Studying on the strictly self-compatibility mechanism of 'Liuyefeitao' peach (Prunus persica L.).
Ontology highlight
ABSTRACT:
SUBMITTER: Liu W
PROVIDER: S-EPMC6070229 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
Studying on the strictly self-compatibility mechanism of 'Liuyefeitao' peach (Prunus persica L.).
Liu Wei W Pei Maosong M Zhang Anning A
PloS one 20180801 8
Peach (Prunus persica L.) generally exhibits self-pollination, however, they can also be pollinated by other varieties of pollen. Here we found two varieties that are different from other peaches: 'Daifei' and 'Liuyefeitao'. 'Daifei' produces less pollen, which needs artificial pollination, honeybee pollination, and the fruit setting depends on other varieties of peach pollen. 'Liuyefeitao' exhibits strictly self-pollination, hence pollen from other species is rejected. To explore the mechanism ...[more]
Similar Datasets
Project description:Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
| S-EPMC7527504 | biostudies-literature
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:The cultivated/domesticated peach (Prunus persica var. persica; Rosaceae, subgenus Amygdalus; synonym: Amygdalus persica) originated in China, but its wild ancestor, as well as where, when, and under what circumstances the peach was domesticated, is poorly known. Five populations of archaeological peach stones recovered from Zhejiang Province, China, document peach use and evolution beginning ca. 8000 BP. The majority of the archaeological sites from which the earliest peach stones have been recovered are from the Yangzi River valley, indicating that this is where early selection for favorable peach varieties likely took place. Furthermore, peach stone morphology through time is consistent with the hypothesis that an unknown wild P. persica was the ancestor of the cultivated peach. The oldest archaeological peach stones are from the Kuahuqiao (8000-7000 BP) and Tianluoshan (7000-6500 BP) sites and both stone samples segregate into two size groups, suggesting early selection of preferred types. The first peach stones in China most similar to modern cultivated forms are from the Liangzhu culture (ca. 5300 to 4300 BP), where the peach stones are significantly larger and more compressed than earlier stones. Similar peach stones are reported from Japan much earlier (6700-6400 BP). This large, compressed-stone peach was introduced to Japan and indicates a yet unidentified source population in China that was similar to the Liangzhu culture peach. This study proposes that the lower Yangzi River valley is a region, if not the region, of early peach selection and domestication and that the process began at least 7500 years ago.
| S-EPMC4156326 | biostudies-literature
Project description:Almost 30 years have passed since the first publication reporting regeneration of transformed peach plants. Nevertheless, the general applicability of genetic transformation of this species has not yet been established. Many strategies have been tested in order to obtain an efficient peach transformation system. Despite the amount of time and the efforts invested, the lack of success has significantly limited the utility of peach as a model genetic system for trees, despite its relatively short generation time; small, high-quality genome; and well-studied genetic resources. Additionally, the absence of efficient genetic transformation protocols precludes the application of many biotechnological tools in peach breeding programs. In this review, we provide an overview of research on regeneration and genetic transformation in this species and summarize novel strategies and procedures aimed at producing transgenic peaches. Promising future approaches to develop a robust peach transformation system are discussed, focusing on the main bottlenecks to success including the low efficiency of A. tumefaciens-mediated transformation, the low level of correspondence between cells competent for transformation and those that have regenerative competence, and the high rate of chimerism in the few shoots that are produced following transformation.
| S-EPMC7465125 | biostudies-literature
Project description:BACKGROUND: MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. RESULTS: We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. CONCLUSIONS: Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.
| S-EPMC3542160 | biostudies-literature
Project description:We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.
2012-07-03 | GSE38535 | GEO
Project description:We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development. Identification of peach miRNAs and their targets from four different tissues
2012-07-02 | E-GEOD-38535 | biostudies-arrayexpress
Project description:Peach latent mosaic viroid (PLMVd) is a small, single-stranded, circular RNA pathogen that infects Prunus persica trees. As with all other known viroids, the PLMVd genome does not encode any proteins. Consequently, it must interact with host cellular factors in order to ensure its life cycle. With the objective of identifying cellular proteins that interact with PLMVd, Northwestern hybridizations were performed using partially purified peach leaf extracts. Mass spectrometric analysis of the detected RNA-protein complexes led to the identification of six putative RNA-binding proteins. One of these was found to be elongation factor 1-alpha (eEF1A), and because of its known involvement in the replication and translation of various RNA viruses, further characterizations were performed. Initially, the existence of this interaction received support from an experiment that immunoprecipitated the eEF1A from a crude extract of infected peach leaves, coupled with reverse transcription-PCR detection of the PLMVd. Subsequently, eEF1A interaction with PLMVd strands of both polarities was confirmed in vitro by electrophoresis mobility shift assays, fluorescence spectroscopy, and the prediction of an altered PLMVd RNase mapping profile in the presence of the protein. The potential contribution of eEF1A to the molecular biology of PLMVd, including for viroid replication, is discussed.
| S-EPMC2786745 | biostudies-literature
Project description:BackgroundThe application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery.DescriptionThe sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly.ConclusionThe eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.
| S-EPMC3253712 | biostudies-literature
Project description:MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.We identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248?±?72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I M?, M?, and M? subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.Most Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.
| S-EPMC4329201 | biostudies-literature