I am a passionate
plant quantitative geneticist and
computational biologist. My hobbies include astronomy, painting, online blogging, photography, cooking, fixing things around my house :) and working on my car. I have over ten years of research experience in the field of plant breeding, quantitative genetics and high-throughput phenotyping, and possess a strong knowledge and experience in conducting
big data analysis and visualization especially on a large scale phenotypic and genotypic data.
2012–2017 PhD - Plant Breeding, Genetics & Genomics — University of Missouri Columbia, USA
2008–2012 BSc Agricultural Sciences — Truman State University, USA
2018–Present Computational biologist (Postdoc) — Cornell University, Geneva, NY
- Analyzed large-scale genotyping data from Genotyping-by-Sequencing, Amplicon Sequencing, Whole genome sequencing for SNP and haplotype calling, genome alignment, genome assembly and genomic selection and prediction.
- Co-Lead the development of a rhAmpSeq (RNase H2 enzyme-dependent amplicon sequencing) haplotype strategy targeting the collinear core genome to improve marker transferability across a diverse genus.
- Worked with nation-wide grape breeders to apply amplicon sequencing (AmpSeq) marker data for accelerated marker-assisted breeding.
- Built genetic maps (in Lep-Map3) of various Vitis populations, and performed quality control (QC) analysis, interval mapping and genome-wide association (GLM, MLM, FarmCPU).
- Managed grapevine breeding database www.VitisBase.org in collaboration with Boyce Thompson Institute (BTI) and Breeding Insight project (USDA); and led setting up trials and high-throughput phenotype data collection on FieldBook android application.
- Big data visualization in R software using packages such as ggPlot; and CIRCOS (written in PERL)
2017 May–2017 Dec Quantitative Geneticist (Postdoc) — University of Illinois - Urbana-Champaign, IL
Led and managed undergraduate students and technicians in the installation of over 2,000
minirhizotron tubes in field to image and study maize roots with
Bartz imaging systems; and collections of minirhizotron images, moisture data, flowering, above ground biomass and yield harvest. Identified genetics basis for maize root structure and control of plant nutrient relations in Illinois Protein Strain Recombinant Inbred (IPSRI) lines of maize
2012—2017 Graduate Research Assistant (PhD) - University of Missouri Columbia, USA
Involved in the development of novel genetic resource and mapping populations such as near isogenic and synthetic lines derived from domesticated corn and its wild relative, Teosinte. Conducted
Joint linkage QTL analysis and Genome wide association study to elucidate several aspects of genetic diversity in maize; genetic basis of various agronomic, fitness and yield related traits such as seed quality and composition in trials conducted with multiple replications in different environment and year. Investigated gene by gene epistatic interactions for various adaptation and domestication related traits in trials with multiple replications and environment.
2009-2012 Undergraduate Research Assistant (BSc) - Truman State University, USA
Conducted molecular genetic analysis to exploit the biodiversity of exotic inbred lines from Central and South America to develop high amylose corn using SSR markers and gel electrophoresis. Assisted in preparing summer maize nurseries such as plowing field with a tractor, planting seeds with hand and dumping seed in seed planter, pollinating and collecting various agronomic data from field trials, harvesting and analyzing data. Developed gene specific molecular markers to select alleles responsible for high amylose in maize kernels with better yield, which I validated their stability in trials conducted in multiple replications in different environments. Wrote annual USDA-ARS Germplasm Enhancement of Maize (GEM) report and presented at ASTA meeting in Chicago, Illinois.
2008-2012 Cafeteria student worker - Sodexo Inc. , USA
Served and stocked food as well as performed all the cleaning related activities in the cafeteria.
2011-2012 Comparative genomics researcher - Truman State University, USA
Analyzed retained homeologous paralog pairs from syntenic regions in Maize and Sorghum. Visualized genomic data of approximately 1Mb in size in
CIRCOS, and conducted comparative genetic study in online tools such as
GeVo function in CoGe, Annotated genes using
InterProScan and expression analysis data from
Summer 2009 & 2012 NSF TruScholars Research Program - Truman State University, USA
Designed gene specific molecular marker for a novel of starch branching enzyme Ia (SBE-1a) allele involved in high amylose starch in maize. Discovered novel recessive starch branching enzyme 1a (sbe1a) likely plays a significant role in the presence of the ae allele in elevating starch amylose from ~55% to >70% in the germplasm release ‘GEMS-0067’. Conducted linkage based mapping studies to identify QTLs for high amylose starch in maize using SSR markers and
QTL cartographer software. Sequenced starch branching enzyme allele (SBE1a) from high amylose maize line, GEMS-0067; Discovered 8bp insertion site at intron 9 resulting splicing mutation, which putatively resulted in truncated protein product post-translation.
A rhAmpSeq haplotype strategy targeting the collinear core genome improves marker transferability across a diverse genus
Cheng Zou, Avinash Karn, Bruce Reisch, Allen Nguyen, Yongming Sun, Yun Bao, Michael S. Campbell, Deanna Church, Stephen Williams, Timothy P. L. Smith, Anne Fennell, Doreen Ware, Jason Londo, Qi Sun and Lance Cadle-Davidson (2018) (In review) Nature Biotechnology
Computational analysis of AmpSeq data for targeted, high-throughput genotyping of amplicons
Jonathan Fresnedo-Ramírez , Shanshan Yang , Qi Sun, Avinash Karn , Bruce I. Reisch, Lance Cadle-Davidson (2018) (Accepted) Frontiers in Plant Sciences
Genome-Wide Association Study (GWAS) and Linkage Mapping Reveal a Major QTL Underlying Acylated Anthocyanin Levels in Grapevine Hybrid Families
Avinash Karn, Shanshan Yang, Cheng Zou, Fred Gouker, Jonathan Fresnedo-Ramírez, Qi Sun, Jason Londo, Bruce I. Reisch, Gavin Sacks, and Lance Cadle-Davidson (In preparation)
Genetic Analysis of Teosinte Alleles for Kernel Composition Traits in Maize
Karn, Avinash, Gillman, J. D., & Flint-Garcia, S. A. (2017) G3: Genes, Genomes, Genetics
Development of Rigorous Fatty Acid Near-Infrared Spectroscopy Quantitation Methods in Support of Soybean Oil Improvement.
Karn, Avinash, Heim, C., Flint-Garcia, S., Bilyeu, K., & Gillman, J. (2016) Journal of the American Oil Chemists
Breeding Specialty Starch Maize Using Exotic Genetic Resources for Gene Discovery of Novel Alleles and Modifiers with Materials Generated from the USDA-ARS GEM Project (2011)
Karn, Avinash, Brent Buckner, Diane Janick-Buckner, Mark Campbell, Michael Blanco, Marvin Scott, and Adrienne Moran Lauter . Maize Genetics Conference Abstracts
MS Command prompt and
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