CAHNRS Department of Horticulture Genomics Lab

Genomics

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With the sequencing of several genomes, genomics research in non-model plant species has entered a new era. The US West Coast and the State of Washington produce some of the best fruit crops globally. Research in the program focuses on basic and applied aspects of the non-model specialty crops and bioenergy crops for their improvement.

The importance of being . . . green?

Development of a fruit is accompanied by changes in pigment and several secondary metabolic processes are in full swing at this transitional phase. Organelles, namely chloroplast and mitochondria, are the major centers of activity during this period. The basic research emphasis in the program is to understand plastid development and function in Rosaceae fruit and non-model crops. Mature fruit plastids have been found to be involved in the synthesis and storage of important phytonutrients such as carotenoids and tocopherols as well as precursors to volatiles that play a role in organoleptic properties as well as pre- and postharvest fruit quality. Evaluation of diverse plastidial functions in fruit and bioenergy crops is expected to provide clues about energy transduction that can enable understanding and alleviation of several physiological disorders as well as improvement of photosynthetic function for improved productivity.

The applied research in the program is centered on using physiology and phenomics-guided omics (genomics, transcriptomics, proteomics and metabolomics) investigations to identify genes underlying economically important traits in horticultural and specialty crops. Further, as candidate genes are discovered, reverse and forward genetics approaches are used to confirm gene-trait relationships. The information generated from this approach can be practically utilized in developing physiological and chemical-based solutions for existing varieties and new varieties can be developed through accelerated plant breeding and biotechnology approaches.

Plant Genomics Perspectives

The Pear Revival Journey

March 12, 2013

Soon after arriving at WSU in 2006, I embarked on a journey with a passionate set of individuals to revive an industry that has remained in suspended animation since the early 1900s. An email from a pear farmer in Yakima urged me to apply for funding to do pear research. That was my first introduction to a segment of the Pacific Northwest fruit industry that, while long an underdog relative to apples, has long sought to reinvent itself for the 21st century marketplace. Read more.

Issues Facing the Pacific Northwest Pear Industry

December 4, 2011

Watch video.

Innovation Crucial to Pear’s Future

September 2, 2011

This just in from The Packer: “Innovation crucial to pear’s future” In general, the pear industry is making money but is fragile because of a lack of innovation, said Amit Dhingra, a Washington State University horticultural genomicist. Read more.

 

Latest News

Pears, Gooseberries and the Future Foresters

From BBC Radio 4: New research by scientists at Washington State University in the U.S. has discovered ripening compounds that could bring an end to the crunchy unripe pear which suddenly goes bad, without becoming ripe at all. Listen or Read More

The Push to Make Pears the New Apple

Amit Dhingra is on a mission to make America fall in love with the pear.

In a lab at Washington State University, the 45-year-old horticulture researcher has dedicated much of the last decade to the shapely fruit. Building off relationships with pear growers who say their businesses are held back by a lack of scientific understanding of their product, Dhingra has mapped the pear genome, bred new trees, and even found a way to ripen the notoriously stiff fruit. Read More Here

by Taryn Phaneuf , The Atlantic

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites, now available

CisSERS, open source software for analyzing sequence data, developed at WSU.

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Read the rest of this PLOS article.

 

Citation: Sharpe RM, Koepke T, Harper A, Grimes J, Galli M, Satoh-Cruz M, et al. (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PLoS ONE 11(4): e0152404. doi:10.1371/journal.pone.0152404