Radka Slovak's research while affiliated with University of Oxford and other places

... Here we reviewed different published studies and found that few of them focused their GWAS analysis on identifying genes that determine a differential PR growth between accessions under control conditions, that is, that does not involve exposure to a stress treatment. For instance, Slovak and collaborators (2020) found that the ARABIDOPSIS ADENYL-ATE KINASE 6 (AAK6), a protein important for ribosomal biogenesis, is required for normal cell cycle progression and PR growth [20]. Furthermore, using an epistatic GWA analysis, Lachowiec and collaborators (2015) reported that the transcription factor of the NAC family NAC6 and ATL5, TERMINAL FLOWER1 (TFL1) and another locus that encodes an ankyrin family protein (At3g28880), contribute to PR length [21]. ...

... To discover novel genes involved in PR growth using the natural variation of Arabidopsis, we analyzed the PR length measures under control conditions of nine different studies to perform GWAS. Eight of these GWAS focus on identifying genes involved in PR growth under different stress conditions: salinity [10,11], nutrient deficiencies [14][15][16], hormones responses [13,23] and wound [12] and only one study is focused on obtaining SNPs under control conditions [21]. In some of these studies, the SNPs associated with the PR length under control conditions are not deeply analyzed may be due to a lack of statistical significance [10,13,14,16,23] or that the PR length was only used as a normalizer under a particular stress condition [15]. ...

... Finally, we found a gene annotated as excocyst complex component 7 upregulated in the meristematic zone. Components of the exocyst are involved in directing exocytotic vesicles to fusion sites on the plasma membrane and might be involved in the distribution of the auxin transporter PINFORMED4 in Arabidopsis (37,38). ...

... Penn could be considered to show a constitutive Pi-starvation response in terms of its primary root length, as it has shorter primary roots in Pi sufficiency compared to M82, and no change in root length in limiting Pi. It should be noted, however, that the short root phenotype is multigenic in nature and that a constitutive Pi deprivation is likely not the only factor at play with the short root (Ron et al., 2013;Toal et al., 2018). In limiting Pi conditions, elongation of root hairs was observed in M82 (two-way ANOVA P < 0.0001; Fig. 1c,d). ...

... Refs. 122,123 ). Despite our mixed evidence, adaptive processes could still be important for most of the populations, since the responses of transplants depended on their habitat of origin. ...

... Fe 3+ released by the H + -ATPase protease system enters the cell after forming chelates with chelators in the plant, and the reduction system converts Fe 3+ chelates into Fe 2+ chelates released for plant uptake and utilization. The iron deficiency-induced pea Fe 3+ reductase gene, PsFRO1, was expressed in plant roots, mycorrhizae, stems, and leaves, and the expression was relatively higher in root epidermal cells with Fe 3+ reduction system and Fe 2+ transporter protein system; and the expression of PsFRO1 in the nitrogen fixation zone of root nodules may play a role in plant nitrogen fixation (Waters et al., 2002); natural allelic variation of FRO2 regulates Arabidopsis root growth under iron deficiency conditions (Satbhai et al., 2017). This step is particularly important as it is the limiting step in the mechanism I process. ...

... In these studies, the SNPs associated with PR length under control conditions were not deeply analyzed because PR length is only used as a normalizer to study a particular stress condition or because small sample sizes render few or no statistically associated SNPs [10,[13][14][15][16]. Nevertheless, the intense research on Arabidopsis PR has allowed uncovering some genetic mechanisms underlying root growth and differentiation as well as the response to different environmental conditions [17]. Several genes have been reported to influence PR, such as the transcription factors WUSCHEL-RELATED HOMEOBOX 5 (WOX5), PLETHORA genes (PLTs), SHORT ROOT (SHR), SCARECROW (SCR), cell cycle genes members such as CYCLIN-DEPENDENT KINASES and CYCLINS and also plant hormones that are key regulators of cell division, elongation and cell identity, during PR development [17][18][19]. ...

... High-throughput plant phenotyping is increasingly used in crop breeding (Araus & Cairns, 2014;Ghanem et al., 2015;Watanabe et al., 2017). It also empowers research approaches such as quantitative trait loci mapping and genome-wide association study, which aim to close the genotype-phenotype gap by identifying associations between phenotypic traits and genetic markers across a broad panel of genotypes (Slovak et al., 2015;Zhang et al., 2017). Moreover, computational methods that can identify, classify or quantify plant stress symptoms or predict plant trait outcomes based on phenotypic data collected at an earlier stage have been established . ...

... Also, we noted if the seedling age was indicated in days after germination (DAG). The data are represented as the mean PR length in cm (S1 Table) and the studies that had their data in pixels were transformed to cm according to [24] (1 pixel = 21 μm). The studies that displayed root kinetic growth as rate growth was converted to linear growth, adding to the previous value. ...