Abstract
BackgroundThe changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits.ResultsHomologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum.ConclusionsThere is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.
Highlights
The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops
To identify polymorphisms that may contribute to domestication syndrome traits, perenniality and oil content and quality, partial sequences of 30 genes were analyzed in Lepidium
The protein coding sequences of field cress showed a high level of homology to A. thaliana with the sequence identity between A. thaliana and field cress ranging between 81 to 98% with a mean value of 89.2% (Table 2)
Summary
The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Domestication is the process of selecting genetic polymorphisms for traits that suit human needs. The use of genomic tools and resources can speed up a domestication process as breeders can select plants bearing desirable traits before the traits have been expressed, using appropriate DNA markers and high-throughput precise phenotyping. While farming systems with annual crops have provided us with unprecedented yield, they have contributed to ecosystem problems such as soil erosion and water runoff [2]. Perennial crops normally have deeper root systems that can prevent soil erosion, reduce water runoff and nutrient leakage. There are currently interesting attempts to develop perennial oil crops such as sunflower [5]
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