Abstract
Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise comparisons of rtcs and wild-type embryo transcriptomes identified 131 transcription factors among 3526 differentially expressed genes [false discovery rate (FDR) <5% and |log2Fc|≥1]. Among those, functional annotation highlighted genes involved in cell cycle control and phytohormone action, particularly auxin signaling. Moreover, in silico promoter analyses identified putative RTCS target genes associated with transcription factor action and hormone metabolism and signaling. Significantly, non-syntenic genes that emerged after the separation of maize and sorghum were over-represented among genes displaying RTCS-dependent expression during seminal root primordia formation. This might suggest that these non-syntenic genes came under the transcriptional control of the syntenic gene rtcs during seminal root evolution. Taken together, this study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
Highlights
Specialized root systems in plants are vital for growth and adaptation because they provide mechanical support, mediate water and nutrient uptake, and interact with the rhizosphere
This study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation
Histological analyses revealed that at 25 dap no seminal root primordia were initiated in wild-type embryos, while early primordia were visible at 30 dap and fully developed primordia were formed at 35 dap under our growth conditions (Fig. 1A)
Summary
Specialized root systems in plants are vital for growth and adaptation because they provide mechanical support, mediate water and nutrient uptake, and interact with the rhizosphere (reviewed in Hawkes et al, 2007; Lynch, 2013; Villordon et al, 2014). The embryonic root system includes a primary root and a variable. Number of seminal roots, while shoot-borne and lateral roots are formed post-embryonically (reviewed in Hochholdinger et al, 2004; Yu et al, 2016). Primary roots are initiated at the basal pole of the embryo and emerge 2–3 days after germination. Seminal roots are initiated at the scutellar node between 22 and 40 days after pollination and emerge in germinating seeds soon after the primary root (Sass, 1977; Erdelska and Vidovencova, 1993). The number of seminal roots in maize varies within a genotype and between different genotypes, and ranges from 0 to 13 (Erdeska and Vidovencova, 1993; Burton et al, 2013; Tai et al, 2016)
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