High-Density Genetic Linkage Mapping of Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes.

has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of , , and their interspecific F mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (s) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight s, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp () to 20.4 Mpb (). The following major correspondence between the eight Lepidium s ( to ) and the five () chromosomes (-) was revealed through comparative genomics analysis: _, _-&, _, _&, _&, _, and _. This analysis revealed that at least 66% of the sequences of the s showed high collinearity with chromosomes. The sequence identity between the corresponding regions of the s and chromosomes ranged from 80.6% () to 86.4% () with overall mean of 82.9%. The map positions on of the homologs of 24 genes that regulate various traits in were also identified. The eight s revealed in this study confirm the previously reported (1) haploid chromosome number of eight in and and (2) chromosomal fusion, translocation, and inversion events during the evolution of = 8 karyotype in ancestral species shared by and to = 5 karyotype in . This study generated highly useful genomic tools and resources for that can be used to accelerate its domestication.