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Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
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Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone
Hao Wu1, Philip W Becraft1,2
1Dep. of Genetics, Development & Cell Biology, IA State Univ., Ames, IA, 50011, USA.
The Plant Genome
|July 29, 2021
Summary
Maize endosperm development genes nkd1, nkd2, and thk1 control aleurone cell layers. Nkd1,2 and Thk1 regulate cell division, while Nkd1,2 also impacts auxin signaling for proper development.
Area of Science:
- Plant Biology
- Molecular Genetics
- Developmental Biology
Background:
- The naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are key regulators of maize endosperm development.
- Mutations in these genes lead to abnormal aleurone (AL) cell layer formation and differentiation.
Purpose of the Study:
- To comparatively analyze the transcriptomes of nkd1,2 and thk1 mutants.
- To elucidate how these genes regulate gene networks controlling AL layer specification and cell differentiation.
Main Methods:
- Comparative transcriptome analysis of nkd1,2 and thk1 mutant maize endosperm.
- Weighted gene coexpression network analysis integrated with laser capture microdissected transcriptome data.
- Identification and analysis of differentially expressed genes and auxin response factor (ARF) targets.
Main Results:
- Both Nkd1,2 and Thk1 regulate cell cycle and division in AL development.
- Nkd1,2, but not Thk1, regulates auxin signaling pathways.
- 61 AL-preferential genes, potentially regulated by NKD-modulated ARFs, were identified and linked to hormone crosstalk, lipid metabolism, and growth.
- Auxin signaling reporter expression was elevated in nkd1,2 mutants, confirming negative regulation by Nkd1,2.
Conclusions:
- Nkd1,2 and Thk1 restrict AL development to a single layer by limiting cell division.
- Nkd1,2 negatively regulates auxin signaling in AL, maintaining normal cell patterning and differentiation.
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