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.
Highlights
Today’s major crop species are the results of thousands of years of intentional and unintentional selection of traits that brought genetically determined changes in the ancestral wild plant species (Burger et al, 2008)
Advanced generation sequencing technologies allow identification of thousands of polymorphic markers that have various applications including the determination of genetic diversity and development of high-density genetic linkage map in plant species
The present study revealed an average observed heterozygosity (Ho) of
Summary
Today’s major crop species are the results of thousands of years of intentional and unintentional selection of traits that brought genetically determined changes in the ancestral wild plant species (Burger et al, 2008). Domestication of a crop species is generally a very slow and long-term process that leads to significant changes in major traits that are regarded as “domestication syndrome” traits, such as determinate growth habit, increased seed size, loss of seed dormancy, and reduced pod shattering (Harlan et al, 1973; Doebley et al, 2006; Weeden, 2007; Burger et al, 2008). Progress in genomic research that include comparative genomics, gene identification, annotation of whole genome sequences (WGS), development of genomewide molecular markers, and genome-wide association studies (GWAS) for various crops led to deep insight into the process of plant domestication and evolution (Geleta and Ortiz, 2016). Through the use of these tools and resources and the analyses of the genetics of “domestication syndrome” traits, a good insight into the evolutionary changes that have occurred during plant domestication have been gained and can be used to facilitate a rapid domestication of new plant species
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