Integration of Sweet Orange Genetic and Physical Maps Using BAC End Sequence Based SNPs and GoldenGate Assay

Recent genome research and explorations have been revolutionized over the past decade due to rapidly evolving and widely used next-gen sequencing technologies and many freely available genomic resources. But efficient application of genomic information into genetics and breeding is still very limited, and relies on improvement of fragmented genome assembly and gene-trait linkage coverage. Integration of sweet orange genetic and BAC physical maps would greatly facilitate the improvement. In this report, SNPs were mined out from sweet orange BAC end sequences (BES) using 454 reads of the genome. After validation by sequencing and SNaPshot assay, 1536 SNPs well distributed in the available sweet orange BAC physical map were selected to develop Illumina GoldenGate SNP platform, and used to genotype a citrange population. Using the segregating data, a BES SNP genetic map of sweet orange was constructed, and the integrated genetic and physical maps are being used to improve a fragmented sweet orange assembly.