Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-Reared Bombyx mori Hybrids
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1212033 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Bombyx mori parental strains Lat21 and B221 from the Department of Science and Technology - Cordillera Administrative Region (DOST-CAR) Sericulture Facility in La Trinidad, Benguet are crossed to produce the hybrids NC144 (Lat21♀ X B221♂) and CN144 (B221♀ X Lat21♂). These hybrids exhibited heterosis in field studies conducted in the 1980s. This study aims to provide evidence for the observed heterosis in the molecular basis for heterosis in B. mori hybrids NC144 and CN144 through RNA sequencing of whole silkworm larvae. Withe the sequencing data, it was possible to identify differentially expressed genes (DEGs) among: 1) the parental strains and their hybrids, and 2) the two hybrids. DESeq2 found 384 DEGs in the hybrids (reference: Parents; 202 upregulated, 182 downregulated) and 819 DEGs in NC144 (reference: CN144; 66 upregulated, 753 downregulated). Amon these are DEGs encoding for heat shock proteins and antimicrobial peptides, which have potentials use as markers for marker-assisted breeding. Additionally, the inducible nature of these genes in the presence of stressors like extreme temperature and bacteria, suggests that they could also be used as diagnostic tools for stress assessment.
2025-02-25 | GSE287287 | GEO
Project description:Global profiling of genes expressed in silk glands of Philippine-reared mulberry silkworm (Bombyx mori)
| PRJNA763387 | ENA
Project description:This study aims to bridge the gap in our knowledge of Philippine-reared silkworm by analyzing the gene expression profiles in the silkworm silk glands through next generation sequencing. RNA was isolated from the silk glands of 5th instar larvae and mRNA-enriched libraries were sequenced with NextSeq 500 (Illumina). To compare gene expression profiles of strains from CAR (Benguet) and TCMO (Misamis Oriental), DESeq2 analysis was performed. DESeq2 found 476 differentially expressed genes (222 upregulated, 254 downregulated) in CAR strains when compared to TCMO strains. Genes were mapped to protein IDs from the NCBI nr database and GO terms were assigned by mapping to the latest annotation data from KAIKObase. Enrichment of GO terms was analyzed using R package goseq. Among the top DEGs are myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of juvenile hormone. GO term enrichment analysis reveals overrepresentation of GO terms related to the biological processes nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, and molecular functions related to nucleotide binding, protein binding, and metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. This study provides for the first time valuable information on the transcriptome of B. mori strains in the Philippines, which are adapted to the tropical environment. The transcriptome assemblies may serve as a resource for studies intended to improve local strains, particularly for increasing silk production.
2022-07-31 | GSE184152 | GEO
Project description:we compared the change of transcritome between the parents and their F1 hybrids showing different heterosis level and obtained the potential index for predicting the heterosis level between rice parental lines.
2024-10-21 | GSE186372 | GEO
Project description:Chinese and Philippine strains of the blood fluke Schistosoma japonicum present clear and distinctive phenotypes in areas of fecundity, pathology, drug sensitivity and immunology. Despite these differences large scale sequencing efforts have focused solely on Chinese mainland strain of the parasite. We have undertaken a comparative genomic hybridisation (CGH) approach to highlight some of the structural differences in the genome of two of the major geographical isolates of S. japonicum. We identified seven distinct regions of the S. japonicum genome that present differential CGH between Chinese and Philippine strains of the blood fluke Schistosoma japonicum, representing either deletion or duplication regions in the Philippine strain. Within these regions, genes that may be related to phenotypical differences are identified and discussed. Genomic DNA was isolated from adult (7 week post cercarial challenge) Schistosoma japonicum Chinese and Philippine isolates and separate maleand femalesamples comparatively hybridised on an Agilent customn designed oligo microarray.
2012-07-13 | E-GEOD-39329 | biostudies-arrayexpress
Project description:Chinese and Philippine strains of the blood fluke Schistosoma japonicum present clear and distinctive phenotypes in areas of fecundity, pathology, drug sensitivity and immunology. Despite these differences large scale sequencing efforts have focused solely on Chinese mainland strain of the parasite. We have undertaken a comparative genomic hybridisation (CGH) approach to highlight some of the structural differences in the genome of two of the major geographical isolates of S. japonicum. We identified seven distinct regions of the S. japonicum genome that present differential CGH between Chinese and Philippine strains of the blood fluke Schistosoma japonicum, representing either deletion or duplication regions in the Philippine strain. Within these regions, genes that may be related to phenotypical differences are identified and discussed.
2012-07-14 | GSE39329 | GEO
Project description:Through genome-wide comparative transcriptome analysis of 63 samples, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.
2020-05-08 | GSE150052 | GEO
Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.
2022-01-05 | GSE186603 | GEO
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased.
2012-03-06 | GSE36273 | GEO
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased. Whole plants in Col, C24, and their F1 hybrids with two replications
2012-03-06 | E-GEOD-36273 | biostudies-arrayexpress