W332
The Genome Sequence of Walnut (Juglans regia L.) cv “Chandler”

Date: Saturday, January 10, 2015
Time: 11:23 AM
Room: Pacific Salon 3
Pedro J Martínez-García , Department of Plant Sciences University of California, Davis, CA
Marc Crepeau , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD
Daniel Gonzalez-Ibeas , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Kristian Stevens , Department of Evolution and Ecology, University of California, Davis, Davis, CA
Jeanne Whalen , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Tim Butterfield , UCDAVIS, DAVIS, CA
Russell Reagan , UCDAVIS, DAVIS, CA
Monica T. Britton , UC Davis Genome Center, Davis, CA
Randi Famula , Dept. Plant Sciences University of California Davis, Davis, CA
Charis Cardeno , University of California, Davis, Davis, CA
Mallikarjuna Aradhya , USDA National Clonal Germplasm Repository, Davis, CA
Charles Leslie , University of California - Davis, DAVIS, CA
Abhaya Dandekar , University of California Davis, Davis, CA
Steven L Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD
Jill Wegrzyn , Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
Charles H. Langley , Department of Evolution and Ecology, University of California, Davis, Davis, CA
David Neale , Dept. Plant Sciences University of California Davis, Davis, CA
The Persian walnut (Juglans regia), also known as the English or common walnut, is native to the mountainous regions of Central Asia and distinguished from other walnut species by its dehiscent husk, thin shells and thin septum separating the kernel halves, traits which greatly facilitate kernel extraction. Annual worldwide Persian walnut production is estimated at 3.2 million MT. The leading producers are China (1.7 million MT) followed by Iran, the United States, and Turkey (FAO, 2014). US production is located almost entirely in the state of California which has nearly 325,000 acres of walnut orchards (USDA NASS, 2014) producing 450,000 in-shell MTs annually. The Walnut Improvement Program (WIP) at UC Davis is one of the most important classical breeding programs for this species. A new collaborative group of researchers is working to increase the genomic tools and resources available for walnut in order to facilitate transition of the classical phenotype-based breeding effort into a genomics-based program. The first result of this undertaking is the recent draft genome sequence for the selected target cultivar, ‘Chandler’. This is the most widely grown and commercially important cultivar in California with annual production exceeding 200,000 MT (USDA NASS, 2014). In addition, Chandler is one of the most commonly used parental genotypes in breeding new selections. This genome presents a highly heterozygous sequence. Two different assembly methods (SOAPdenovo2 and MaSuRCA) were used. The final assembly contained 27,032 scaffolds over 1000 bp, with a total length of 667 Mbp and an N50 scaffold size of 415,376 (based on a 620 Mbp genome size). The draft consensus sequence has been annotated by over 1.2M SNPs. Two candidate genes, associated with biosynthesis and oxidation of polyphenols in walnuts, have been mapped to the draft sequence located in two scaffolds, super369 and jcf7180001214880. Walnut genome sequence information will facilitate diversity characterization of Juglans regia wild germplasm and breeding program material. The advances in genomics are beginning to provide walnut breeders with new tools and methodologies that will accelerate the breeding process and allow genetic dissection of complex traits.
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