Whole-genome mapping reveals QTLs linked to key agronomic traits in bi-parental populations of field cress (Lepidium campestre)

Abstract

Abstract Background Field cress, Lepidium campestre, is an oil and catch crop undergoing domestication for the Nordic region. In this study, the genetic bases of domestication-related traits of field cress are identified using three bi-parental F2 mapping populations (MPs). The MPs were phenotyped for plant height (PH), inflorescence length (IL), pod density (PD), seed yield per plant (SYPP), seed dormancy (SD), and pod shattering measured with two different parameters (PSH1 and PSH2). Results The MPs were genotyped, with a targeted Genotyping-by-sequencing (GBS) method, SeqSNP, using 9,378 Single Nucleotide Polymorphisms (SNP) spanning across eight linkage groups (LGs) of field cress. There was wide phenotypic variation among the individuals for the agronomic traits measured in all MPs. A linkage map was constructed for each MP by mapping high-quality SNPs spanning 607 cM, 893 cM, and 732 cM to the eight field cress LGs, in each of the respective MPs. Quantitative trait loci (QTLs) mapping identified nine QTLs linked to PSH2, three for PH, two for SYPP, and one each for SD, IL, and PD distributed across all LGs. Taking advantage of field cress genome synteny with Arabidopsis thaliana chromosomes, annotation of the genes found within a major QTL for PSH2 found in LG5 (for MP3) revealed putative roles related to flowering, seed, and siliques development, cellulose and lignin biosynthesis, and water loss prevention. Conclusion This study identified QTLs for multiple domestication-related traits and provides genomic resources useful for applying novel breeding tools to accelerate field cress domestication and improvement.

Keywords

• De novo domestication
• Domestication-syndrome traits
• Genotyping-by-sequencing
• Linkage group
• SeqSNP
• Single nucleotide polymorphism