WALNUT GENOME ANALYSIS

The goal of this project is to build a set of comprehensive genomic tools for walnut. These will facilitate a more precise evaluation of breeding populations and will accelerate development of improved walnut cultivars to address the needs of both California growers and the consumers of this important agricultural commodity. Development of these tools includes (1) construction of a physical map of the walnut genome, (2) a detailed survey of walnut gene expression, and (3) fine-scale genetic and association mapping of economically important traits. Two bacterial artificial chromosome (BAC) libraries comprising a total of 129,024 clones (64,512 each) were constructed from Persian walnut (Juglans regia cv. Chandler) DNA. Average insert lengths were 135 kb (HindIII) and 120 kb (MboI) for the two libraries respectively, providing approximately 20x genome coverage. To date 124,890 BAC clones have been fingerprinted using the five-color SNaPshot HICF technology. The fingerprints have been edited, and 113,073 could be used for contig assembly with the FPC program. A total of 916 contigs and 4,830 singletons were obtained. A total of 54,912 BAC end sequences (BES) have also been produced, one BES per BAC. A mapping population of 265 progeny of the cross Chandler’ x ‘Idaho that segregates for all commercially important walnut traits was evaluated with 15 SSRs to verify the parentage of F1 progeny. In addition, the genetic structure of 399 trees among 204 diverse accessions, including 62 elite germplasm used for breeding, was employed in the development of a population for association mapping of walnut traits. A total of 21 cDNA libraries were constructed for the characterization of the walnut transcriptome using next generation DNA sequencing. These genomic tools will significantly strengthen ongoing California walnut breeding efforts by facilitating marker-assisted selection strategies. The use of well-defined markers will significantly increase selection efficiency, the discovery of new genes, and rapid integration of these genes into genetic backgrounds adapted to California environmental conditions, thus accelerating the development of improved walnut cultivars. PROJECT OBJECTIVES