Biology subjects

Tregear, J.

Publications and source records attributed to Tregear, J..

3 recordsLinked to original sources

bioRxiv2026

Connecting gene expression and cytokinin signaling during meristem determinacy transition in the rice panicle

Structural complexity in the rice inflorescence (panicle) is determined by the activity of indeterminate meristems, which allow sequential branching events to occur but later acquire a determinate character that precludes the initiation of new growth axes. To better understand the underlying regulatory processes, we combined a detailed time-course of panicle development with tissue-specific sampling of meristems before and after the determinacy switch, monitoring global gene expression programs and hormone accumulation. This allowed the delineation of three dynamic transcriptional modules and the inference of gene regulatory networks highlighting hormone regulatory hubs associated with the indeterminate-to-determinate meristem transition. Our data confirm the importance of known regulators of inflorescence development and identify novel actors, notably genes encoding transcription factors, that were not previously described in the regulation of flowering. The combined biochemical and transcriptomic data support a model in which cytokinin signalling is particularly active during the proliferative branching phase, during which meristem maintenance is promoted while a feedback mechanism is also triggered, ultimately leading to the acquisition of determinate meristem fate later in development. HighlightInvestigating the molecular nature of rice inflorescence meristem determinacy, we studied temporal and spatial gene expression alongside hormone accumulation, identifying novel regulatory interactions and a key role for cytokinins.

plant biology↗

bioRxiv2023

African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the identification of key QTLs

BackgroundDeveloping high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The genetic interactions that govern the diversity of panicle complexity within and between the two species are still poorly understood. ResultsTo identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapo. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12 and QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. ConclusionOur analysis led to the detection of genomic variations between O. sativa cv. Caiapo and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.

plant biology↗

bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗