Shrub willow (Salix section Vetrix), is a dioecious, short rotation coppice, bioenergy crop. While there are thousands of genes involved in sex dimorphism in shrub willow, there is an interest in identifying the master regulator genes for sex and the pathways through which sex dimorphism is mediated. Here we report on analysis of catkin and shoot tip expression data from Salix purpurea, an economically important and model shrub willow species with a ZW sex determination system and homomorphic sex chromosomes. RNA-Seq data were obtained from 90 males and 90 females and small RNA data from 22 males and 22 females in an F2 population and aligned to the recent version 5.1 genome assembly. Aligned reads were subsequently utilized to perform eQTL mapping, differential expression, and network analysis. These data were used to identify gene associations and networks strongly associated with sex, and to develop hypotheses regarding master regulator genes of sex. We discuss the methods and challenges of RNA-Seq mapping and analysis between homomorphic sex chromosomes with high similarity. We present the differential expression profiles between sexes of major gene families, sex-associated network modules, and enriched metabolic pathways. Finally, we use these data to hypothesize mechanisms of sex determination and dimorphism via candidate master regulator genes. This study is the first transcriptome-wide network analysis in Salix floral tissue and represents a significant step towards understanding sex determination in this genus. Results from this study can also provide valuable insight and knowledge of sex determination in the related genus Populus, as well as other dioecious plant species.
Coauthors: Craig Carlson – Cornell University;Guanqiao Feng – Texas Tech University;Matt Olson – Texas Tech University;Stephen DiFazio – West Virginia University;Brian Sanderson – West Virginia University;Ran Zhou – West Virginia University;David Macaya-Sanz – West Virginia University;Ken Keefover-Ring – University of Wisconsin-Madison;Lawrence Smart – Cornell University