Source: UNIVERSITY OF CALIFORNIA, RIVERSIDE submitted to
BREEDING HEAT TOLERANT VARIETIES OF COWPEA BY EXPLOITING ASSOCIATION STUDIES AND LEGUME SYNTENY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
1000346
Grant No.
2013-67011-21132
Project No.
CA-R-00008687
Proposal No.
2013-03350
Multistate No.
(N/A)
Program Code
A7101
Project Start Date
Sep 1, 2013
Project End Date
Aug 31, 2015
Grant Year
2013
Project Director
Lucas, M. R.
Recipient Organization
UNIVERSITY OF CALIFORNIA, RIVERSIDE
(N/A)
RIVERSIDE,CA 92521
Performing Department
Botany and Plant Sciences
Non Technical Summary
This project will contribute new knowledge concerning the inheritance, genetic control, and breeding of traits important for agricultural production in the face of unpredictable climates. The aim is to study responses to heat during reproductive development using cowpea, a warm-season legume with a legacy as a model for studying heat tolerance. A broad assessment of allelic variation important for tolerance to heat during reproductive development will be captured using an unstructured diversity panel, SNP genotyping, and knowledge of legume synteny. This knowledge will be reconciled with previously developed marker-trait associations to design breeding indices and mating schemes aimed at developing enhanced varieties of cowpea. Furthermore, knowledge gained from cowpea will be used to help describe heat-tolerance associated regions in related crop genomes including soybean and common bean.
Animal Health Component
10%
Research Effort Categories
Basic
60%
Applied
10%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20104301081100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
0430 - Climate;

Field Of Science
1081 - Breeding;
Goals / Objectives
Professional Development Design critical elements of a plant breeding initiative. Attend and participate in conferences including PAG and CSSA meetings. Comunicate research strategy and findings by publication and presentation. Research Survey heat tolerance among a diversity panel of cowpea samples during a greenhouse trial. Perform a genome-wide association study to identify allelic variation important for the inheritance of heat tolerance. Reconcile marker-trait associations to design a breeding scheme. Pursue marker-assisted breeding. Describe genomic regions important for heat tolerance.
Project Methods
Approach A diversity panel of ~200 cowpea lines will be chosen from the UCR collection and grown under hot greenhouse conditions in the fall of 2013. These lines will be chosen among a larger group of ~700 lines which were already genotyped using an EST-derived SNP genotyping platform developed by our group and some lines which are interesting but have yet to be genotyped. An experimental trial will be conducted during short days in order to mitigate potentially different photoperiod responses. Plants will be deconstructed at maturity and evaluated for tolerance to heat during reproductive development (stage II) by measuring the number of pods per peduncle. DNA will be gathered from lines yet to be genotyped and sent to a service provider for finger printing. Genotype data for the diversity panel will be used to identify population structure including genepools, migrants, admixture, duplicates, and to develop coancestry estimates (Pritchard et al., 2000; Earl and vonHoldt, 2012; Evanno et al., 2005; Jakobsson and Rosenberg, 2007; and Rosenberg, 2004) to be used as a covariate in association mapping provided by TASSEL (Bradbury et al., 2007). Marker-trait associations identified using the diversity panel will be combined with associations I previously identified using a recombinant-inbred population (Lucas et al., 2012a) to identify SNP haplotypes associated with tolerance to heat during reproductive development. These trait-associated regions will also be compared to knowledge of other trait-associated regions including seed size (unpublished), resistance to foliar thrips (Lucas et al., 2012b), and resistance to fungi (Pottoroff et al., 2012; Muchero et al., 2011). Haplotype variation at heat tolerance associated regions will be assessed by surveying previously genotyped materials. An index weighted in favor of heat tolerance will be developed to calculate genome estimated breeding values for lines yet to be phenotyped. Lines with the highest breeding values will eventually be tested and incorporated into a mating design capable of stacking trait determinants. Broader diversity provided by an unstructured population will provide a more comprehensive assessment of allelic variation contributing to the inheritance of tolerance to heat when compared to a bi-parental population. Such a design would facilitate the discovery and tagging of novel trait-determinants. This project will also aim to capture favorable allelic diversity using marker-assisted approaches to selection including genomic selection and marker-assisted backcrossing. If relatively few genes with major effect are identified a backcrossing approach will be pursued to combine heat tolerance into high-quality grain and biotic stress resistant backgrounds. If several genes contributed by several sources with minor phenotypic effects are identified genomic selection will be designed and pursued in order to breed a variety with the highest predicted breeding values based on known marker-trait associations. Twelve milestones will be used to verify the project is on schedule and to assure that objectives are being met. The targeted timeframe for the completion of these milestones within the life of the funded project are provided in TABLES 1 and 2 for fiscal years 2014 and 2015, respectively. Milestones for Objective 1 are those concerning professional development which includes experimental design, networking, and communication of findings and strategy of the project. Milestones for Objective 2 contribute to the development of technical competence by primarily focusing on the utilization of genomic technologies to help develop new crop varieties capable of enhanced production in marginal environments typically affected by unpredictable climates. *Milestones for Objective 1 1a) Design critical elements of a modern plant breeding scheme. 1b) Attend and participate in conferences, including PAG and CSSA meetings in 2013 - 2015. 1c) Communicate research strategy and findings by publication and presentation. Milestones for Objective 2 2a) Conduct a greenhouse trial using a diversity panel to measure agronomically important traits. 2b) Utilize service providers to obtain genotype data. 2c) Identify and account for population structure of the diversity panel. 2d) Identify marker-trait associations through GWAS. 2e) Reconcile knowledge with previous association studies. 2f) Describe genomic regions of related crops likely to harbor trait determinants. 2g) Plant parents for mating, make crosses, and advance to F2. 2h) Make selections based on genotype knowledge. * See original application for timeline of milestones.

Progress 09/01/13 to 08/31/15

Outputs
Target Audience:Farmers in the San Joaquin Valley of California, USA. Domestic and international plant breeders. Industry leaders. Undergraduate and graduate students. University affiliates. Attendees at scientific conferences. Readers of primary literature. Changes/Problems:I completed my graduate program at the end of December 2014 and left the host university in January 2015 to join Syngenta as a professional plant breeder in late January 2015. What opportunities for training and professional development has the project provided?The most memorable interactions I had during conferences I attended include:Ainong Shi who is a cowpea breeder at the University of Arkansas. Matthew Blair who is a legume genomics expert at Tennessee state. Mike Thompson who is the Director of Agriculture Market Development at Illumina. Jamie O'rourke who is a legumes expert at Iowa State. I also met indusry leaders from Syngenta, Monsanto, and Nunhems in attempt to establish a professional career in plant breeding. This fellowship was a major component of my professional development which helped me prepare for my new position as a pepper breeder working for Syngenta. How have the results been disseminated to communities of interest?Publication, oral presentation, training new student at the University. Communication of strategy and results with colleagues. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Professional Development: 1. Design critical elements of a plant breeding initiative. Work with service providers and members of the crop community to establish breeder-friendly DNA technologies. Develop diversity panels based on genotype knowledge. Designed a QTL introgression back-cross breeding program. Selected markers to tag trait-associated and recurrent parent loci in backcross breeding. Design field trial to screen breeding populations. 2. Attend and Participate in Conferences Invited speaker in the Legumes Workshop at the 2015 Plant and Animal Genome Conference. Presented three posters at the 2015 Plant and Animal Genome Conference. Oral presentation at the UC Riverside Genetics, Genomics, and Bioinformatics Symposium. 3. Communicate research strategy and findings by publication and presentation. Published backcross breeding in technical journal. Abstract for poster and oral presentations published in conference proceedings. Dissertation published online. Research 1. Survey heat tolerance among a diversity panel of cowpea samples during a greenhouse trial. Screened cowpea germplasm accessions during two greenhouse trials. Identified lines with potential tolerance to high temperatures. 2. Reconcile marker-trait associations to design a breeding scheme. Compared allelic variation within breeding and parental lines to select individuals for selfing and intermating. 3. Pursue marker-assisted breeding. Made crosses based on allelic variation and sampled tissue for DNA extraction and genotyping. Interpreted genotype information to identify lines with heat tolerance associated alleles. 4. Describe genomic regions important for heat tolerance. Assessed the impact of heat QTLs on the inheritance of seed size.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Lucas MR, Huynh BL, Roberts PA, and Close TJ. 2015. Introgression of a Rare Haplotype from Southeastern Africa to Breed California Blackeyes with Larger Seeds. Frontiers in Plant Science.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lucas MR. 2015. Identification and Introgression of Mozambican Cowpea Alleles to Breed California Blackeyes with Larger Seeds. Plant and Animal Genome Conference XXIII Poster Session.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lucas MR, Huynh BL, Roberts PA, Close TJ. 2015. Introgression of a Rare Haplotype from Southeastern Africa to Breed Cowpeas with Larger Seeds. Plant and Animal Genome Conference XXIII Legumes Workshop.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Lucas MR. 2015. Using Genomic Resources to Breed Cowpeas with Larger Seeds. Proquest.


Progress 09/01/13 to 08/31/14

Outputs
Target Audience: During the first year of my USDA NIFA project, support provided by this fellowship promtoed my interactions with numerous students, professional and academic scientists, government representatives, university affiliates, and the general public. Among the most notable audiences reached include farmers and members of a commodity board in the San Jaoquin Valley of California, many of which represent diverse and underrepresented groups including hispanics and women. Research activies supported by NIFA were communicated during my participation at several domestic and international conferences in which I was an invited guest speaker or presented a poster including the International Conference on Legume Genetics and Genomics in Saskatoon Canada, the 2nd Plant Genomics Congress in St. Louis MO, the Crop Science Societies of America Annual meeting in Tampa FL, the Plant and Animal Genome Conference in San Diego CA, the Genetics Genomics and Bioinformatics Symposium in Riverside CA, among others in which my colleagues represented my work during their attendance to international meetings. Research conducted during this fellowship became important in helping to train and integrate new members of our research team including a woman from Senegal, a woman form Spain, a Chinese-american woman, a woman from California, and an African-American male. This award was widely recognized and disseminated to the broader public through interactions with the University of California, Riverside Office of Research and has been communicated to program officers and representatives for the Bill and Melinda Gates Foundation, the United States Agency for International Development, the Consultative Group on International Agricultural Research, the United States Department of Agriculture, and to a number of for-profit organizations including Monsanto, Syngenta, and Bayer. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Trained numerous new students and visiting scientists. Developed writing, presentation, and other communication skills during participation in international conferences. Built technical competence for a career as a plant breeder. How have the results been disseminated to communities of interest? Through publication, presentation (including field days), training, and collaboration. What do you plan to do during the next reporting period to accomplish the goals? Lead paper through the publication process. Train new members to build upon initiatives. Improve knowledge by reviewing recent developments in the literature. Collaborate with experts to expand the scope and impact of the project. Advocate for improved infrastructural capabilities to enhance research efforts. Search and build applications for a position as a professional plant breeder.

Impacts
What was accomplished under these goals? Professional Development: Designed and pursued a marker-assisted backcrossing scheme. Utilized field and greenhouse resources, outsourced service providers. Participated in PAG, CSSA, ICLGG, and PGCA conferences. Published abstracts of presentations, technical paper under review. Research: Breeding scheme designed and pursued. Introgression lines evaluated during the summer of 2014 for performance. Determined linkage of heat tolerance genetic factors to previously annotated traits.

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: 2014 IFLRC VI & ICLGG VII. Using SNPs to Breed Cowpeas with Larger Seeds. Lucas MR, Huynh BL, Roberts PA, and Close TJ.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: 2014 2nd Plant Genomics Congress. Impact of NGS on Application Oriented Cowpea Genetic Research. Lucas MR, et al.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: 2014 Plant and Animal Genome Conference (PAG). Identification and Introgressions of African Cowpea Alleles to Develop Larger Seeded California Blackeyes. Lucas MR, Bao-Lam Huynh, Roberts PA, and Close TJ.