Extensive Functional Pleiotropy ofREVOLUTASubstantiated through Forward Genetics    

Abstract

In plants, genes may sustain extensive pleiotropic functional properties by individually affecting multiple, distinct traits. We discuss results from three genome-wide association studies of approximately 400 natural poplar (Populus trichocarpa) accessions phenotyped for 60 ecological/biomass, wood quality, and rust fungus resistance traits. Single-nucleotide polymorphisms (SNPs) in the poplar ortholog of the class III homeodomain-leucine zipper transcription factor gene REVOLUTA (PtREV) were significantly associated with three specific traits. Based on SNP associations with fungal resistance, leaf drop, and cellulose content, the PtREV gene contains three potential regulatory sites within noncoding regions at the gene's 39 end, where alternative splicing and messenger RNA processing actively occur. The polymorphisms in this region associated with leaf abscission and cellulose content are suggested to represent more recent variants, whereas the SNP associated with leaf rust resistance may be more ancient, consistent with REV's primary role in auxin signaling and its functional evolution in supporting fundamental processes of vascular plant development.

BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of REVOLUTA

“…REV plays multiple and pleiotropic roles in plant development, including tissue patterning, secondary wall formation, and vascular cambium development (Robischon et al, 2011;Schuetz et al, 2013;Porth et al, 2014) and has recently been shown to play a role in modulating plant development according to light availability by interacting with light signaling pathways to mediate the shade avoidance response (Brandt et al, 2012). These findings support a role for REV in modulating plant development in response to environmental inputs.…”

Genome‐wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

“…The repeated occurrence of ecophysiology traits associated with pleiotropic loci was notable (Table 6), particularly as these had little or no correlative relationship to biomass and/or phenology traits. Other examples of potentially pleiotropic loci have also been uncovered in P. trichocarpa (Porth et al, 2014), including a set of genes affecting phenology, wood fiber properties and disease resistance (I. Porth & J. Kl ap st e, unpublished).…”

“…involving a number of genes or gene networks), GWAS using high genome coverage of single nucleotide polymorphisms (SNP) markers has been very effective for identifying the genetic architecture underlying variability in these traits (Eckert et al ., ; Parchman et al ., ; Riedelsheimer et al ., ; Morris et al ., ; Porth et al ., ). GWAS can also uncover loci with potential pleiotropic effects that may be important to natural variation within species and their capacity for adaptation (Mackay et al ., ; Stapley et al ., ; Porth et al ., ).…”

“…GWAS can also uncover loci with potential pleiotropic effects that may be important to natural variation within species and their capacity *These authors contributed equally to this work. for adaptation (Mackay et al, 2009;Stapley et al, 2010;Porth et al, 2014).…”

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

“…This TF plays an important role in laying down leaf polarity, root and vasculature [73]. REV is a part of a complex regulatory system involving auxin, transcription factors, miRNAs and carrier complex and is the key regulatory gene in plant morphogenesis [74]. Transcriptional variant of REV was regulated by miR165 and miR166 families.…”