negus, Li-Ling Chen, and Chin-Feng Hwang, QTL mapping of malic acid in a Vitis aestivalis-derived 'Norton' population, 45th American Society for Enology and Viticulture-Eastern Section Annual Conference, via Zoom, July 7-8, 2021 - An Oral Presentation Kavya Tummala, Li-Ling Chen and Chin-Feng Hwang, Marker-Assisted Selection to determine the introgression of Rpv-3 mediated downy mildew resistance in 'Chambourcin' X 'Cabernet Sauvignon' grapevine population, 45th American Society for Enology and Viticulture-Eastern Section, via Zoom, July 7-8, 2021-An Oral Presentation Chin-Feng Hwang, Li-Ling Chen and Jacob Schneider, Grapevine Breeding Program Updates at Missouri State University, VitisGen2 Online Annual Meeting on January 5-7, 2022 - An Oral Presentation Jacob Schneider, Li-Ling Chen and Chin-Feng Hwang, Genetic Study of Grapevine Rooting Ability from Dormant Hardwood Cuttings, 2022 Show Me Grape and Wine Symposium, March 9, 2022 - An Oral Presentation What do you plan to do during the next reporting period to accomplish the goals?1. Maintain the existing mapping populations of Norton x Cabernet Sauvignon at MSFES. 2. Construct a high-resolution Norton linkage map with rhAmpSeq-based SNP markers. 3. Analyze the rooting ability phenotyping data using WinZHIZO software 4. Localize the QTLs for rooting ability related traits. 5. Continue to teach "Plant Breeding &Genetics" and "Plant Breeding &Genetics Lab" with input from students and advisory committee. 6. Implement SNP technology and rooting ability phenotyping protocols into VESTA online courses 7. Submit annual report in April 2023
Impacts
What was accomplished under these goals?
Objective 1 - Build Research Capacity for Grapevine Improvement at MSU and MU 1.1. Construct a Norton linkage map using both SSR and rhAmpSeq-based SNP markers Based on a set of ubiquitous 2,000 RNase H2-dependent amplicon sequencing (rhAmpSeq) markers of the Vitis genome, the mapping population of'Norton' x 'Cabernet Sauvignon' with 273 progeny, plus parents were genotyped. The haplotype variants were analyzed using a custom analyze_amplicon.pl Perl scrip. The four most frequency haplotype alleles for each marker were obtained and converted to a variant call format (VCF) file using a custom Perl script, haplotype_to_VCF.pl. The VCF file was further imported into Trait Analysis by a SSociation Evolution and Linkage (TASSEL) for genotype imputation. Out of 2000 rhAmpSeq marker panel, a total of 1,981 makers were identified and saved as a VCF file. These identified rhAmpSeq markers will be going through a post-imputation, a genotype with > 90% and markers with >10% missing data across each individual will be excluded. We will then integrate the remaining rhAmpSeq with the identified SSRs markers to develop a high-resolution consensusmap. 1.2. Conduct a two-year segregation analysis of the entire F1 mapping population for rooting ability from the hardwood dormant cuttings Dormant cuttings of uniform size (14.5 g average) with >3 nodes were taken from 199 hybrids ofVitis aestivalis-derived 'Norton' xV. vinifera'Cabernet Sauvignon' by Jacob Schneider, on January 07, 11, 12, and 13, 2022 from the Missouri State Fruit Experiment Station (MSFES) vineyard at Mountain Grove. Five cuttings were taken from each F1individual as well as parents. The canes were left in a cool dark room (approximately 40°F) for one month to ensure dormancy, then planted on February 9 and 11, 2022. Four rooting beds were filled with commercial growing mix (Fafard growing mix, Agawam, MA) composed of 50-55% composted pine bark, Canadian Sphagnum peat, perlite, vermiculite, and dolomitic limestone. The cuttings were treated with a low concentration (0.2%) of Indole-3 butyric acid (IBA), bundled in groups of 5 and stuck 4-6 inches deep into 10-inch-deep rooting beds. Each rooting bed was bottom- heatedto promote root development. The heating coils were set at 80°F, placed in sand and covered with a weed barrier. With the growing mix added the beds held a temperature of ~70°F. The rooting beds are in a dark, unheated room to keep the upper portion of cuttings cool and unexposed to light so to avoid early bud break. The 4' x 4' rooting beds were supplied with 3.5 gallons of water per bed per week. Harvesting of the roots was completed on March 28 and 30, 2022. Multiple traits were recorded and measured both on-sight and using WinRhizo imaging software. Measured traits include the longest main root, lateral root length, total root length, root number, and morphological rank of overall rooting ability (0-4). Each trait will be analyzed for its potential use as a quantitative phenotype for trait-genotype interaction/correlation. 1.3. Identify DNA markers associated with the rooting ability for future marker-assisted selection For the first-year data, root number was the initial phenotype selected to check for trait-marker associations. A linkage map was constructed with 189 F1 genotypes in JoinMap 4.1 using 411 SSR markers. Using QTL 6 to analyze the SSR markers, linkage group (LG) 1 showed the highest peak with an LOD of 6.13. The flanking SSR markers for possible QTL are ctg8034 and VMCN2g7. Analysis for the other rooting traits will be conducted in like manner along with the second-year data. Objective 2 - Build Educational Capacity of MSU and MU 2.1. Incorporate rooting ability phenotyping concept in the "Plant Breeding and Genetics" course Dr. Hwang continues to offerthe Plant Breeding and Genetics course, which serves as a general introduction to the principles of classical breeding and biotechnology. Eight (7 undergraduate and 1 graduate) students registered for this course in Spring 2022. Lectures on the development of SSR and SNP marker in grapevine, marker-assisted selection for F1 hybrid identification, rooting ability phenotyping using WinZHIZOsoftware and linkage mapping are emphasized. The feedback from students indicates that knowledge of the cutting-edge molecular breeding technology is integral for their competitiveness in the job market. 2.2. Offer hands-on experience on grapevine interspecific hybrid identification using DNA markers in the "Plant Breeding and Genetics Lab" course Dr. Hwang and Li-Ling Chen, Clinical Instructor, continue to offer the576/AGP 676 laboratory hands-on coursein Spring 2022 to teach the general techniqueincluding 1) isolation of DNA from grape leaves, 2) determination of the concentration of isolated DNA using a NanoDrop, 3) performance of PCR, 4)visualization of DNA via electrophoresis and 5) running a DNA fragment analysis via capillary electrophoresis. These procedures are used to verify the true hybrids at the seedling stage by using SSR markers.Six (5 undergraduate and 1 graduate) students will complete the course. 2.3. Provide two graduate assistantships to work on grape molecular breeding program Two new MS students, Coy Greenwood and Priyanka Devkota, were recruited into the Plant Science graduate program starting June and August 2021, respectively. However, Coy decided to leave the program at the end of training, August 2021. Due to the Covid-19, Priyanka could not obtain the required visa to join us. Instead, we have used the graduate assistantship affiliated with this project to support an undergraduate student, Sydney Moore, for her hourly wage. She has learned laboratory skills including DNA extraction, PCR, and analysis of SSRs via capillary electrophoresis. She also assisted in acquiring the hardwood cuttings for the rooting ability experiments. We have recently recruited a new graduate student, Tabinda Shahid, starting August 2022. Jacob Schneider, a second-year collaborative Ph.D. student with Texas A&M University, continues the second-year rooting ability experiment described in Objective 1.2 above. Objective 3 - Build Experiential Extension and Viticulture Capacity at MSU and MU 3.1. Provide graduate students experiential Extension opportunities with grape growers, workshops and conferences Five graduate students and one undergraduate student participated in the Show Me Grape and Wine Symposium (in person) on March 9, 2022 in Columbia, MO. The graduate students were from MSU (2), MU (2) and Saint Louis University. The undergraduate participating in the Symposium was part of a senior Capstone project in Dr. Volenberg's program. Further this undergraduate was selected in a competitive process to participate in Undergraduate Research Day at the Missouri State Capital on April 4, 2022. The Conference and Symposium as well as the Undergraduate Research Day provided students the opportunity to interact and learn first-hand from grape growers as well as academics in the viticulture industry and leading stakeholders. 3.2. Provide graduate students experiential viticulture opportunities in commercial vineyards and MSU and MU vineyards The first vineyard opportunity will take place on June 21, 2022 as part of the Missouri Grape Growers Association Viticulture Field Day. This day will provide students the opportunity to learn about vineyard establishment, pruning one year old vines, irrigation installation, weed management in non-bearing vineyards, the value of grow tubes, and deer abatement. Students will also participate in tailgate meetings that are scheduled in different locations throughout the state. Thisshort duration twilight meetinginvolveslocal grape growers in a main topic that is pertinent to the phenology of the grapevines. Students get to see first-hand how an Extension Specialist works with growers solving viticulture problems.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Karlene L. Negus, Li-Ling Chen, Jonathan Fresnedo-Ram�rez, Heather A. Scott, Gavin L. Sacks, Lance Cadle-Davidson and Chin-Feng Hwang (2021). Identification of QTLs for Berry Acid and Tannin in a Vitis aestivalis-derived 'Norton'-based population. Fruit Research 1: 8.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2021
Citation:
Karlene L. Negus: Identification of QTLs for Berry Acids and Sugar in a Vitis aestivalis-derived Norton-based population.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2021
Citation:
Kavya Tummala: Marker-assisted Selection to Determine the Introgression of Rpv-3 Mediated Downy Mildew Resistance in Chambourcin X Cabernet Sauvignon Grapevine Population
|
Progress 05/01/20 to 04/30/21
Outputs
Target Audience:This research will lead to the construction of the first genetic linkage map with both SSR and SNP markers for the Norton grape. The integration of both SSR and SNP markers to construct a high-resolution Norton linkage map will greatly assist in improving marker-density and serve as a foundation for future grape breeding. Due to the Covid-19 pandemic, no research data has been presented at any conferences or meetings except VitisGen2 Annual Advisory meeting. However, research results have been communicated with advisors from Missouri Wine and Grape Research Board to better educate growers on the value of molecular breeding and the benefits of improving grapevines. In addition, MSU maintains an on-line Blog at MSFES; the new knowledge produced from this study also has been disseminated to the general public through it. Changes/Problems:None What opportunities for training and professional development has the project provided?Linking the educational, research and extension resources with the V. aestivalis-derived 'Norton' grape breeding program within the College of Agriculture (COAG) at Missouri State University (MSU), Grape and Wine Institute (GWI) at University of Missouri (MU) and VitisGen2 program at Cornell University, this proposed work includes interdisciplinary training opportunities for students in plant breeding, genetics, genomics and metabolomics with a specific focus on grapevine rooting ability traits. The following are the core competencies that have been provided. Build Research Capacity 1. Mapping population maintenance 2. SNP marker development via rhAmpSeq technology 3. Linkage map construction using both SSR and SNP markers 4. Conduction of a segregation analysis for root ability related traits 5. Utilization of molecular markers to be applied for future marker-assisted selection Build Educational Capacity 1. Comprehension of the basics and application of various molecular marker techniques 2. Acquaintance with grapevine rooting ability assessments 3. Familiarity with SSR and SNP markers applications in grapevine breeding 4. Implementation of marker-assisted selection into teaching materials for students to understand the plant molecular breeding concept 5. Ability to make public presentations and write reports and manuscripts for publication Build Experiential Extension and Viticulture Capacity All proposed experiential Extension and viticulture capacity proposed were dependent on travel and face-to face learning. The Covid-19 pandemic resulted in travel restrictions, remote learning for students and limited as well as strongly advised against any face-to-face meetings. Student Training Opportunities Provided Undergraduates: Students were invited to attend a virtual viticulture and enology conference conducted through the University of Missouri Grape and Wine Institute on March 1-4, 2021. Graduate Students: Karlene Negus (June 2019 - Present): Genetic Characterization of Acidity in Vitis aestivalis-derived 'Norton'-based Population Kavya Tummala (January 2020 - Present): Rpv-3 Mediated Downy Mildew Resistance in Vitis Interspecific Hybrid 'Chambourcin'-based Population How have the results been disseminated to communities of interest?Dr. Hwang, Li-Ling Chen (Clinical Instructor) and two students (Karlene Negus and Jacob Schneider) attended the VitisGen2 Online Annual Meeting on January 6-8, 2021. Negus presented a talk entitled "Identification of QTLs for Berry Acid and Tannin in aVitis aestivalis-derived 'Norton'-based Population". Due to the Covid-19, all the business travels including attending conferences are all banned by Missouri State University and University of Missouri. What do you plan to do during the next reporting period to accomplish the goals?1. Maintain the existing mapping populations of Norton x Cabernet Sauvignon at MSFES. 2. Construct a high-resolution Norton linkage map with rhAmpSeq-based SNP markers. 3. Analyze the rooting ability phenotyping data using WinZHIZO software 4. Conduct the 2nd year segregation analysis for rooting ability related traits. 5. Continue to teach "Plant Breeding and Genetics" and "Plant Breeding and Genetics Lab" courses with input from students and advisory committee. 6. Implement SNP technology and rooting ability phenotyping protocols into VESTA online courses 7. Submit annual report in April 2022
Impacts
What was accomplished under these goals?
Objective 1 - Build Research Capacity for Grapevine Improvement at MSU and MU 1.1. Construct a Norton linkage map using both SSR and rhAmpSeq-based SNP markers An ideal mapping population size for establishing a framework genetic map is approximately 200 progenies. As of April 2021, we have established a mapping population of 273 F1 progeny from crosses between Vitis aestivalis-derived 'Norton' and V. vinifera 'Cabernet Sauvignon'. This F1 population has been maintained at the Missouri State Fruit Experiment Station (MSFES) in Mountain Grove, Missouri. A total of 1,157 simple sequence repeat markers (SSR) were tested, 859 were amplified via PCR and 413 were polymorphic for at least one parent.The consensus map consisted of 411 markers on 19 linkage groups with a total distance of 1,678.6 cM. For SNP marker development via rhAmpSeq technology, leaf tissues from 'Norton' x 'Cabernet Sauvignon' 273 F1 progeny plus parents, were shipped to the VitisGen2 project at Cornell University in June 2020. All 273 genotypes were proven to be interspecific hybrids between 'Norton' and 'Cabernet Sauvignon'. The manufacturers protocol has been used for rhAmpSeq amplification of the 2000 marker panel. PCR products were indexed, pooled, cleaned, and quantified prior to sequencing using an Illumina (Illumina, San Diego, CA, USA). The rhAmpSeq sequencing data will be analyzed using an optimized pipeline for read de-multiplexing and variant haplotyping. We anticipate constructing the rhAmpSeq-based SNP linkage map by the end of 2021. 1.2. Conduct a two-year segregation analysis of the entire F1 mapping population for rooting ability from the hardwood dormant cuttings Three-node dormant cuttings of uniform size were taken from 199 hybrids of Vitis aestivalis-derived 'Norton' x V. vinifera 'Cabernet Sauvignon' by Jacob Schneider, on January 04, 2021 from the Missouri State Fruit Experiment Station (MSFES) vineyard at Mountain Grove. Five cuttings were taken from each F1 individual along with parents. The canes were left in a cool dark room (approximately 40 °F) for one month to ensure dormancy, then planted on February 2, 2021. The rooting bed was filled with commercial growing mix (Fafard growing mix, Agawam, MA) composed of 50-55% composted pine bark, Canadian Sphagnum peat, perlite, vermiculite, and dolomitic limestone. Additional perlite and vermiculite were added (~10% by volume) to ensure adequate moisture and drainage during the watering schedule and to make for easier root harvesting. The cuttings were treated with a low concentration (0.2%) of Indole-3 butyric acid (IBA), bundled in groups of 5 and stuck 6 inches deep into 10-inch-deep rooting beds. Each of the three rooting beds were supplied with bottom heat set at 80 °F to promote root development over bud break or shoot growth. With temperatures set at 80 °F, placement of the heating coils in sand and then covered with a weed barrier resulted in the growing mix holding a temperature of 70 °F. The rooting bed is in a dark and unheated room (around 40 °F) to keep the upper portion of cuttings cool so to avoid early bud break. The 4' x 4' rooting beds were supplied with 4 gallons of water per bed per week. Harvesting of the roots completed on March 24, 2021. Multiple traits will be recorded and measured both on-sight and using WinRhizo imaging software. Measured traits include the longest main root, lateral root length, total root length, root number, morphological rank of overall rooting ability (0-4), and root dry weight. Each trait will be analyzed for its potential to be used as a quantitative phenotype for trait-genotype interaction/correlation. Objective 2 - Build Educational Capacity of MSU and MU 2.1. Incorporate rooting ability phenotyping concept in the "Plant Breeding and Genetics" course Dr. Hwang offers the Plant Breeding and Genetics course, which serves as a general introduction to the principles of classical breeding and biotechnology. The main purpose of this course is to examine concepts relevant to students in plant breeding, genetics, biotechnology, crop sciences and allied fields of plant pathology. The course content presents a broad range of applicable information pertaining to the modification and improvement of a wide range of agronomic and horticultural crops. Twelve (9 undergraduate and 3 graduate) students registered for this course in Spring 2021. Lectures on the development of SSR and SNP marker in grapevine, marker-assisted selection for F1 hybrid identification, rooting ability phenotyping using WinZHsoftware and linkage mapping are emphasized. The feedback from students indicates that knowledge of the cutting-edge molecular breeding technology is integral for their competitiveness in the job market. 2.2. Offer hands-on experience on grapevine interspecific hybrid identification using DNA markers in the "Plant Breeding and Genetics Lab" course Dr. Hwang and Li-Ling Chen, Clinical Instructor, continue to offer the laboratory hands-on course (Plant Breeding and Genetics Lab, AGP 576/AGP 676) in Spring 2021 to teach the general technique required for molecular breeding work including 1) isolation of DNA from grape leaves, 2) determination of the concentration of isolated DNA using a spectrophotometer (NanoDrop 2000, Thermo Scientific), 3) visualization of DNA via electrophoresis, 4) performance of polymerase-chain reaction (PCR) and 5) running a DNA fragment analysis via capillary electrophoresis. These procedures are used to verify the true hybrids at the seedling stage by using SSR markers. Eight (7 undergraduate and 1 graduate) students will complete the course. The CDC Covid-19 guidelines have been implemented including mask and glove wearing with at least 6-feet social distancing in the laboratory. 2.3. Provide two graduate assistantships to work on grape molecular breeding program Two new MS students, Coy Greenwood and Priyanka Devkota, were recruited into the Plant Science graduate program starting June and August 2021, respectively. Cory will be under the financial support of this project; however, Priyanka will be sponsored by a graduate assistantship from the Plant Science Graduate Program. Their key skills to be learned include emasculation of grapevine flowers, pollination, seed germination, propagation of cuttings, assessment of disease index and berry quality and vineyard management; laboratory skills include DNA extraction, PCR, analysis of SSRs via capillary electrophoresis, analysis of SNPs via TASSEL, R, and Lep-MAP3 software, linkage map construction, phenotyping data collection and QTL mapping. Their anticipated graduation date is in May 2023. Objective 3 - Build Experiential Extension and Viticulture Capacity at MSU and MU 3.1. Provide graduate students experiential Extension opportunities with grape growers, workshops and conferences As a result of the Covid-19 pandemic the University of Missouri and state government instituted both international, national and state travel restrictions that resulted in not being able to undertake objective 3.1. Also hampering the undertaking of objective 3.1 was the move of faculty, staff and students off campus. Faculty and staff that could work from remote locations were strongly advised to limit campus visits. These travel restrictions precluded vineyard visits with students. Thereby efforts will be undertaken to incorporate 3.1 activities into year 2 and 3 to complete the objective. 3.2. Provide graduate students experiential viticulture opportunities in commercial vineyards and MSU and MU vineyards Similar to objective 3.1 above the Covid-19 pandemic resulted in travel restrictions that precluded travel for both faculty and students. Thereby vineyard visits could not occur for both faculty and students. Efforts will be undertaken to incorporate 3.2 activities into year 2 and 3 to complete the objective.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Karlene L. Negus, Li-Ling Chen, Jonathan Fresnedo-Ram�rez, Heather A. Scott, Gavin L. Sacks, Lance Cadle-Davidson and Chin-Feng Hwang (2021). Identification of QTLs for Berry Acid and Tannin in a Vitis aestivalis-derived 'Norton'-based population (Manuscript in Review)
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