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GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)

View ORCID ProfileB Gemeinholzer, O Rupp, View ORCID ProfileA Becker, M. Strickert, C-M Müller
doi: https://doi.org/10.1101/2021.11.30.470612
B Gemeinholzer
aUniversity Kassel, Botany, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
eSystematic Botany, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 38, D-35392 Giessen, Germany
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O Rupp
bBioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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A Becker
cEvolutionary Developmental Biology of Plants, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 38, D-35392 Giessen, Germany
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M. Strickert
dII. Physikalisches Institut, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 1, D 35392 Gießen
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C-M Müller
eSystematic Botany, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 38, D-35392 Giessen, Germany
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Abstract

The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost transcriptome analysis (mRNA-GBS) with reduced complexity and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. The use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Our mRNA-GBS approach revealed too many additional short mRNA sequences, hampering sequence alignment depth and SNP recovery. Optimizations are being discussed. Nevertheless, our study design across different regions in Germany was also challenging as the use of differential expression analyses with reduced complexity, in which mRNA is fragmented at specific sites rather than randomly, is most likely counteracted under natural conditions by highly complex plant reactions at low sequencing depth.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted December 02, 2021.
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GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)
B Gemeinholzer, O Rupp, A Becker, M. Strickert, C-M Müller
bioRxiv 2021.11.30.470612; doi: https://doi.org/10.1101/2021.11.30.470612
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GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)
B Gemeinholzer, O Rupp, A Becker, M. Strickert, C-M Müller
bioRxiv 2021.11.30.470612; doi: https://doi.org/10.1101/2021.11.30.470612

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