Parallel gene loss underlies success in a colonizing Arabidopsis lineage
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Arabidopsis Thaliana
SUBMITTER: Max Planck Institute for Plant Breeding Research
PROVIDER: PRJEB44201 | EVA | 2022-01-11
REPOSITORIES: EVA
Similar Datasets
Project description:In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments.
2014-09-01 | GSE36844 | GEO
Project description:In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments.
2014-09-01 | GSE36845 | GEO
Project description:In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments.
2014-09-01 | GSE47490 | GEO
Project description:Optimised flowering time is an important trait ensuring successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors known to play important roles in flowering control in many plants. This includes the best characterised eudicot model Arabidopsis thaliana (Arabidopsis) where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to the similar floral-inductive cues of extended cold (vernalisation) followed by warm long days, as winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes; one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly-repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long and short day photoperiods, with and without prior vernalization, compared with wild type. On the other hand, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild type background. Here, we describe the generation of Mtsoc1 triple mutant plants by CRISPR-Cas9 gene editing. Two independent Mtsoc1 homozygous triple mutants were non-flowering and bushy in floral inductive VLD. Phenotyping and gene expression analyses by RNA-seq and RT-qPCR indicate that the Mtsoc1 triple mutants remain vegetative. Thus overall, the Mtsoc1 triple mutants are dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.
2024-02-26 | GSE247931 | GEO
Project description:Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well known. Due to global warming, understanding this ambient temperature pathway has become increasingly important. FLOWERING LOCUS M (FLM) is one critical flowering regulator of this pathway in Arabidopsis thaliana. We identified the Arabidopsis accession Kil-0 as an early flowering strain when compared to the common reference accession Col-0. Genetic mapping of this trait identified a causative region of around 31 kb at the bottom of chromosome one. Within this region, only FLOWERING LOCUS M (FLM) was expressed at a significantly lower level in Kil-0 when comparing RNA-seq (RNA sequencing) data from 10-day old Kil-0 and Col-0 plants grown at 21C. Furthermore, FLM was also the gene with the greatest reduction in gene expression between Kil-0 and Col-0 when we specifically analyzed 267 genes with a role in flowering time regulation what strongly suggested that FLM is the major locus that results in accelerated flowering in Kil-0.
2015-08-28 | E-MTAB-4473 | biostudies-arrayexpress
Project description:Small RNA sequences from Arabidopsis lyrata flowering tissues, as isolated from flowering tissues of two biological replicates. These data were analyzed to 1) discover new micoRNAs in A. lyrata 2) examine microRNA processing accuary in A. lyrata and 3) to examine patterns of 24nt siRNA accumulation in A. lyrata.
2010-04-22 | GSE20442 | GEO
Project description:Plants display remarkable developmental and phenotypic plasticity in order to adapt to their environment. It has long been postulated that epigenetics plays a key role in these processes, but with one or two exceptions, solid evidence for the role of epigenetic variation in these processes is lacking. A key impediment to understanding these processes is the lack of information on the extent of epigenetic variation and how it relates to genetic and phenotypic variation in natural population, both over the lifecycle of an individual, and over evolutionary time. Here we show that genetic variants under selection in the north of Sweden appear to drive variation in DNA methylation, which in turn is highly correlated with local climate. Selective sweeps and genetic variants associated with adaptation to the local environment have previously been identified within the Swedish Arabidopsis population. Our finding that they harbour variants responsible for climate associated epigenetic variation strongly supports the role of epigenetic processes in local adaptation. These findings provide a basis for further dissecting the role of epigenetics in local adaptation at the molecular level
2015-03-28 | GSE65685 | GEO
Project description:Spring frost is a growing risk to temperate fruit production as warmer winter conditions can lead to earlier bloom, increasing the chance of damaging cold temperatures. One strategy to minimize the impacts of frost is to breed late-flowering cultivars to avoid the frost risk period. In this study, we analyzed Late-Flowering Peach (LFP) germplasm and showed its floral buds require longer chilling and warming periods during dormancy than the control cultivar, ‘John Boy’ (JB). We identified a 983-bp deletion in an AP2 gene, dubbed euAP2a, present only in LFP but not in 14 other peach genomes analyzed. This mutation eliminates an miR172 binding site, possibly allowing the euAP2a transcript to accumulate preferentially during chilling. These findings together with an early report that a deletion in the same euAP2a causes increasing floral petals, a morphological mark that also occurs in LFP, implies that the 983-bp deletion may contribute to the late-flowering phenotype. Furthermore, RNAseq data revealed that that two chilling- and three warm-responsive co-expression modules, which were collectively composed of 2,931 genes, were differentially activated at four of 13 dormancy stages. This activation was concurrent with a transient, stage-specific down-regulation of euAP2a. However, the mutated euAP2a in LFP did not exhibit the periodic downregulation events observed in JB and the concurrent activation of the five modules, leading to potential loss of activation of two chilling-responsive modules and an 8–12-day delay of three warm-responsive modules, which corresponds to the longer chilling requirement and delayed flowering time in the LFP buds. These findings support euAP2a as a potential regulator to control both floral development and bloom time in peach. Our findings provide important insight into the mechanisms underlying flowering time in peach, as well as a novel regulatory pathway that may operate in other plants. The results provide new insights to facilitate the breeding of new cultivars with late-flowering frost-avoidance traits.
2024-02-09 | GSE244570 | GEO
Project description:Small RNA sequences from Arabidopsis lyrata flowering tissues, as isolated from flowering tissues of two biological replicates. These data were analyzed to 1) discover new micoRNAs in A. lyrata 2) examine microRNA processing accuary in A. lyrata and 3) to examine patterns of 24nt siRNA accumulation in A. lyrata. Two small RNA libraries from flowering tissues of two biological replicates were analyzed using an Applied Biosystems SOLiD™ System
2010-04-22 | E-GEOD-20442 | biostudies-arrayexpress