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Research article - Peer-reviewed, 2020

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

Geleta, Mulatu; Gustafsson, Cecilia; Glaubitz, Jeffrey C.; Ortiz, Rodomiro

Abstract

Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 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 L. campestre 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 F2 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 (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1–Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.

Keywords

contig tag haplotype; field cress; genetic linkage mapping; genotyping by sequencing; Lepidium; linkage group; single-nucleotide polymorphism

Published in

Frontiers in Plant Science
2020, volume: 11, article number: 448

Authors' information

Geleta, Mulatu Dida (Dida, Mulatu Geleta)
Swedish University of Agricultural Sciences, Department of Plant Breeding
Gustafsson, Cecilia (Hammenhag, Cecilia)
Swedish University of Agricultural Sciences, Department of Plant Breeding
Glaubitz, Jeffrey C.
Cornell University
Ortiz, Rodomiro (Ortiz Rios, Rodomiro Octavio)
Swedish University of Agricultural Sciences, Department of Plant Breeding

UKÄ Subject classification

Genetics and Breeding
Botany
Genetics

Publication Identifiers

DOI: https://doi.org/10.3389/fpls.2020.00448

URI (permanent link to this page)

https://res.slu.se/id/publ/105355