Development of High-Density Intra-Specific Linkage Map Using Genotyping By Sequencing (GBS) in Lettuce

Genotyping by sequencing (GBS) has been developed as an affordable application of NGS for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. In this study we employed a double restriction enzyme digestion protocol (HindIII and NlaIII) to study a RIL mapping population generated from a cross of Salinas88 × La Brillante cultivars.  Libraries were generated as 96-plex pools. The library was sequenced on an Illumina Hiseq machine producing a total of 374 M reads.  A total of 83,318 high quality SNPs were identified as polymorphic between the parents and evaluated in the RIL population. Redundant genotyping information was condensed per scaffold producing haplotyping data for a total of 4,452 scaffolds. After filtering based on missing data and number of SNPs per scaffold, a total of 1,798 scaffolds were selected as markers to construct the linkage map. The resultant linkage map consists of 1,773 scaffolds mapped to 15 linkage groups (Lg) with a total length of 1,840 cM.  QTL analysis confirmed a major QTL for shelf life on linkage group 4 and revealed additional QTLs on Lg1, Lg3 and Lg5.