Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

Zeratsion Abera Desta,Bozena Kolano,Zeeshan Shamim,Susan J Armstrong,Monika Rewers,Elwira Sliwinska,Sandeep Kumar Kushwaha,Isobel A P Parkin,Rodomiro Ortiz,Dirk-Jan De Koning

doi:10.1038/s41598-019-53320-0

Abstract

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

Highlights

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted
Our results provide the first glimpse of the genome of field cress and have posited on how to integrate multiple techniques – genetic map to comparative and molecular cytogenetic maps – elucidating the resources to effectively assign two linkage groups (LGs) to their chromosomes
Strikingly similar regions of the chromosome inert for crossovers were detected in both species including their hybrid individual, suggesting that these regions may be derived from their progenitor’s chromosomal rearrangements of these two species

Summary

Introduction

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably. Field cress could reduce fertilizer dependency (e.g. nitrogen fertilizer), which maintains the soil quality, thereby mitigating the current and future challenges of climate change. These www.nature.com/scientificreports foundational features of the species suggest the possibilities that could arise from domestication of field cress which has yet been underutilized and has been the focus of limited research. Linkage maps are further employed to detect quantitative trait loci (QTL), to anchor and orient annotated genome assemblies, and to locate candidate genes in fine mapping

Methods

Results

Conclusion