Joseph L. Kepiro
PO Box 12355
Beaumont, TX 77726
USA
Home +1 (409) 781-2716
Email: citrus61@yahoo.com

Career Goals

My goal is to obtain full time employment as a Plant Breeder/Research Geneticist. I am experienced with molecular markers (AFLP, SSR, etc.), phenotyping populations, trait-marker association mapping and QTL data analysis and mapping.

Academic Background

Ph.D. (Plant Genetics/Plant Breeding/Plant Cell and Developmental Biology) 1997-2003 University of California, Riverside CA.

BS (Botany) 1993 University of Washington, Seattle.

AA degree (Math and Science) 1981 Spokane Falls Community College, Spokane WA.

Knowledge, Skills and Abilities

Molecular Techniques
- Bulked Segregant Analysis using AFLP markers for efficient identification of markers linked to traits
- DNA Extraction and Purification
- PCR/RTPCR
- Molecular Markers: SSRs and Genomic AFLP
- Sequencing
- RNA/mRNA Extractions and Purification
- cDNA-AFLP/Expression Analysis (EST's)
- Cloning linked markers
- BAC library screening
- Light and fluorescent microscopy

Software
- JoinMap version 4.0
- MapQTL version 5.0
- Windows QTL Cartographer 2.5
- Excel and Quattro-Pro database creation and management
- Microsoft PowerPoint
- SAS analyst
- StatView Statistical Analysis
- Saga MX version 3.2 AFLP scoring software (Li-Cor)
- WinSeedle (Image Analysis)
- Adobe Photoshop

Research Experience

Oct 2003 to Present
Molecular Genetics Post-doc project for the USDA-ARS at the Rice Research Unit in Beaumont Texas

"QTL Mapping of Milling Yield in Southern U.S. Rice with Amplified Fragment Length Polymorphism (AFLP) and Micro-Satellite (SSR) Markers."

Major Duties
I performed a wide range of duties to generate data, map QTLs and create regression models related to the complexly inherited trait of rice milling yield. Specific duties included: applying high-throughput methodologies to generate marker profiles; modification of existing methods of genetic analysis or developing new techniques in order to improve accuracy and efficiency; evaluating and performing calculations and analysis according to established principles and evaluating the adequacy of the results; participating in the preparation of data for scientific technical reports; undertaking the routine care, maintenance, and calibration of moderately complex laboratory equipment; and keeping abreast of current scientific advancements through literature reviews and attending approved meetings, workshops, and conferences.

Project Overview
The objective of this project was to find molecular markers linked to the major components of the complex trait "milling yield" for rice grown in the Southern Plains region of the United States. I coordinated and helped plan planting. During the growing season I monitored the crop, collected samples and relevant data. I worked with seed separating and processing equipment. I personally performed most of the lab work and processed grain samples through stages that required particular attention to detail.

Linkage Mapping
I extracted DNA and verified its quality. I used SSR markers to cull lines possessing non-parental alleles. I processed DNA into AFLP templates for mapping. I used AFLP system II for small genomes and IRD-labeled primers to screen a subset of the population with 256 primer combinations. I used multi-plex PCR and a Li-Cor genetic analyzer to identify primer combinations producing the maximum number of polymorphisms per primer combination. Using JoinMap 3.0, I created a genetic map placing approximately 540 AFLP markers into groups and anchored them onto the 12 chromosomes of the rice genome witt well characterized SSR markers .

Statistics
I used a StatView statistical analysis program (SAS) to generate descriptive statistics. I created models with forward stepwise regression to identify the significant components with partial R-squared values for each trait significantly contributing to the variance of milling yield. I used SAS analyst to run forward regression and create models with partial R-squared for each sub-component trait found significantly contributing to milling yield.

QTL analyses
Significant variables of the regression model were used in QTL analyses with MapQTL 5.0 to identify markers linked to milling yield with interval and MQM mapping. I further verified the location and LOD significance with WinQTL Cartographer interval and composite interval mapping.

Career Development
I researched and initiated the purchase of new equipment. I introduced new lab techniques and products to increase productive, reduce errors, and expand the Research Unit's ability to conduct state of the art research. I developed my skills for quality control, and polished my skills as a supervisor while supervising 3-5 employees performing various tasks with impact on this project. I developed and communicated clear, unambiguous guidelines for quality and production goals. To ensure quality data for QTL analysis, sample integrity was protected from compromise and repeatability increased by standardized machinery settings, standard operating procedures and check samples. I designed simple and easily followed experimental designs to removed sources of error.

Bulk Segregant Analysis
I screened a population for Rice Blast resistance by performing AFLP bulked segregant analysis to successfully identify and sequence markers linked to the resistance.

1997-2003
Dissertation Project at the University of California, Riverside

"The Molecular Genetic Analysis of Nucellar Embryony (Apomixis) in Citrus."

Project Overview
I scored a BC1 population for the trait of nucellar embryony (apomixis). I used multi-plexed PCR and a Li-Cor 4200 sequencer to generate AFLP markers for mapping. I used bulked segregant analysis to find markers linked to apomixis. I constructed a genetic map from ~ 700 AFLP markers and identified markers linked to a major and minor locus of nucellar embryony by QTL analysis. I cloned markers into E. coli. I sequenced the inserts using a Li-Cor 4200 sequencer. I screened a citrus BAC Library using those clones as 32P labeled probes to identify BAC clones carrying the linked markers and verified the BAC were carrying the fragment by amplifying with the AFLP primers.

cDNA-AFLP and Expression Analysis
I extracted total RNA, purified it to mRNA and made dscDNA for cDNA-AFLP template generation. I used an Expression Analysis kit from Li-Cor to screen bulks of the dscDNA templates for differential expression. I identified a number of up-regulated and/or unique transcripts and sequenced the most relevant. I screened a BAC library to identify clones with the sequences hybridizing to the differentially expressed transcripts.

Investigation of Thorns in Citrus
I searched the databases for varieties with different classification of thorniness, made crosses, collected the seed and planted them for a future study.

1995-1997
Research Technician for the Oregon State University Southern Oregon Experiment Station in Medford Oregon

I worked as a level two Research Technician for the agronomy department. I was involved in irrigation, collection of samples, and recording of data. I helped to design and set up experiments and trials. I operated various field equipment including tractors with implements, harvesters, trenchers, and sprayers. I applied herbicide and held an Oregon State applicator's and consultant's license. I conducted herbicide trials to establish agronomic practices for new and alternative crops. I worked with seed separating and processing equipment.

1991-1993
Domestic Observer for the Ground Fish Program of the National Marine Fisheries Service (NMFS)

I worked in Alaska under the auspices the NMFS sampling and collecting data aboard commercial fishing vessels at sea in the northern Pacific Ocean and Bering Sea.

Awards and Other Honors

• USDA-ARS "Superior Performance Award 2005 Rating Period": Rated as Exceeds Fully Successful for conceiving, planning and conducting research and for resource management accomplishments.

• USDA-ARS "Spot Award 2005": For development and implementation of protocols expanding the research capabilities of the Rice Research Unit.

• Best Poster: 2001 UCR Botany and Plant Sciences graduate student retreat.

• United States Marine Corps: Certificate of Commendation 1986

• United States Marine Corps: Meritorious Unit citation (highest supply effectiveness in the US Navy and Marine Corps for 3 consecutive years).

• United States Marine Corps: Honor man of two inter-service digital electronic technical schools.

• Future Farmers of America: Placed first at the Eastern Washington Crops judging contest.

Professional Organizations

• International Society for Plant Molecular Biology (ISPMB)

• American Society of Plant Biologists (ASPB)

• American Society for Horticultural Science (ASHS)

• International Society of Citriculture (ISC)

Other Academic Activities

• Graduate Student Representative for the Botany Department at the campus level

• Graduate Student Representative for the Campus Research Integrated Safety Committee

• Graduate Student member on the Curriculum Committee for the Botany and Plant Sciences Dept.

Continuing Education

• Workshop on Genomic Mapping For Agricultural & Biological Research Applications. October 25 & 26, 2006. USDA, ARS, Cropping Systems Research Laboratory, Lubbock, TX

• Practical Workshop in the Analysis and Genotypic Data, April 1 & 2, 2004. Institute for Plant Genomics and Biotechnology Laboratory for Plant Genome Technology, Norman Borlaug Center Texas A & M University, College Station Texas

Publications, Presentations and Posters

Publications

Kepiro, J.L., Roose, M.L., AFLP Markers Closely Linked to a Major Gene Essential for Nucellar Embryony (Apomixis) in Citrus maxima x Poncirus trifoliata Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA (Submitted to Journal of Tree Genetics and Genomes, being reviewed as of July 2007).

Kepiro, J.L., McClung, A.M., Chen, M.H., Yeater, K.M., and Fjellstrom, R.G., Mapping QTLs for Milling Yield and Grain Characteristics in a Tropical japonica Long Grain Cross (Submitted to Journal of Cereal Science, revisions submitted July 2007).

Kepiro, J.L., Roose, M.L., QTL analysis of Nucellar Embryony in Poncirus trifoliata Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA (being prepared for journal submission).

Kepiro, J.L., Fjellstrom, R.G., McClung, A.M., and Yeater, K. M., Forward Regression Modeling of Milling Yield Components and Their Relationship to Grain Quality and Agronomic Traits in Long Grain japonica Rice (being prepared for journal submission).

Newsletter article: " AFLP Markers Linked with Long Grain Milling Yield ", Research Update in RiceCAP News University of Arkansas, April 2007 Volume 3 Issue 7 pp 4-6.

Newsletter article: "Molecular Markers for Milling Yield", in Texas Rice newsletter, Texas A&M University, August 2006, Vol. VI, No. 6.

Kepiro, J.L., Roose M.L., Nuceller Embryony. In: Khan I (ed) Citrus Genetics, Breeding and Biotechnology. CABI Publishing, a division of CAB International (the "Publishers") of Nosworthy Way, Wallingford, Oxon OX10 8DE, UK.

Seminars

The 31st Technical Working Group, Feb 26- March 1, 2006; The Woodlands, TX: Seminar title: Molecular Markers for Milling Yield in Southern U.S. Long Grain Rice.

Plant and Animal Genome XI, 2003; San Diego CA: Seminar W161: Molecular Genetic Analysis of Nucellar Embryony (Apomixis) in Citrus maxima x Poncirus trifoliata using AFLP

Posters

Plant and Animal Genome XV, 2007; San Diego CA: Poster title: Modeling of Milling Yield Components and Their Relationship to Grain Quality QTLs in Long Grain japonica Rice.

The 31st Rice Technical Working Group, 2006; The Woodlands, TX: Poster title: Evaluating Milling Yield in a Cypress × Panda Cross with Traditional, Re-milling and Re-wetting Techniques

Plant and Animal Genome XIV, 2006; San Diego CA: Poster title: QTLs for Milling Yield in Tropical Japonica Long Grain Rice.

Plant and Animal Genome XIV, 2006; San Diego CA: Poster title: Mapping Sheath Blight Resistance QTL(S) In Rice (co-author).Kepiro J.L, McClung A.M., and Fjellstrom R.G., (2004)

QTL Mapping of Milling Yield in Southern U.S. Rice with Amplified Fragment Length Polymorphism (AFLP) and Micro-Satellite (SSR) Markers, in the Proceeding of Food and Agriculture Panel Meeting December 11-18, 2004; 33rd U.S. and Japan Natural Resources (UJNR) Cooperative Program.

Plant and Animal Genome XIII, 2005; San Diego CA: Poster title: QTL Mapping of Milling Yield in Southern U.S. Rice with Amplified Fragment Length Polymorphism (AFLP) and Micro-Satellite (SSR) Markers.

Plant and Animal Genome XI, 2003; San Diego CA: Poster titles: 1) “Molecular Genetic Analysis of Apomixis in Citrus”; 2) “Using cDNA-AFLP to Identify an Up-regulated Transcript in Citrus Ovules 10 DAA”; 3. “Genomic AFLP Maps of Citrus maxima and Poncirus trifoliata useful in QTL Analysis of the Nucellar Embryony Form of Apomixis.”

Plant and Animal Genome IX, 2001 San Diego CA: Poster title “Molecular Genetic Analysis of Apomixis in Citrus”.

International Society of Citriculture Ninth Congress, Dec 2000, Orlando FL: Poster title “Molecular Genetic Analysis of Apomixis in Citrus”.

References: Available on request

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