Research Summary

Plants have the fascinating ability to constantly adapt their development according to changes in the surrounding environment. This plasticity is provided by meristems, small groups of undifferentiated self-regenerating stem cells, continuously formed throughout development. Meristem number, position and activity are a major source of variability in the architecture of different plant species, since they determine if, when and how branches and flowers are formed during both vegetative and reproductive development. Plant architecture, extensively modified during the domestication of crop species, still represents a major target of selection in modern breeding. In particular, in cultivated grasses, the major worldwide food source, vegetative and reproductive branching represents a major component of yield. 

Our research is aimed at understanding: i) how pluripotent meristematic cells are formed during development; ii) how meristem fate and organ initiation are regulated; iii) the role of the plant hormone auxin in shaping plant architecture and regulating meristem function (; iv) the molecular mechanisms of plant domestication and evolution.  

In my laboratory we investigate the molecular mechanisms behind the formation and activity of meristems, by combining the strength of traditional forward and reverse genetics with molecular biology. We use maize mutants affected in branch and flower formation to identify and understand the genes and gene networks controlling plant architecture. We isolated several genes affecting branching in both tassels and ears, the male and female inflorescences of maize. Among these, we identified two transcription factors (BARREN STALK1 and BARREN STALK FASTIGIATE1), an auxin biosynthetic enzyme (SPARSE INFLORESCENCE1) involved in the formation of new meristems, and a transcriptional corepressor (RAMOSA1 ENHANCER LOCUS2) that regulates the decision of meristems to form either a branch or a flower during development. To move towards a systemic understanding of the molecular mechanisms regulating plant architecture, it is essential to achieve a more comprehensive view of the relationships of these genes and pathways, and for this purpose we are using different genomic approaches. We also pursue functional comparative analysis, by using different model plant systems (maize and Arabidopsis thaliana) to highlight the similarities and differences at the origin of the variability in plant architectures observed in natural and domesticated environments.

Currently funded projects:

IOS-1546873 Genomic and synthetic approaches linking auxin signaling to functional domains in maize

IOS-1456950  Characterizing the role of transcriptional repression in maize development and domestication


Recent Publications

O’Malley, RC, S.C. H, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.  2016.  Cistrome and epicistrome features shape the regulatory DNA landscape. Cell. 165:1280-1292. AbstractWebsite
The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.
Galli, M and Gallavotti, A.  2016.  Expanding the regulatory network for meristem size in plants. Trends in Genetics. 32(6):372-383. AbstractWebsite
The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop was established as being essential for regulating the size of shoot meristems by maintaining a delicate balance between stem cell proliferation and cell recruitment for the differentiation of lateral primordia. Recent research in various model species (Arabidopsis, tomato, maize, and rice) has led to discoveries of additional components that further refine and improve the current model of meristem regu- lation, adding new complexity to a vital network for plant growth and productivity.
Galli, M, Liu Q, Moss BL, Malcomber S, Li W, Gaines C, Federici S, Roshkovan J, Meeley R, Nemhauser J et al..  2015.  Auxin signaling modules regulate maize inflorescence architecture. Proc Natl Acad Sci USA. 112:13372-13377. AbstractWebsite
In plants, small groups of pluripotent stem cells called axillary meristems are required for the formation of the branches and flowers that eventually establish shoot architecture and drive reproductive success. To ensure the proper formation of new axillary meristems, the specification of boundary regions is required for coordinating their development. We have identified two maize genes, BARREN INFLORESCENCE1 and BARREN INFLORESCENCE4 (BIF1 and BIF4), that regulate the early steps required for inflorescence formation. BIF1 and BIF4 encode AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins, which are key components of the auxin hormone signaling pathway that is essential for organogenesis. Here we show that BIF1 and BIF4 are integral to auxin signaling modules that dynamically regulate the expression of BARREN STALK1 (BA1), a basic helix-loop-helix (bHLH) transcriptional regulator necessary for axillary meristem formation that shows a striking boundary expression pattern. These findings suggest that auxin signaling directly controls boundary domains during axillary meristem formation and define a fundamental mechanism that regulates inflorescence architecture in one of the most widely grown crop species.
Gallavotti, A. and Whipple, CJ.  2015.  Positional cloning in maize (Zea mays subsp. mays, Poaceae). Applications in Plant Sciences. 3:1400092.gallavotti_and_whipple_2015.pdfWebsite