Co-expression Network Analysis in Carya illinoinensis cvs. ‘Tiny Tim’ and ‘Mahan’ Identifies Cell Wall Remodeling and Inositol Metabolism Modules Associated with Nut Size

Pecan is a tree nut crop native to the United States and Mexico, with a global market of over 2 billion USD. Nut size has been the most important target trait for crop improvement during the very limited breeding cycles. However, relatively little is known about the molecular basis of pecan nut ontogeny and the mechanisms underlying pecan nut sizing. Besides nut size, pecan fruit faces myriad physiological disorders throughout the growing season, making knowledge of essential genes at each growth stage a necessary first step in developing new cultivars and management practices to overcome these issues. To develop a deeper understanding of pecan fruit development and identify candidate genes underlying the large fruit phenotype, a time-course transcriptomic study of pecan fruit in two genotypes, ‘Mahan’ and ‘Tiny Tim’, was conducted. Weighted Gene-Coexpression Network Analysis (WGCNA) was employed to group transcripts into functional clusters, and hub transcripts were identified through module correlation analysis to select those that are potential drivers of these functional clusters. Modules related to cell wall biosynthesis, cell wall organization, and inositol metabolism in ‘Mahan’, and proteolysis and abscisic acid response in ‘Tiny Tim’ were found to be associated with nut size.