Regulatory variation controlling architectural pleiotropy in maize

Plant architecture is central to yield and has been at the core of crop domestication and improvement. In cereals, inflorescence branching and leaf angle are important traits that contribute to planting density and yield potential. Several classical maize mutants show disruptions in both traits, suggesting a core regulatory network underlies pleiotropy between them. Here, we investigate regulatory modules that contribute to architectural pleiotropy between tassel branch number (TBN) and leaf angle (LA) in maize by defining transcriptional networks that function in lateral organ boundaries to promote development of these morphologically distinct organs. Using a set of nine mutants with specific developmental defects in one or both traits, we generated dynamic, context-specific gene regulatory maps that describe ligule and tassel branch development at the molecular level. Mutants introgressed into B73 and control plants were grown in environmentally controlled chambers and precisely-staged tassel primordia were hand-dissected at two stages: right before and after first primary branches initiated. Two stages capturing early development of the ligular region, including the shoot apical meristem, were also collected from mutants with LA defects. RNA-seq was performed on 140 samples and integrated into gene regulatory and co-expression networks, which were extended to include publicly available transcription factor occupancy maps for important developmental regulators, chromatin accessibility maps and natural variation to help prioritize novel genes and regulatory elements underlying diversity in LA and tassel branching phenotypes. We also used these transcriptional networks to guide multi-trait genome-wide association studies (GWAS) based on three years of field phenotyping TBN and LA traits in over 500 diverse maize lines. Various network-assisted GWAS approaches were used to identify polymorphisms in candidate genes that associate with these architecture traits and the pleiotropy between them. Our data provide novel insight into regulatory mechanisms controlling architectural pleiotropy that can be used for targeted crop improvement. Overall design: We use a set of 9 maize mutants (lg1, lg2, ra1, ra2, fun, Wab1-R, wab-rev, bin2-RNAi, bri1-RNAi) to generate 140 poly-A+ RNA-seq libraries from tassel primordia, apex2 and apex1 tissues.