Regulatory modules controlling maize inflorescence architecture

Abstract

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.

Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation

“…Maize ramosa1 (ra1) mutants are characterized by abnormal branching in the ear, a phenotypic anomaly that mimics the branching patterns normally observed in the developing tassel (Gallavotti et al, 2010). Recent data show that LG1 accumulates in the axils of tassel branches (Eveland et al, 2014;Lewis et al, 2014). lg1 mutants exhibit reduced tassel angle and three SBP genes, including lg1, are implicated in tassel branching, suggesting that LG1 functions in boundary specification in the tassel (Brown et al, 2011;Eveland et al, 2014;Lewis et al, 2014).…”

“…Of 96 genes that are DE in lg1-R mutant primordia, 45 were also DE in ra1 ears and 26 were DE in tassel versus ear primordia (P < 1e-2 for all comparisons) (Supplemental Figures 4C and 4D). Given that lg1 is ectopically expressed in the highly branched ra1 mutant ear primordia, but not in wild-type ears (Eveland et al, 2014), it is likely that DE genes common to both lg1-R and ra1 mutants act downstream of LG1 and are involved in branching.…”

“…Recent data show that LG1 accumulates in the axils of tassel branches (Eveland et al, 2014;Lewis et al, 2014). lg1 mutants exhibit reduced tassel angle and three SBP genes, including lg1, are implicated in tassel branching, suggesting that LG1 functions in boundary specification in the tassel (Brown et al, 2011;Eveland et al, 2014;Lewis et al, 2014). Our finding that genes such as CUC2-like have specific expression patterns at the blade-sheath boundary and other developmental boundaries prompted us to ask if other genes that are DE at the blade-sheath boundary are also implicated in lateral branching.…”

“…We compared transcripts that are DE specifically in preligule tissue and lg1-R mutants to genes that are either DE between branched tassel and unbranched ear primordia or DE in ra1 mutant ears compared with the wild type (Supplemental Figure 4) (Eveland et al, 2014). Of 619 genes that are DE in preligule tissue, 227 were also DE in ra1 ear primordia relative to wild-type ears and 151 were DE in tassel primordia relative to ear primordia (Supplemental Figures 4A and 4B).…”

“…Our finding that genes such as CUC2-like have specific expression patterns at the blade-sheath boundary and other developmental boundaries prompted us to ask if other genes that are DE at the blade-sheath boundary are also implicated in lateral branching. Thus, we looked for overlap between our transcriptomic data sets and genes implicated in lateral branching (Eveland et al, 2014). Genes that are common in multiple data sets are likely to play evolutionarily conserved roles during regulation of developmental processes.…”