Project description:Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.
Project description:Upon virus infections, the transcriptomic profile of host plants markedly changes. The rapid and comprehensive transcriptional reprogramming is critical to ward off virus attack. To learn more about transcriptional reprogramming in tobamovirus-infected pepper leaves, we carried out transcriptome-wide RNA-Seq analyses of pepper leaves following Obuda pepper virus (ObPV) and Pepper mild mottle virus (PMMoV)-inoculations.
Project description:The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.
Project description:A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage. To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage.
Project description:Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.
Project description:Background The first branch angle (FBA) is a critical trait influencing plant architecture, yield, and mechanized harvesting efficiency in pepper (Capsicum annuum L.). However, the genes and regulatory processes involved remain largely unclear. Results The phenotypic evaluation of 220 pepper accessions revealed significant genetic variation in FBA, with a broad-sense heritability of 93.26%, indicating a strong genetic foundation and making it a stable trait for selection. A genome-wide association study (GWAS) with mixed linear model and FarmCPU detected 25 significant SNPs related to FBA. Several candidate genes were identified, encompassing components of brassinosteroid signaling, gibberellin signaling, serine/threonine-protein kinase signaling, and cell wall modification. To functionally contextualize these genetic findings, two accessions with divergent FBAs (compact B010 and loose B003) were selected for cytological and hormonal analyses. The paraffin sections stained with Periodic Acid-Schiff showed that the compact B010 exhibits more starch granules in endodermal amyloplasts, while the loose B003 has larger cell size on the adaxial side. Hormonal analysis based on HPLC-MS/MS revealed higher auxin levels in the compact B010 and higher gibberellin, cytokinin, brassinosteroid, and strigolactone levels in the loose B003. These results suggest a mechanism whereby brassinosteroid/gibberellin-mediated cell expansion, potentially through the action of cell wall modification genes, drives the loose architecture of B003. Furthermore, RNA-Seq and qRT-PCR confirmed the coordinated regulation of the key phytohormone pathways (auxin signaling; cytokinin, gibberellin, and brassinosteroid biosynthesis) and serine/threonine-protein kinase signaling. Therefore, our work integrates multi-layered analyses to propose a regulatory framework for FBA in pepper: genetic loci associate with alterations in phytohormone regulation, kinase activity, and cellular traits, which orchestrate the transcriptomic, hormonal, and cytological changes that collectively determine branch architecture.
Project description:Pepper(Capsicum annuum L.) fruit development is a complex and genetically programmed process, a comparative study of transcriptome and proteome changes during two varieties of pepper development（IMG, MG, Br and MR） has been carried out by using RNA-Seq and Lable-free quantitation technology.
