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Functional genetics of rice PISTILLATA genes reveals new roles and target genes in flowering time, female fertility and parthenocarpy

ABSTRACT:

Diversification of transcription factors and of their downstream targets can contribute to new organ morphologies. An example is rice lodicule, a small fleshy petal analogue that aids floret opening, thus facilitates pollination and fertility. To understand the mechanism underlying its specification, we investigated the developmental functions of the rice PISTILLATA (PI) paralogs, OsMADS2 and OsMADS4. Null osmads2 mutants reiterated OsMADS2 nonredundant lodicule specification roles and importantly revealed new roles in flowering time and floral organ number and fate in multiple whorls. Doubly perturbed osmads2d8/d8 osmads4kd florets had severe abnormalities and initiated parthenocarpy. Remarkably, ubiquitous OsMADS4 overexpression rescued osmads2 abnormalities, though impaired anther development and seed setting. Target genes whose (in)direct regulation can contribute to OsMADS2 functions were discovered by identifying its genome-wide binding regions and by transcriptome profiling. Several OsMADS2 targets are implicated in lodicule and stamen development, floral organ number, cell wall, cell shape and osmotic homeostasis processes. Altogether, we reveal novel roles for the rice PI paralogs, e.g. panicle exsertion and embryo sac differentiation and provide mechanistic insights on their diversification and functions in floral organ specification.

ORGANISM(S): Oryza sativa

PROVIDER: GSE260916 | GEO | 2025/09/14

REPOSITORIES: GEO

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Project description:The emerging picture of transcriptional regulation is one of unexpected complexity. It is now clear that single transcription factors control hundreds, if not thousands, of direct targets by binding their genomic loci, but it is not understood how many of these are major players and how many are supporting cast. To address this, we leverage a well-characterized developmental network in Arabidopsis and map genome-wide binding of related proteins in multiple tissues. The transcription factor APETALA2 (AP2) has numerous functions, including roles in floral organ identity, seed development and stem cell maintenance. We focus on the role of AP2 in the floral transition and map direct targets on a genome-wide scale. We show that ap2 mutants flower early in long and short days, and that AP2 binds to many loci, most prominently floral pathway integrators, microRNAs and floral organ identity genes, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two developmental microRNA genes that control AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We also seek conserved targets by comparing the genome-wide direct target repertoire of AP2 with that of SCHLAFMÜTZE (SMZ), another member of the AP2-like miR172 target clade that shares partial redundancy, as evidenced by a hexuple mutant for the entire clade that flowered extremely early. Clear similarities and divergence are exposed in the AP2 and SMZ direct target repertoires. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions both as a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE 15 (AGL15), and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). ChIP-Seq of two biological replicates for ATH-AP2 and respective control samples

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Functional genetics of rice PISTILLATA genes reveals new roles and target genes in flowering time, female fertility and parthenocarpy

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