AUTHOR=Geleta Mulatu , Gustafsson Cecilia , Glaubitz Jeffrey C. , Ortiz Rodomiro 

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

JOURNAL=Frontiers in Plant Science

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.00448

DOI=10.3389/fpls.2020.00448

ISSN=1664-462X

ABSTRACT=<p><italic>Lepidium campestre</italic> has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of <italic>L. campestre</italic>, <italic>Lepidium heterophyllum</italic>, and their interspecific F<sub>2</sub> 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 <italic>L. campestre</italic> 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<sub>2</sub> 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 (<italic>LG</italic>s) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight <italic>LG</italic>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 (<italic>LG-4</italic>) to 20.4 Mpb (<italic>LG-7</italic>). The following major correspondence between the eight Lepidium <italic>LG</italic>s (<italic>LG-1</italic> to <italic>LG-8</italic>) and the five <italic>Arabidopsis thaliana</italic> (<italic>At</italic>) chromosomes (<italic>Atx-1</italic>–<italic>Atx-5</italic>) was revealed through comparative genomics analysis: <italic>LG-1&amp;2</italic>_<italic>Atx-1</italic>, <italic>LG-3</italic>_<italic>Atx</italic>-<italic>2</italic>&amp;<italic>3</italic>, <italic>LG-4</italic>_<italic>Atx-2</italic>, <italic>LG-5</italic>_<italic>Atx-2</italic>&amp;<italic>Atx-3</italic>, <italic>LG-6</italic>_<italic>Atx-4</italic>&amp;<italic>5</italic>, <italic>LG-7</italic>_<italic>Atx-4</italic>, and <italic>LG-8</italic>_<italic>Atx-5</italic>. This analysis revealed that at least 66% of the sequences of the <italic>LG</italic>s showed high collinearity with <italic>At</italic> chromosomes. The sequence identity between the corresponding regions of the <italic>LG</italic>s and <italic>At</italic> chromosomes ranged from 80.6% (<italic>LG-6</italic>) to 86.4% (<italic>LG-8</italic>) with overall mean of 82.9%. The map positions on <italic>Lepidium LGs</italic> of the homologs of 24 genes that regulate various traits in <italic>A. thaliana</italic> were also identified. The eight <italic>LG</italic>s revealed in this study confirm the previously reported (1) haploid chromosome number of eight in <italic>L. campestre</italic> and <italic>L. heterophyllum</italic> and (2) chromosomal fusion, translocation, and inversion events during the evolution of <italic>n</italic> = 8 karyotype in ancestral species shared by <italic>Lepidium</italic> and <italic>Arabidopsis</italic> to <italic>n</italic> = 5 karyotype in <italic>A. thaliana</italic>. This study generated highly useful genomic tools and resources for <italic>Lepidium</italic> that can be used to accelerate its domestication.</p>