Dataset Information

Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop.

ABSTRACT:

Background

The 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.

Results

Homologues 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.

Conclusions

There 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.

SUBMITTER: Gustafsson C

PROVIDER: S-EPMC5975587 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Parallels exist between the domestication of new species and the improvement of various crops through selection on traits which favor the sowing, harvest and retention of yield potential and the directed efforts to improve their agronomics, disease resistance and quality characteristics. Common selection pressures may result in the parallel selection of orthologs underlying these traits and homologies between crop species can be exploited by plant breeders to improve germplasm. Perennial grains and oilseeds are a class of proposed crops for improving the diversity and sustainability of agricultural systems. Maximilian sunflower (Helianthus maximiliani Schrad.) is a perennial crop wild relative of sunflower (Helianthus annuus L.) and a candidate perennial oilseed species. Understanding parallels between cultivated H. annuus and H. maximiliani may provide new tools for the development of Maximilian sunflower and other wild relatives of sunflower as crops to enhance functional diversity in cropping systems. F2 populations of Maximilian sunflower segregating for traits associated with the domestication ideotype of cultivated sunflower including branching architecture, capitulum morphology and flowering time were developed to investigate parallels between H. maximiliani and H. annuus. Genotype-by-sequencing (GBS) was employed to genotype novel Maximilian sunflower populations and perform quantitative-trait-loci (QTL) analysis. A total of 11 QTL in five regions were identified across 21 linkage groups using 4142 GBS derived single nucleotide polymorphism markers called using the sunflower reference genome as a guide. A major QTL on linkage group 17b, associated with aspects of floral development and apical dominance, was discovered and corresponds with a known domestication QTL hotspot in H. annuus and candidate genes were identified. This suggests the potential to exploit orthologs for neo-domestication of H. maximiliani for traits such as branching architecture, timing of anthesis, and capitulum size and morphology for the development of a perennial oilseed crop from wild relatives of cultivated sunflower.