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

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Abstract

Key message

Accurate genomic prediction of yield within and across generations was achieved by estimating the genetic merit of individual white clover genotypes based on extensive genetic replication using cloned material.

Abstract

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 genotypes and 170 rhizobium inocula. 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.

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Availability of data and material

RNA-seq reads were deposited in the Sequence Read Archive with bioproject ID PRJNA661141.

Code availability

The workflow for mapping and variant calling can be found at: https://github.com/MarniTausen/WhiteCloverRNAseq. All scripts used for statistical analyses and visualisation of data are available at: https://github.com/cks2903/White_Clover_GenomicPrediction_2020.

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Acknowledgements

We thank Finn Pedersen, Nanna Walther, Mike Ladefoged Damholdt and Karina A. Kristensen for plant work and greenhouse tending, M. Izabel C. Alves, Trine F. Gadeberg, Caroline Benfeldt, Camous Moslemi and Leandro A. Escobar-Herrera for help in the greenhouse, and Marc Clausen for implementing the technical part of the imaging system.

Funding

This work was funded by grant no. 4105-00007A from Innovation Fund Denmark (S.U.A.).

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Author notes

  1. Sara Moeskjær and Cathrine Kiel Skovbjerg have equally contributed to the work.

Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark

    Sara Moeskjær, Cathrine Kiel Skovbjerg, Rune Wind & Stig U. Andersen

  2. Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark

    Marni Tausen

  3. DLF, 4660, Store Heddinge, Denmark

    Niels Roulund

  4. Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus C, Denmark

    Marni Tausen & Luc Janss

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  1. Sara Moeskjær
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Contributions

S.U.A. and S.M were involved in conceptualization; C.K.S., S.M., S.U.A. and L.J. helped in methodology; C.K.S., L.J., M.T, S.M. and R.W. contributed to software; C.K.S., M.T., S.M., S.U.A. and L.J. were involved in validation; C.K.S., S.M., M.T. and R.W helped in formal analysis; S.M., C.K.S, M.T. and N.R. contributed to investigation; L.J., S.U.A. and N.R. were involved in resources; C.K.S., S.M. and M.T. helped in data curation; C.K.S. and S.M. contributed to writing—original draft; S.U.A., C.K.S. and S.M. were involved in writing—review & editing; S.M. and C.K.S. helped in visualisation; S.U.A. and L.J. contributed to supervision; S.U.A. was involved in project administration and funding acquisition.

Corresponding authors

Correspondence to Cathrine Kiel Skovbjerg or Stig U. Andersen.

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Conflict of interest

DLF has developed and marketed the cultivars Brianna, Klondike, Rabbani, Riesling, Silvester and Violin that were analysed in this study.

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Communicated by Matthew N Nelson.

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Moeskjær, S., Skovbjerg, C.K., Tausen, M. et al. Major effect loci for plant size before onset of nitrogen fixation allow accurate prediction of yield in white clover. Theor Appl Genet 135, 125–143 (2022). https://doi.org/10.1007/s00122-021-03955-3

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