Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic selection to enhance tilapia breeding

ABSTRACT: This project aims to develop and apply genomic tools to enhance selective breeding of Nile tilapia, with a focus on disease resistance.

INSTRUMENT(S): Illumina HiSeq X Ten

ORGANISM(S): Oreochromis Niloticus

SUBMITTER: The Roslin Institute, University of Edinburgh

PROVIDER: PRJEB38548 | EVA | 2020-06-01

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	tilapia_snp_array.accessioned.vcf.gz	Vcf
	tilapia_snp_array.vcf.gz	Vcf
	tilapia_snp_array.vcf.gz.tbi	Vcf

Items per page:

1 - 3 of 3

Similar Datasets

Project description:Genomic selection to enhance tilapia breeding

| PRJEB38548 | ENA

Local ancestry inference provides insight into Tilapia breeding programmes

Project description:Local ancestry inference provides insight into Tilapia breeding programmes

| PRJEB38387 | ENA

Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding

Project description:Advancements in -omics techniques provide powerful tools to assess potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering causes changes in plants that go beyond the changes introduced by conventionally plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis (Bt) genes that developed by genetic engineering and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines. Metabolome profiling analysis found several new metabolites in GE rice lines when compared to the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both genetic engineering and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and HPLC-MS technology to assess the unintended changes in new rice varieties, and the results suggest that genetic engineering does not cause unintended effects that go beyond conventional cross-breeding in rice.

2020-10-01 | GSE152572 | GEO

Comparative wheat phosphoproteome profiling pinpoints high temperature-associated breeding markers

Project description:Elevated temperatures resulting from climate change are adversely impacting natural and crop ecosystems, necessitating the development of heat-tolerant crops. We established a framework to precisely identify wheat protein-phosphorylated sites associated with varying temperature sensitivities. Our findings demonstrate that the phosphorylation state of a specific set of proteins creates a unique signature for heat stress tolerance. These findings aid the identification of targets for breeding or genome editing to enhance heat tolerance.

2024-12-02 | PXD047670 | Pride

Project description:Genomic consequences of selective breeding in Nile Tilapia (Oreochromis niloticus)

| PRJNA1039171 | ENA

sandflies breeding sites

Project description:bacterial diversity of sandflies breeding sites

| PRJNA966793 | ENA

Multi-organ transcriptomic profiles and gene-regulation network underlying vibriosis resistance in tongue sole

Project description:Vibrio spp. are major pathogens responsible for mortality and disease in various marine aquaculture organisms. Effective disease control and genetic breeding strategies rely heavily on understanding host vibriosis resistance mechanisms. The Chinese tongue sole (Cynoglossus semilaevis) is economically vital but suffers from substantial mortalities due to vibriosis. Through continuous selective breeding, we have successfully obtained vibriosis-resistant families of this species. In this study, we conducted RNA-seq analysis on three organs, including liver, spleen and intestine from selected resistant and susceptible tongue soles. Additionally, we integrated these data with our previously published RNA-seq datasets of skin and gill, enabling the construction of organ-specific transcriptional profiles and a comprehensive gene co-expression network elucidating the differences in vibriosis resistance. Furthermore, we identified 12 modules with organ-specific functional implications. Overall, our findings provide a valuable resource for investigating the molecular basis of vibriosis resistance in fish, offering insights into target genes and pathways essential for molecular selection and genetic manipulation to enhance vibriosis resistance in fish breeding programs.

2024-06-26 | GSE270251 | GEO

Exploring selective breeding in common bean (Phaseolus vulgaris L.) landraces

Project description:Selective breeding for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.)

| PRJEB81566 | ENA

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fiber length, lint percentage, and Fusarium wilt resistance

Project description:Sea Island cotton (Gossypium barbadense) is the source of the world’s finest fiber-quality cotton, yet relatively little is understood about the genetic variation among diverse germplasm, the genes underlying important traits, and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fiber quality, yield, disease resistance, maturity, and plant architecture. The highest number of associated loci was for fiber quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments we confirmed the role of five candidate genes regulating four key traits, i.e., disease resistance, fiber length, fiber strength, and lint percentage. Geographical and temporal considerations demonstrate selection for the superior fiber quality (fiber length and fiber strength), and high lint-percentage in improving G. barbadense in China. Pedigree selection breeding wholly increased Fusarium wilt disease resistance, and separately improved fiber-quality and yield. Our work provides a foundation for understanding genomic variation in and selective breeding of Sea Island cotton.

2022-04-13 | GSE184965 | GEO

Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance

Project description:Crop breeding aims to balance disease resistance with yield; however, single resistance (R) genes can lead to resistance breakdown, and R gene pyramiding may affect growth fitness. Here we report that the rice Pigm locus contains a cluster of genes encoding nucleotide-binding leucine-rich repeat (NLR) receptors that confer durable resistance to the fungus Magnaporthe oryzae without yield penalty. Among these NLR receptors, PigmR confers broad-spectrum resistance, whereas PigmS competitively attenuates PigmR homodimerization to suppress resistance. PigmS expression, and thus PigmR-mediated resistance, are subjected to tight epigenetic regulation. PigmS increases seed production to counteract the yield cost induced by PigmR Therefore, our study reveals a mechanism balancing high disease resistance and yield through epigenetic regulation of paired antagonistic NLR receptors, providing a tool to develop elite crop varieties.

2017-06-15 | GSE83522 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data