Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume.
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ABSTRACT:
SUBMITTER: Zhang M
PROVIDER: S-EPMC8319914 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X-76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA-LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.
| S-EPMC6972806 | biostudies-literature
Project description:We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis.
2012-12-27 | GSE40162 | GEO
Project description:We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis. Five RNA pools were created corresponding to different tissues of the Prunus mume.
2012-12-27 | E-GEOD-40162 | biostudies-arrayexpress
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next season’s growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. ‘Nanko’ vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release.
2014-03-26 | GSE49368 | GEO
Project description:Prunus mume, belonging to the Prunus genus, is an Asian tree, and its common names are Chinese plum and Japanese plum. P. mume are cultivated for fruit production as well as ornamental purposes. In this study, we conducted de novo transcriptome assembly for two selected P. mume cultivars referred to as Takada and Wallyoung (commercially important cultivars for fruit production and ornamental trees, respectively) by RNA-sequencing. We obtained 9.14 GB and 9.48 GB sequence data from Takada and Wallyoung (NCBI accession numbers: SRX1187101 and SRX1187169), respectively. De novo transcriptome assembly identified 130,989 and 116,941 transcripts for Takada and Wallyoung, respectively. In addition, we identified 96,681 and 91,429 proteins from Takada and Wallyoung, respectively, by TransDecoder program. We performed BLASTP against the NCBI non-redundant (nr) datasets to annotate identified proteins. This study provides transcriptomes and proteomes for two different P. mume cultivars, which might be useful for comparative transcriptome analyses and assist development of genetic markers.
| S-EPMC4664763 | biostudies-literature
Project description:Bud dormancy is a critical developmental process for perennial plant survival, and also an important physiological phase that affects the next seasonM-bM-^@M-^Ys growth of temperate fruit trees. Bud dormancy is regulated by multiple genetic factors, and affected by various environmental factors, tree age and vigor. To understand molecular mechanism of bud dormancy in Japanese apricot (Prunus mume Sieb. et Zucc.), we constructed a custom oligo DNA microarray covering the Japanese apricot dormant bud ESTs referring to peach (P. persica) genome sequence. Because endodormancy release is a chilling temperature-dependent physiological event, genes showing chilling-mediated differential expression patterns are candidates to control endodormancy release. Using the microarray constructed in this study, we monitored gene expression changes of dormant vegetative buds of Japanese apricot during prolonged artificial chilling exposure. In addition, we analyzed seasonal gene expression changes. M-bM-^@M-^XNankoM-bM-^@M-^Y vegetative buds collected in November, and those exposed to chilling for 40 or 60 days were used as microarray samples. Among the 58539 different unigene probes, 2345 and 1059 genes were identified as being more than two-fold up-regulated and down-regulated, respectively, following chilling exposure for 60 days (P value < 0.05). The down-regulated genes included P. mume DORMANCY-ASSOCIATED MADS-box genes, which supported the previous quantitative RT-PCR and EST analyses showing that these genes are repressed by prolonged chilling treatments. The genes encoding lipoxygenase were remarkably up-regulated by prolonged chilling. Cluster analysis suggested that the expression of the genes showing expression changes by artificial chilling exposure were coordinately regulated by seasonal changes. Our parametric analysis of gene set enrichment suggested that genes related to jasmonic acid (JA) and oxylipin biosynthesis and metabolic processes were significantly up-regulated by prolonged chilling, whereas genes related to circadian rhythm were significantly down-regulated. The results obtained from the microarray analyses were verified by quantitative RT-PCR analysis of selected genes. Taken together, this study raised the possibility that the microarray platform constructed in this study is applicable for deeper understanding of molecular network related to agronomically important bud phisiologies including dormancy release. In this study, we used chilling exposed bud samples (0, 40, 60 days starting at November) and seasonal monthly bud samples (June to March). For the samples in dataset 1 (three different time points during chilling treatment), three technical replicates (60K M-CM-^W 3 per sample) with three biological replicates were averaged, whereas three technical replicates were averaged for the samples in dataset 2 (10 different seasonal time points)
2014-03-26 | E-GEOD-49368 | biostudies-arrayexpress
Project description:Prunus mume (mei), which was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced. Here, we assemble a 280M genome by combining 101-fold next-generation sequencing and optical mapping data. We further anchor 83.9% of scaffolds to eight chromosomes with genetic map constructed by restriction-site-associated DNA sequencing. Combining P. mume genome with available data, we succeed in reconstructing nine ancestral chromosomes of Rosaceae family, as well as depicting chromosome fusion, fission and duplication history in three major subfamilies. We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P. mume, including its regulation of early blooming in endodormancy, immune response against bacterial infection and biosynthesis of flower scent. The P. mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of fruit trees.
| S-EPMC3535359 | biostudies-literature
Project description:MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.
| S-EPMC9355595 | biostudies-literature
Project description:BackgroundMei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume 'Fenban' and Prunus mume 'Kouzi Yudie' to identify high-quality polymorphic markers between the two cultivars on a large scale.ResultsA total of 1464.1 Mb and 1422.1 Mb of 'Fenban' and 'Kouzi Yudie' sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent's SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny.ConclusionsA large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between 'Fenban' and 'Kouzi Yudie' using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.
| S-EPMC3851432 | biostudies-literature
Project description:TCP proteins, belonging to a plant-specific transcription factors family, are known to have great functions in plant development, especially flower and leaf development. However, there is little information about this gene family in Prunus mume, which is widely cultivated in China as an ornamental and fruit tree. Here a genome-wide analysis of TCP genes was performed to explore their evolution in P. mume. Nineteen PmTCPs were identified and three of them contained putative miR319 target sites. Phylogenetic and comprehensive bioinformatics analyses of these genes revealed that different types of TCP genes had undergone different evolutionary processes and the genes in the same clade had similar chromosomal location, gene structure, and conserved domains. Expression analysis of these PmTCPs indicated that there were diverse expression patterns among different clades. Most TCP genes were predominantly expressed in flower, leaf, and stem, and showed high expression levels in the different stages of flower bud differentiation, especially in petal formation stage and gametophyte development. Genes in TCP-P subfamily had main roles in both flower development and gametophyte development. The CIN genes in double petal cultivars might have key roles in the formation of petal, while they were correlated with gametophyte development in the single petal cultivar. The CYC/TB1 type genes were highly detected in the formation of petal and pistil. The less-complex flower types of P. mume might result from the fact that there were only two CYC type genes present in P. mume and a lack of CYC2 genes to control the identity of flower types. These results lay the foundation for further study on the functions of TCP genes during flower development.
| S-EPMC5005400 | biostudies-literature