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Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays

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Abstract

Key message

Polymorphic probes identified via a sequence-based approach are suitable to infer the genotypes of recombinant inbred lines from hybridisation intensities of GeneChip ® transcript profiling experiments.

Abstract

The sequences of the probes of the ATH1 GeneChip® exactly match transcript sequences of the Arabidopsis thaliana reference genome Col-0, whereas nucleotide differences and/or insertions/deletions may be observed for transcripts of other A. thaliana accessions. Individual probes of the GeneChip® that show sequence polymorphisms between different A. thaliana accessions may serve as single-feature polymorphism (SFP) markers, provided that the sequence changes cause differences in hybridisation intensity for the accessions of interest. A sequence-based approach identified features on the high-density oligonucleotide array that showed sequence polymorphisms between A. thaliana accessions Col-0 and C24. Hybridisation intensities of polymorphic probes were extracted from genome-wide transcript profiles of Col-0/C24 and C24/Col-0 recombinant inbred lines and assessed after standardisation via sliding window analyses to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and the resulting data were integrated with information, which had been established previously with single nucleotide polymorphism and insertion/deletion markers, to enrich the linkage map of the Col-0/C24 and C24/Col-0 recombinant inbred populations. Congruence between the molecular marker map and the sequence maps of the A. thaliana Col-0 chromosomes proved the reliability of the genotype information which was deduced from the transcript profiles of the Col-0/C24 and C24/Col-0 recombinant inbred lines.

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Abbreviations

DAF:

Days after flower opening

eQTL:

Expression quantitative trait loci

GS:

Gap size

GEO:

Gene Expression Omnibus

IM:

Invariant match

Indel:

Insertion/deletion

PM:

Perfect match

RA:

Ratio

RIL:

Recombinant inbred line

SFP:

Single-feature polymorphism

SNP:

Single nucleotide polymorphism

VM:

Variant match

WS:

Window size

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Acknowledgements

Aspects of this study were funded through BMBF grant GABI-OIL (0315053G).The authors thank Dmitri Pescianschi for support during the custom C++ script development and Jahnavi Koppolu for her contribution to the analysis of plant phenotypes. Kristin Langanke and Angelika Flieger are acknowledged for skilful technical assistance.

Author information

Author notes

  1. Hieu Xuan Cao

    Present address: Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany

  2. Renate Schmidt and Anastassia Boudichevskaia equally contributed to this study.

Authors and Affiliations

  1. Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany

    Renate Schmidt, Anastassia Boudichevskaia, Hieu Xuan Cao, Sang He & Jochen Christoph Reif

  2. Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany

    Rhonda Christiane Meyer

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  1. Renate Schmidt
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Corresponding author

Correspondence to Renate Schmidt.

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The authors declare that they have no conflict of interest.

Additional information

Communicated by Dr. Jim Register.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file 1: Identification of probe sets containing VM and IM probes. (DOCX 17 kb)

299_2017_2200_MOESM2_ESM.xlsx

Supplementary file 2: RA values of recombinant inbred lines and parental lines Col-0 and C24. For the parental lines values for three replicates each are given, for the RILs a single replicate each was analysed. (XLSX 29898 kb)

Supplementary file 3: Strategy for identification of putative SFP markers and genotype assignment. (DOCX 17 kb)

299_2017_2200_MOESM4_ESM.xlsx

Supplementary file 4: Alignment of ATH1 probe sequences to the Col-0 and C24 genomes that provided the basis for SFP marker identification. Column “Best hit note” summarises the results of sequence alignments with Bowtie, only alignments containing up to three mismatches but no Indels are listed for each probe. IM, invariant match denotes a probe that shows unique perfect matches when compared to the Col-0 and C24 genomes; PM, unique perfect match; MisM, unique match containing between one and three mismatches but no Indel(s); NoM, no match or matches that contain Indels and/or more than three mismatches; VM, variant match refers to probes that reveals a unique perfect match when compared to the Col-0 genome whereas the C24 genome shows at least one mismatch or no alignment at all. For the VM probes the positions and identity of SNPs in the oligonucleotide sequences are indicated in the column “C24 SNPs”. (XLSX 6445 kb)

299_2017_2200_MOESM5_ESM.xlsx

Supplementary file 5: Graphical genotypes of recombinant inbred lines. Thresholds determined with different sliding window parameters were used to deduce the RIL genotypes for the different SFP markers. WS 5/GS 2* and WS 3/GS 1* refer to consensus genotype scores that were based on eight different parameter combinations of the sliding window analysis (WS 2/GS 2, WS 3/GS 1, WS 3/GP 2, WS 4/GS 1, WS 4/GS 2, WS 5/GS 0, WS 5/GS 1, WS 5/GS 2). SFP markers were ordered according to their position on the chromosome sequence maps of the reference accession Col-0 with the exception of the 23 unreliable SFP markers which are shown at the end of the compilation. Col-0 and C24 genotypes are denoted “a” and “b”, respectively. Putative double-recombination events that were identified by a single SFP marker are shown in italics and are marked with the postfix “-DR”. “NDR” marks those scores for which genotypes were not assigned. (XLSX 11659 kb)

Supplementary file 6: Construction of the bin map (DOCX 76 kb)

299_2017_2200_MOESM7_ESM.xlsx

Supplementary file 7: Molecular marker map of recombinant inbred lines. The cumulative genetic distances are given for all markers which were used for the bin map in cM. For each marker it is indicated whether it represents an SNP, Indel or SFP marker. SFP marker names correspond to the probe set they were derived from (XLSX 26 kb)

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Schmidt, R., Boudichevskaia, A., Cao, H.X. et al. Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays. Plant Cell Rep 36, 1871–1881 (2017). https://doi.org/10.1007/s00299-017-2200-6

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