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INVESTIGATOR: Nimmakayala, P.

PERFORMING INSTITUTION:
WEST VIRGINIA STATE UNIVERSITY
PO BOX 1000
INSTITUTE, WEST VIRGINIA 25112

SUMMER ACADEMY OF PLANT BREEDING: A PLATFORM TO DEVELOP MINORITY WORKFORCE IN MOLECULAR PLANT BREEDING

NON-TECHNICAL SUMMARY: Traditionally, crop improvement has been practiced more like an art rather than well-structured science. Breeding is an evolving science that traces back to the possibly unintentional domestication of plants and animals c. 10,000 years ago, to the breeding/hybridization societies and later, by elucidation of the laws of genetics which subsequently merged with quantitative genetics to bring science to bear on breeding. Although clear methods were available in quantitative genetics to identify lines with superior combining ability and methods to estimate heritabilities that will allow prediction of realizable genetic advance of quantitative traits such as yield and resistance, those modules were very cumbersome to teach in the class room environment. The application of science to the breeding process has been incredibly successful, as evidenced by selections in early generation seedlings using high-throughput genomic technologies. With genomics, it is possible to identify all the genes in a plant and then to begin to understand the genetic properties and networks that contribute to the development of a superior plant. Genomics has facilitated interesting teaching tools in the classroom to teach modern plant breeding. In the current proposal, we plan to develop a full time summer course " Modern Plant Breeding Methods" and offer it to all students studying at various other 1890 land-grant schools. It will be further combined with special summer workshops for faculty, graduate students and undergraduate levels for extensive training on marker-assisted selection and Genome Wide Association Study (GWAS).

OBJECTIVES: The main aim of this proposal is to consolidate the University's crop science focus by assimilating and strengthening existing proficiency in analysis of breeding/genomic resources, and plant breeding methods. Specifically, our intent is to: 1) develop a summer course "Introduction to Crop Improvement" with the modern sequencing and genotyping methods that can impact "Modern Breeding" and offer the course for all the WVSU students and the other students coming from various other 1890 land-grant schools and 2) organize special summer workshops for faculty, graduate students and undergraduate levels for extensive training on marker assisted selection and GWAS (Genome -wide association studies) pipelines.

APPROACH: We are proposing a dual level course on methods in molecular breeding. The content makes this course useful not only to students interested in working in crop improvement programs, but also to those who are interested in other careers such as core genomics. Upon completion of this 3-credit course of combined lecture and laboratory, students will be able to: 1. Understand theory and practice of modern plant breeding 2. Understand principles of crop improvement 3. Principles of linkage disequilibrium mapping 4. Complete problem-solving exercises to demonstrate knowledge of the course material. The second objective is to organize special summer workshops for faculty, graduate students and undergraduate levels for extensive training on marker assisted selection and GWAS (genome-wide association studies). Mainly this workshop deals with identification of markers linked to various yield, quality and resistance traits using association mapping. Since this objective aims to teach all steps of association mapping, participants will also learn the conditions of mapping spurious associations between candidate markers and phenotypes that can result from the presence of population structure. Association mapping analysis will be taught using the freely useable software TASSEL 2.1 (www.maizegenetics.net). After attending this workshop, graduate students will be working on independent research projects. Our goal is to allow students to develop GWAS projects and then we will help him/her by devising series of experiments that would fit in the pipeline and perform LD and association mapping analysis, which would finally enable them to gather evidence to support or refute their hypothesis. New assessments will be created with an eye toward going beyond this level and perhaps approach Application, Analysis, and Synthesis. We strive to create structured learning teams that experience active and cooperative inquiry during their independent research projects. The evaluation plans include annual evaluation of: 1) existing genomic infrastructure at WVSU; 2) number of students registered for the improved crop improvement summer course; 3) evaluation of products used in the program (Sequence panels developed for various crop germplasm diversity analysis, methods of bioinformatics successfully used for GWAS pipeline teaching and student experimentation, and 4) assessment of student experimentation outcomes and summer intern evaluations. The ultimate measure of success of the program is not just in numbers of graduates but also in numbers that become professionally active in crop genetics, genomics and molecular breeding after graduation. A secondary measure will be an increase in the quality and quantity of research publications resulting from genomic research projects. Specific evaluation criteria will include, in increasing order of importance, 1) number of requests for class and course-related materials, and 3) employment success of trainees

PROGRESS: 2013/09 TO 2017/08
Target Audience:Graduate and Undergraduate students Faculty and graduate students from other 1890 universities Local high-school students and teachers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Various teaching modules developed using this teaching grant are currently being taught in Biotechniques (BT 571), Crop Diversity (Biol 599) and Crop Genomics (Biol 399). In addition, this grant helped us to incorporate these techniques in 7 graduate thesis research projects and 12 undergraduate research projects. Summer workshops provided an opportunity for both students and facultyto establish education linkages with other Universities. How have the results been disseminated to communities of interest?Workshops, presentations and emails. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

IMPACT: 2013/09 TO 2017/08
What was accomplished under these goals? As per the objectives, a dual level summer course on Crop genome analysis (Biol 399) has been developed and taught during summer 2014 and 2015. Various high throughput modules like genotyping by sequencing, association mapping and genomic selection) were incorporated in crop genomics curricula. Using this teaching capacity building grant, We also developed various modules for genome assisted selection, marker development, hands on genotyping using high throughput techniques, field level plant breeding and metabolite quantification for enhancing the crop improvement curriculum at West Virginia State University. We built genome wide association mapping pipeline at WVSU that is being taught at several levels including Crop Evolution and Biodiversity and Biotechniques. We have organized lab classes and workshops on GMO products - the science and technology in developing GMO for 10th and 11th grade students in local high schools. Some schools have already introduced Biotechnology in their curriculum for 9-12th grade students. Around 400 highschool and middel school students were exposed to the latest DNA technologies. We conducted hands on summer workshops for WVSU and other 1890 land-grant universities in the areas of plant breeding, genomics and applied plant breeding. Recently, we have organized a national level Molecular Breeding and genomics workshop (27th to 30th June, 2017) for undergraduate, graduate students and faculty from 10 different universities (Alabama A&M University, Alcorn State University, Arizona State University, California state university, Delaware State University, Florida A&M University, Tennessee State University, Fort Valley State University, Kansas State University, Inter-American University of Puerto Rico). All the participants appreciated the exhaustive molecular techniques taught in such a short time. This workshop provided an opportunity for WVSU faculty and grad students to establish education linkages with other Universities.

PUBLICATIONS (not previously reported): 2013/09 TO 2017/08
1. Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ghimire B., Saminathan T., Bodunrin A., Hass A., Nimmakayala P and Reddy U. K. Mining Candidate Genes for Tolerance of Acid Coal-mine Water Toxicity by Conditional Genome-Wide Association Mapping. 1890 Land-Grant Universities Association of Research Directors, Inc. 18th Biennial Research Symposium, Atlanta, Georgia, April 1 - 4, 2017.
2. Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Yadav L., Saminathan T., Nimmakayala P and Reddy U. K. Characterization of Ankyrin Gene Family and Other Genes Involved in Pepper Fruit Size and Capsaicin Content. 1890 Land-Grant Universities Association of Research Directors, Inc. 18th Biennial Research Symposium, Atlanta, Georgia, April 1 - 4, 2017.
3. Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Nimmakayala P.2017. Genome-wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. 1890 Land-Grant Universities Association of Research Directors, Inc. 18th Biennial Research Symposium, Atlanta, Georgia, April 1 - 4, 2017
4. Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Krittika Tonapi, Lakshmi Abburi, Umesh Reddy, Professor and Padma Nimmakayala. 2016. Association Mapping for Fruit Traits in Capsicum chinense. Annual conference of the American Society for Horticultural Science, August 7-11, 2016, Atlanta, Georgia.

PROGRESS: 2015/09/01 TO 2016/08/31
Target Audience:Graduate and Undergraduate students Local highschool students Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The teaching modules developed using this grant are currently being taught in Biotechniques (BT 571), Crop Diversity (Biol 599) andCrop Genomics (Biol 399). In addition, this grant helped us to incorporate these techniques in 7 graduate thesis research projects and 12 undergraduate research projects. We used this teaching grant for developing capacity to perform genomic research in watermelon, melon, pumpkin, pepper and cotton. How have the results been disseminated to communities of interest?Through workshops and emails. What do you plan to do during the next reporting period to accomplish the goals?We recently got an instrumentation grant funded by Department of Defence. Using this, we obtained Nextseq 500, a Nextgen sequencing machine from Illumina and Irys mapper, a third generation sequencing from Bionano Company. We wish to invite our high school students and teachers, faculty from 1890 land-grant universities and our undergraduates and graduate students to participate in summer workshop during the summer of 2017. Similarly a set of independent projects will be executed so that the results can be used to publish new journal articles.

IMPACT: 2015/09/01 TO 2016/08/31
What was accomplished under these goals? Using this teaching capacity building grant, we developed various modules for genome assisted selection, marker development, hands on genotyping using high throughput techniques, field level plant breeding and metabolite quantification for enhancing the crop improvement curriculum at West Virginia State University. We built genome wide association mapping pipeline at WVSU that is being taught at several levels including Crop Evolution and Genome Level Diversity, Current Concepts of Biotechnology and Biotechniques. In addition to genome assisted plant breeding, we developed several modules in phenomics to be used various courses. We conducted hands on summer workshops for graduate and undergraduate students in the areas of plant breeding, genomics and applied plant breeding. We have organized a three day summer workshop for 93 high school students on GMO products - the science and technology in developing GMO and identification of GMO food items for 10th, 11th and 12th grade students from local high schools.

PUBLICATIONS: 2015/09/01 TO 2016/08/31
1. Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Nimmakayala, P., Venkata l. Abburi, Lavanya Abburi, Suresh Babu Alaparthi, Robert Cantrell, Minkyu Park, Doil Choi, Gerald Hankins, Sridhar Malkaram and Reddy UK. 2014. Linkage disequilibrium and population structure analysis among Capsicum annuum L. cultivars for use in association mapping. Molecular Genetics and Genomics, DOI 10.1007/s00438-014-0827-3
2. Type: Journal Articles Status: Published Year Published: 2014 Citation: Reddy, U. K., A. Almeida, V. L. Abburi, S. B. Alaparthi, Nimmakayala P et al., 2014. Identification of Gene-Specific Polymorphisms and Association with Capsaicin Pathway Metabolites in Capsicum annuum L Collections. PLoS ONE 9: e86393
3. Type: Journal Articles Status: Published Year Published: 2016 Citation: 3. Nimmakayala P, Abburi VL, Saminathan T, Almeida A, Davenport B, Davidson J, Reddy CM, Hankins G, Ebert A, Choi D, Stommel J, Reddy U (2016) Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms. Frontiers in Plant Science 7 (1646). doi:10.3389/fpls.2016.01646

PROGRESS: 2014/09/01 TO 2015/08/31
Target Audience:Graduate and Undergraduate students Local highschool students Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The modules developed from this grantare currently being taught in Biotechniques (BT 571), Crop Diversity (Biol 599) and Crop Genomics (Biol 399). How have the results been disseminated to communities of interest?Through workshops and emails. What do you plan to do during the next reporting period to accomplish the goals?Special summer workshop in plant breeding with special reference to GWAS will be organized (2016) for faculty, graduate students and undergraduate levels for extensive training on marker assisted selection and Genomic selection pipelines. Summer course will be taught on crop genomics.

IMPACT: 2014/09/01 TO 2015/08/31
What was accomplished under these goals? As per the objectives, a dual level summer course on Crop genomics and evolution (Biol 399) has been developed and taught during summer. We have developed crop diversity and genetic analysis modules in the currently being taught in Biotechniques (BT 571), Crop Diversity (Biol 363) and Crop Genomics (Biol 399/599). We have organized plant breeding workshops and regular lab classes. Recently we developed large scale SNP datasets for melon, watermelon, cotton and pepper. We have organized lab classes on GMO products - the science and technology in developing GMO and identification of GMO food items for 10th, 11th and 12th grade students in local high schools. We have also organized a summer workshop on Molecular markers and marker assisted selection (MAS) in 2015 for local high school students and ourundergraduate students.Using this teaching capacity building grant, we developed various modules for genome assisted selection, marker development, hands on genotyping using high throughput techniques, field level plant breeding and metabolite quantification for enhancing the crop improvement curriculum at West Virginia State University.We built genome wide association mapping pipeline at WVSU that is being taught at several levels including Crop Evolution and Genome Level Diversity, Current Concepts of Biotechnology and Biotechniques.?

PUBLICATIONS: 2014/09/01 TO 2015/08/31
No publications reported this period.

PROGRESS: 2013/09/01 TO 2014/08/31
Target Audience: Graduate and undergraduate students of WVSU. Local high school students and teachers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Various genomic tools are currently being taught in Biotechniques (BT 571), Crop Diversity (Biol 599) and Crop Genomics (Biol 399). How have the results been disseminated to communities of interest? Workshops and regular lab classes What do you plan to do during the next reporting period to accomplish the goals? Special summer workshop will be organized for faculty, graduate students and undergraduate levels for extensive training on marker assisted selection and GWAS (Genome -wide association studies) pipelines.Summer course will be taught on crop genomics.

IMPACT: 2013/09/01 TO 2014/08/31
What was accomplished under these goals? As per the objectives, a dual level summer course on Crop genomics and evolution (Biol 399) has been developed and taughtduring summer 2014 (06/16/14 to 7/25/14). Four graduate students and one undergraduate attended the course. Various high throughput modules like genotyping by sequencing, genomic selection and Best Linear Unbiased Predictors (BLUPs) were incorporated in crop genomics curricula. We traditionally teach plant breeding highlighting the importance of traits with high heritability and genetic advance. Newly developed modules for BLUPs use the concept of genomic selection to locate highvalue breeding lines and best combiners. We extended this concept for various crops that we are currently using for our teaching and research. We have organized lab classes on GMO products – the science and technology in developing GMO for 10th and 11th grade students in local high schools. Some schools have already introduced Biotechnology in their curriculum for 9-12th grade students. We will be organizing a summer workshop on Molecular markers and marker assisted selection (MAS) in 2015 for local high school teachers other 1890 faculty and graduate students.

PUBLICATIONS: 2013/09/01 TO 2014/08/31
No publications reported this period.