Walnut Genome Analysis

The goal of this project is to build a set of comprehensive genomic tools to facilitate a more precise evaluation of breeding populations as well as to access unique germplasm for the walnut improvement program. A remaining deliverable was a genetic map that can be used to map phenotypic traits of significance for walnut quality and production. This map can be used to align any phenotypic trait to linkage groups that represent discreet regions on walnut chromosomes. Single nucleotide polymorphisms (SNPs) were used to create the map. These SNPs were identified by comparing three different sources of DNA sequence data, BAC end sequences, SOLiD shotgun genome sequence and RNAseq data obtained from 20 different cDNA libraries representing various walnut tissues. This comparison revealed ~6000 SNPs that were then processed by Illumina to create an Infinium array that was then used to create the linkage map by analyzing 352 progeny from a Chandler x Idaho cross. The data was processed and generated a very dense map with 35 linkage groups by assigning 1600 SNPs. The genetic map will accelerate development of improved walnut cultivars to address the needs of both California growers and the consumers of this important agricultural commodity. A total of 20 cDNA libraries were sequenced using next generation DNA sequencing to define the walnut transcriptome and over a billion reads were processed to obtain 85,045 consensus sequences or genes that define the gene space. 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.