Additional file 13: Table S5. of Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping
Creators: name: Lars-Gernot Otto
name: Prodyut Mondal
name: Brassac, Jonathan
name: Preiss, Susanne
name: Degenhardt, Jörg
name: He, Sang
name: Reif, Jochen
name: Sharbel, Timothy
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: BLAST alignment results* for 5 and 13 sequences harbouring SNPs significantly associated with flowering time (FT) and alpha-bisabolol, respectively. * BLAST alignment results threshold: BLAST-score of &gt; = 80 with a sequence identity of &gt; = 80%/75% and an E-value &lt;1.33 × 10−13; (in brackets): results below the threshold (minimum BLAST-score of &gt;55 with a sequence identity of &gt; = 75% and an E-value &lt;1 × 10−4. The blastn algorithm was used for the analysis of the data, since the results obtained from tblastx were similar to the ones from blastn. Tblastx achieved not more hits above the significance threshold than blastn at the NCBI database. ** A more general annotation approach, an HMM (hidden Markov model) search through the Protein families database, did also not yield any results for sequence 6153. *** tblastx. The BLAST alignment of the 5 sequences harbouring significantly associated SNPs to FT (Additional file 12: Table S4) against the NCBI nucleotide collection of flowering plants identified 2 sequences with significant hits to potential candidate genes in multiple plant species (BLAST-score threshold see above, with a sequence identity of &gt; = 80%). Below the significance threshold, for 3 sequences an alignment to plant species could be done, but not for sequence 6153. (1) Jankowsky E. RNA Helicases at work: binding and rearranging. Trends in biochemical sciences. 2011;36(1):19–29. doi: 10.1016/j.tibs.2010.07.008 . (2) Kurasawa K, Matsui A, Yokoyama R, Kuriyama T, Yoshizumi T, Matsui M, Suwabe K, Watanabe M, Nishitani K. The AtXTH28 gene, a xyloglucan endotransglucosylase/hydrolase, is involved in automatic self-pollination in Arabidopsis thaliana. Plant Cell Physiol. 2009; 50(2):413–22. doi: 10.1093/pcp/pcp003 . From the above 13 alpha-bisabolol associated sequences, one has been described as microsatellite sequence (1379). For the remaining 12 sequences, specific gene products were described in multiple plant species: “722” ascorbate peroxidase 2-like protein, 3 species; “1139” glutamate receptor, 2 species; “1732” predicted: probable carboxylesterase 6, 5 species; “1998” predicted: nuclear fusion defective 4-like (NFD4; LOC109841189) protein, 2 species; “3218” ammonium transporter 3 member 1-like, 2 species;, “3223” U-box domain-containing protein 13 and armadillo/beta-catenin repeat family protein, 3 species; “3249” probable pre-mRNA-splicing factor ATP-dependent RNA helicase, 23 species; “4194” mostly asparagine synthetase, 60 species; “5721” chaperone protein ClpB1/ heat shock protein, 42 species; “6386” lipase, 1 species; “6598” malate dehydrogenase, chloroplastic-like, 19 species; “6654”, mainly reticulon-like protein B2, 24 species. (3) Portereiko MF, Sandaklie-Nikolova L, Lloyd A, Dever CA, Otsuga D, Drews GN NUCLEAR FUSION DEFECTIVE1 encodes the Arabidopsis RPL21M protein and is required for karyogamy during female gametophyte development and fertilization. Plant Physiol. 2006; 141:957–965. (4) Caverzan A, Passaia G, Rosa SB, Ribeiro CW, Lazzarotto F, Margis-Pinheiro M. Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection. Genetics and Molecular Biology. 2012;35 (4 Suppl):1011–1019. (5) Forde BG, Roberts MR. Glutamate receptor-like channels in plants: a role as amino acid sensors in plant defence? F1000Prime Reports. 2014;6:37. doi: 10.12703/P6-37 . (6) Sharma M, Pandey A, Pandey GK. β-catenin in plants and animals: common players but different pathways. Frontiers in Plant Science. 2014;5:143. doi: 10.3389/fpls.2014.00143 . (7) Lee U, Rioflorido I, Hong SW, Larkindale J, Waters ER, Vierling E.: 2007. The Arabidopsis ClpB/Hsp100 family of proteins: chaperones for stress and chloroplast development. Plant J. Jan;49(1):115–27 (DOCX 24 kb)