Campus Units
Statistics
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2017
Journal or Book Title
Journal of Experimental Botany
Volume
68
Issue
3
First Page
403
Last Page
414
DOI
10.1093/jxb/erw422
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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.
Copyright Owner
The Authors
Copyright Date
2016
Language
en
File Format
application/pdf
Recommended Citation
Tai, Huanhuan; Opitz, Nina; Lithio, Andrew; Lu, Xin; Nettleton, Dan; and Hochholdinger, Frank, "Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.)" (2017). Statistics Publications. 178.
https://lib.dr.iastate.edu/stat_las_pubs/178
Included in
Agronomy and Crop Sciences Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Statistical Models Commons
Comments
This article is published as Tai, Huanhuan, Nina Opitz, Andrew Lithio, Xin Lu, Dan Nettleton, and Frank Hochholdinger. "Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.)." Journal of experimental botany 68, no. 3 (2016): 403-414. doi: 10.1093/jxb/erw422.