High-Density Genetic Linkage Mapping of Lepidium 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.