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Title: Development of a high-density intra-specific linkage map of lettuce using genotyping by sequencing (GBS)

item GALEANO, CARLOS - University Of California
item FROENICKE, LUTZ - University Of California
item DUITAMA, JORGE - International Center For Tropical Agriculture (CIAT)
item KOZIK, ALEXANDER - University Of California
item REYES-CHIN-WO, SEBASTIAN - University Of California
item CARRASQUILLA-GARCIA, NOELIA - University Of California
item Simko, Ivan
item Hayes, Ryan
item MICHELMORE, RICHARD - University Of California

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/6/2013
Publication Date: 1/13/2014
Citation: Galeano, C.H., Froenicke, L., Duitama, J., Kozik, A., Reyes-Chin-Wo, S., Simko, I., Hayes, R.J., Michelmore, R. 2014. Development of a high-density intra-specific linkage map of lettuce using genotyping by sequencing (GBS). Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, California. P686.

Interpretive Summary: Rapid advances in “next-generation” DNA sequencing technology have changed the way populations are genotyped. Genotyping by sequencing (GBS) has been developed as a rapid and robust approach for reduced-representation sequencing of multiplexed samples that combines genome-wide molecular marker discovery and genotyping .The flexibility and low-cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. The objective of this study was to use GBS technology in lettuce (Lactuca sativa L.) to saturate the genetic map of a RIL population from Salinas x La Brillante and confirm the localization of a QTL for decay of cut lettuce. The GBS protocol described allows the identification of large numbers of high quality SNPs in lettuce in a cost-effective manner. The GBS protocol and pipeline are suited to the analysis of any species for which a reference genome is available.

Technical Abstract: Genotyping by sequencing (GBS) has been developed as an affordable application of next-generation sequencing 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 Salinas 88 × La Brillante (SLB) 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 9 linkage groups (Lg) with a total length of 1,827 cM. QTL analysis confirmed a major QTL for shelf life on linkage group 4 and revealed additional QTLs on Lg1, Lg3, Lg5 and Lg9.