Whole Genome Profiling Based Physical Map of Field Pea

Field pea (Pisum sativum L.) has an expected genome size of 3947 to 4397Mbp and the estimated size of repetitive sequences is 85% of the genome size. The primary objective of this study is to construct a sequence-based physical map of pea to address the repetitive sequences which are difficult to handle with traditional restriction digestion based physical maps. Whole genome profiling (WGP, Keygene^TM), a technology based on generation of short sequence tags from terminal ends of restriction fragments of individual BAC clones, is used for the physical map construction. A total of 295,680 BAC clones were pooled in a multi-dimensional manner. DNA from individual pool is restriction digested with EcoRI and MseI restriction enzymes. The EcoRI restriction site ends of the fragments were sequenced using the Illumina Hiseq2000 with 100nt read length. A total of 825.2 million deconvolutable reads were generated, of which 1.11 million reads were unique and are considered as WGP tags. These tags corresponded to 220,013 BACs. The sequence tagged BACs were used to assemble individual BAC clones into contigs and superBACs using modified FPC software (Keygene N.V.). Of the 220,013 BACs, 213,719 BACs were grouped into 13,040 contigs with an average contig size of 0.33Mbp. The N₅₀ contig size is 42 BACs and 0.62 Mbp. Other 6,294 BACs remained as singletons. The Mbp coverage of BAC contigs and singletons is 4294 Mbp. The order and estimated size of the physical map will be compared with the estimated genetic distances of a high density SNP linkage map of Cameor x China recombinant inbred line mapping population.