Biology subjects

Skovbjerg, C. K.

Publications and source records attributed to Skovbjerg, C. K..

5 recordsLinked to original sources

bioRxiv2024

Genome-wide association studies identify promising QTL for freezing tolerance in winter and early spring as a basis for in-depth genetic analysis and implementation in winter faba bean (Vicia faba L.) breeding

Interest in faba bean as a locally adapted high-protein grain legume crop has increased in Europe over the past decade. Winter faba bean, which can make use of soil moisture from autumn to spring and partially escape summer droughts, exhibit greater yield potential than the spring-type. However, due to insufficient winter hardiness, winterkill is a major constraint that prevents large-scale production of current winter-type cultivars in Central and Northern Europe. Here, we extend the understanding of freezing tolerance, the main component trait of winter hardiness, during winter and against late-frost in early spring and define genomic target regions for marker-assisted selection. Comparative analysis of genome-wide association studies revealed 13 treatment-specific major QTLs with partially pleiotropic effect on four freezing tolerance related traits. In addition, we identified five treatment-unspecific pleiotropic QTLs, including two major freezing tolerance loci on chromosomes 1 and 5. Our results thus indicate both a distinct and common genetic control of tolerance to winter- and late-frost in winter faba bean. In combination with the promising prediction abilities obtained from marker score-based prediction, our work highlights the potential for marker-assisted and genomic selection toward improved freezing tolerance and winter hardiness in winter faba bean breeding programs.

genetics↗

bioRxiv2021

Major effect loci for plant size before onset of nitrogen fixation allow accurate prediction of yield in white clover

White clover is an agriculturally important forage legume grown throughout temperate regions as a mixed clover-grass crop. It is typically cultivated with low nitrogen input, making yield dependent on nitrogen fixation by rhizobia in root nodules. Here, we investigate the effects of clover and rhizobium genetic variation by monitoring plant growth and quantifying dry matter yield of 704 combinations of 145 clover and 169 rhizobium genotypes. We find no significant effect of rhizobium variation. In contrast, we can predict yield based on a few white clover markers strongly associated with plant size prior to nitrogen fixation, and the prediction accuracy for polycross offspring yield is remarkably high. Several of the markers are located near a homolog of Arabidopsis thaliana GIGANTUS 1, which regulates growth rate and biomass accumulation. Our work provides fundamental insight into the genetics of white clover yield and identifies specific candidate genes as breeding targets.

plant biology↗

bioRxiv2019

Evaluation of yield, yield stability and yield-protein trade-off in commercial faba bean cultivars

Faba bean is a legume crop with high protein content and large potential for cultivation in the Northern latitudes. However, it has a reputation for being an unstable crop with large inter-annual variability, mostly explained by yearly variation in rainfall. Consequently, the objective is to breed cultivars with high seed yield and high yield stability. In this study, 17 commercial cultivars of faba bean were evaluated for seed yield, yield stability and trade-off between seed yield and protein content in four locations in Denmark and Finland during 2016-2018. We found that location and year effects accounted for 72% of the total seed yield variation. Cultivar by environment interactions (GxE) were found to be small and did not cause re-ranking of cultivars in different environments. Yield stability contributed little to the mean yield of the cultivars because high-yielding cultivars consistently outperformed the lower yielding genotypes, even under the most adverse conditions. The latter was also the case for total protein yield quantified as total yield multiplied by seed protein percentage. Although we found a strong negative correlation of -0.64 between yield and protein content, a few cultivars produced high yields while maintaining a relatively high protein content, suggesting that these traits may to some degree be genetically separable.

plant biology↗

bioRxiv2019

Syntenizer 3000: Synteny-based analysis of orthologous gene groups

MotivationThe amorphous nature of genes combined with the prevalence of duplication events makes establishing correct genetic phylogenies challenging.\n\nSince homologous gene groups are traditionally formed on basis of sequence similarity, both orthologs and paralogs are often placed in the same gene group by existing tools. Certain tools such as PoFF take syntenic relationship of genes into consideration when forming gene groups. However, a method to form gene groups consisting of only true syntelogs has not yet been developed.\n\nIn order to obtain orthologous gene groups consisting of the most likely syntelogs we need a method to filter out paralogs. If one strain has two or more copies of the same gene in a gene group we want to keep only the true syntelog in the group, and remove the paralogous copies by distinguishing between the two using synteny analysis.\n\nResultsWe present a novel algorithm for measuring the degree of synteny shared between two genes and successfully disambiguate gene groups. This synteny measure is the basis for a number of other useful functions such as gene neighbourhood visualisation to inspect suspect gene groups, strain visualisation for assessing assembly quality and finding genomic areas of interest, and chromosome/plasmid classification of contigs in partially classified datasets.\n\nAvailabilityThe latest version of Syntenizer 3000 can be downloaded from the GitHub repository at https://github.com/kamiboy/Syntenizer3000/\n\nConsult the manual.pdf file in the repository for instructions on how to build and use the tool, as well as a in depth explanation of the algorithms utilised.

bioinformatics↗

bioRxiv2018

Extreme genetic signatures of local adaptation during plant colonization

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with the recent colonization of Japan by Lotus japonicus. We carefully track the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We characterize the loss of diversity during this process and identify genomic regions with extreme genetic differentiation. Next, we perform population structure-corrected association mapping of phenotypic traits measured in a common garden and discover a number of genome-wide significant associations. Contrasting these analyses, we find that there is a strong concordance between phenotypic variation and extreme differentiation for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection by local adaptation during the colonization process and point to associated candidate genes.

evolutionary biology↗