Development of Pineapple (Ananas comosus L.) Genetic Map with Restriction Site Associated DNA (RAD) Markers

Pineapple is the third most cultivated tropical fruit in the world with a worldwide gross production value of USD $9.9 billion in 2011. The global pineapple industry has heavily relied on a single cultivar, “Smooth Cayenne”, for more than a century in fresh fruit production and canning. Breeding research of new diseases-resistance cultivars with desirable fruit traits can be enhanced with the availability of genomic and genetic resources. The pineapple genome was sequenced using an integrative whole genome shotgun approach generating a scaffold N50 of 401kb and an assembly that covers 333Mb of the estimated 525Mb genome. To facilitate the scaffold anchoring and orientation, a high density genetic map was constructed using an F2 population of Ananas comosus var. comosus cultivar “Smooth Cayenne” F153 crossed with Ananas comosus var. bracteatus Hana64, using Restriction site Associated DNA (RAD) markers. 1,240 high quality SNP markers were scored between the parents and 56 offsprings and mapped into 30 linkage groups (LGs), with a combined length of 2,227cM. These markers anchored 318 scaffolds, which represent 153Mb (46%) of the assembled genome. This genetic map facilitates the assembly of pineapple genome and serves as a foundation for mapping economical traits, such as fruit size and spineless leaves in QTL studies.