2016
DOI: 10.1186/s12870-015-0700-5
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CENH3-GFP: a visual marker for gametophytic and somatic ploidy determination in Arabidopsis thaliana

Abstract: BackgroundThe in vivo determination of the cell-specific chromosome number provides a valuable tool in several aspects of plant research. However, current techniques to determine the endosystemic ploidy level do not allow non-destructive, cell-specific chromosome quantification. Particularly in the gametophytic cell lineages, which are physically encapsulated in the reproductive organ structures, direct in vivo ploidy determination has been proven very challenging. Using Arabidopsis thaliana as a model, we her… Show more

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Cited by 255 publications
(257 citation statements)
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References 68 publications
(74 reference statements)
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“…We conducted 20 iterations to assess the stability in detection of the number of clusters. To prevent overfitting when conducting the DAPC, the number of principal components to retain was determined with a cross‐validation approach as implemented by the function xvalDapc() (e.g., Campoy et al., 2016; Van Cann, Virgilio, Jordaens, & De Meyer, 2015; Virgilio et al., 2015) with 100 repetitions.…”
Section: Methodsmentioning
confidence: 99%
“…We conducted 20 iterations to assess the stability in detection of the number of clusters. To prevent overfitting when conducting the DAPC, the number of principal components to retain was determined with a cross‐validation approach as implemented by the function xvalDapc() (e.g., Campoy et al., 2016; Van Cann, Virgilio, Jordaens, & De Meyer, 2015; Virgilio et al., 2015) with 100 repetitions.…”
Section: Methodsmentioning
confidence: 99%
“…In addition, the identification of candidate genes has been achieved using the GWAS approach in several plant species, including Arabidopsis 16, rice17 and soybean18. Recently, high throughput next-generation sequencing technologies such as genotyping-by-sequencing (GBS)10, restriction site associated DNA sequencing (RAD-seq)19 and specific-locus amplified fragment sequencing (SLAF-seq)2021 have provided an opportunity to obtain the required marker coverage in upland cotton cultivars/accessions.…”
mentioning
confidence: 99%
“…Irena Molina and Malin Abrahamsson. Briefly, samples were collected from five sequential developmental stages (classification based on Zhu et al [35]): +PGR (Proliferating cultures + Plant growth regulators (PGR) five days after subculture), —PGR (Proliferating cultures —PGR five days after subculture), EE (Early embryos differentiated after one week on maturation medium); LE1 and LE2 (late early embryos developed after two and three weeks on maturation medium, respectively). Three independent samples were collected for every stage and frozen in liquid nitrogen and stored at −80 °C until extraction.…”
Section: Methodsmentioning
confidence: 99%
“…Expression levels of PaNAC03 was tested by qRT-PCR by using an iQ5 Multicolor Real-Time PCR Detection System (BioRad) and SsoFast EvaGreen Supermix (BioRad) as stated previously and two independent lines (4.1 and 4.2) with expression levels 1.7 times higher than the WT cell line were selected for maturation initiation, RNA sequencing and chemical analysis. The initiation of somatic embryo maturation in the overexpression lines and the control line was done according to the protocol described by Filonova et al [44], briefly for each line pre-weighed pieces of callus was placed on half strength LP medium for a week before the explants were transferred onto the maturation medium, the maturation response was scored after four and six weeks on maturation medium, embryos resembling the LE2, ME1 and ME2 stages [35] were noted.…”
Section: Methodsmentioning
confidence: 99%