Slow Rate of Genome Evolution and Frequent Cycles of WGD followed by Dysploid Reduction in Woody Rosids

Two BAC libraries were constructed for walnut (Juglans regia, 2n=32) and 48,218 BAC end sequences (BES) were generated. SNPs located in coding sequences of BES (cdBES) were discovered and used to construct a walnut 6K Infinium assay. The assay was used to construct a walnut genetic map with 1,524 SNP markers. A total of 124,890 BAC clones was fingerprinted with the SNaPshot fingerprinting technique and assembled into contigs. A total of 561 contigs were anchored on the genetic map, thus generating a physical map of the walnut genome. The estimated genome size on the basis of the physical map was 736.1 Mb, which was close to the 1C walnut genome size of 606 Mb. This comparative physical map contains 15,203 cdBES. They were used to assess synteny between the walnut genome and the grape (Vitis vinifera), poplar (Populus trichocarpa), apple (Malus domestica), Medicago truncatula, and cucumber (Cucumis sativa) genomes. In each comparison, syntenic blocks were delimited and quantified. The quantification revealed that a whole genome duplication (WGD) took place during the evolution of Juglandaceae. Eight pairs of homoeologous chromosomes were identified in the walnut genome. It was confirmed that independent WGDs are in the immediate ancestry of the poplar, apple, and cucumber genomes. Each of these Rosid lineages show cycles of an increase in chromosome number by WGD followed by a decrease in chromosome number by dysploidy. Among Rosid species, quantification of synteny revealed slow genome evolution in the lineages of woody perennials compared to those of herbs.