An Ultra-High Density, Sequencing-Based Genetic Map Improve the Reference Genome of Asian Lotus

Lotus is a basal eudicot and belongs to the genus Nelumbo. This genus consists of two species, Nelumbo nucifera (Asian lotus) and Nelumbo lutea (American lotus). It has been cultivated for 7000 years throughout Asia for ornamental, edible, medicinal and religious purposes. We have assembled the draft genome of Asian lotus ‘China Antique’ which was based on the genetic map of American lotus. However, the genome might not be correctly assembled because of potential chromosomal rearrangements between these two species. In order to optimize the draft genome, we constructed an SNP-based high-density genetic map of Asian lotus and reassembled the genome of ‘China Antique’. An F₂ population of 91 individuals was derived from Nelumbo nucifera ‘Baige’ and ‘Donghe’. A total of 174.2 Gb of raw data were generated by re-sequencing. The coverage of reads on a reference genome was 6.4 x for the parents and 2.2 x for the individuals. From these reads, 321,706 SNPs were identified, and 24,868 valid SNPs for F₂ population were used for genetic map construction. We defined the block of the same genotype across of all individuals as a bin and constructed a genetic map spanning 637.62 cM with bin markers. 1,171 bins including 19,599 SNPs were anchored on eight linkage groups corresponding to eight chromosomes. Based on SNP locations on the reference genome, the bin map was integrated with the genome scaffold. Two of ten top scaffolds, megascaffolds 1 and 2, were misassembled, and should be integrated with megascaffolds 4, 8, 9 and 5, 6, 10 to anchor new scaffolds, respectively. We will continue to reassembly the genome of ‘China Antique’ and improve the reference genome using this genetic map.