High Resolution Detection of Recombination Events in RILs by Genomic Shotgun Sequencing at Low Coverage

The genome of lettuce has been sequenced through a collaboration between the UC Davis Genome Center and BGI, funded by ten breeding companies. The current assembly comprises of ~21,500 scaffolds covering ~90% of the estimated 2.7 Gb genome [https://lgr.genomecenter.ucdavis.edu/].  We used Genotyping by Shotgun Sequencing (GBSS) to analyze a population of Recombinant Inbred Lines (RILs) from a cross of Lactuca sativa x L. serriola.  Genomic reads of parental lines were aligned to reference scaffolds at 10x coverage to identify variants between L. sativa and L. serriola. CLC Genomics Server variant analysis and filtering tools were used to select more than twelve million high quality SNPs segregating in the RIL population. Genomic libraries for one hundred RILs were sequenced at ~1x coverage and reads were aligned to scaffolds of the reference genome to infer the RIL haplotypes. A custom GBSS pipeline and subsequent genetic mapping allowed us to assign ~10,000 of the largest scaffolds (95% of assembled genome) to genetic bins ordered along the nine chromosomal linkage groups. Several hundred recombination events were detected within scaffolds. SNP density and RIL genomic read coverage determined the resolution with which we could locate the point of recombination. The size of the genotype transition regions varied from a few bases to several thousand nucleotides. Points of recombination are being analyzed relative to genic regions, transposable elements, repeat sequences, and other genome elements.  The technical details of the workflow with the use of CLC bio and other tools will be presented.