Genes and pathways selected during animal domestication
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ABSTRACT:
PROVIDER: PRJEB19493 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice
| PRJNA314330 | ENA
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79154 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79155 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE78883 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE78900 | GEO
Project description:Kernel row number (KRN) is not only a key agronomic trait influencing maize yield but also a phenotype that underwent significant changes during maize domestication from its wild ancestor, teosinte. Previous studies have identified multiple quantitative trait loci (QTLs) associated with ear morphology on chromosome 5, among which the molecular basis and domestication role of qKRN5.04b remain unclear. To elucidate the function of qKRN5.04b, we constructed a segregating population through hybridization based on recombinant inbred lines derived from near-isogenic lines. Using high-throughput genotyping technologies and rigorously excluding interference from teosinte-derived chromosomal segments elsewhere in the genome, we narrowed the qKRN5.04b interval to a 3.8 Mb region. Transcriptomic analysis of immature maize ears revealed that differentially expressed genes were predominantly enriched in cis-regulatory RNA synthesis pathways, while KEGG pathway analysis indicated significant enrichment in auxin signal transduction. Functional validation showed that Mu insertion mutants of ZmGrx5 reduced kernel row number by two, suggesting ZmGrx5 as a candidate gene underlying qKRN5.04b. Population genetic analysis further demonstrated that ZmGrx5 is the most strongly selected member within the CC-type glutaredoxin (ROXY) family. Collectively, this study provides preliminary insights into the molecular basis of qKRN5.04b and offers valuable clues for understanding ROXY gene domestication and advancing molecular breeding strategies in maize.
2025-08-27 | GSE306206 | GEO
Project description:Morphotypes of Brassica oleracea are the result of a dynamic interaction between the genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaf patterns, flowering delaying and nutrient quality are some of the characters were potentially selected by humans during domestication. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve crop production. We aim to identify candidate genes that are responsible for kale leaf shape diversity and the evolution of domestic kale. Here we look at the global pattern of expressed genes during one single phase of development in kale, cabbage and TO1000 to gain an understanding of the genome-wide differences among some of the vegetative B. oleracea phenotypes. We identified gene expression patterns that are shared among the phenotypes and estimate the contribution of morphotype-specific gene expression patterns that set each of them apart. Differentially expressed developmental genes that regulate the vegetative to reproductive transition were abundant and present in all comparisons.
2021-01-27 | GSE149483 | GEO
Project description:Domestication of wild animals induces a set of phenotypic characteristics collectively known as the domestication syndrome. However, how this syndrome emerges is still not clear. Recently, the neural crest cell deficit hypothesis proposed that it is generated by a mildly disrupted neural crest cell developmental program, but clear support is lacking due to the difficulties of distinguishing pure domestication effects from preexisting genetic differences between farmed and wild mammals and birds. Here, we use a farmed fish as model to investigate the role of persistent changes in DNA methylation (epimutations) in the process of domestication.We show that early domesticates of sea bass, with no genetic differences with wild counterparts, contain epimutations in tissues with different embryonic origins. About one fifth of epimutations that persist into adulthood are established by the time of gastrulation and affect genes involved in developmental processes that are expressed in embryonic structures, including the neural crest. Some of these genes are differentially expressed in sea bass with lower jaw malformations, a key feature of domestication syndrome. Interestingly, these epimutations significantly overlap with cytosine-to-thymine polymorphisms after 25 years of selective breeding. Furthermore, epimutated genes coincide with genes under positive selection in other domesticates. We argue that the initial stages of domestication include dynamic alterations in DNA methylation of developmental genes that affect the neural crest. Our results suggest a role for epimutations during the beginning of domestication that could be fixed as genetic variants and suggest a conserved molecular process to explain Darwin’s domestication syndrome across vertebrates.
2019-07-09 | GSE125124 | GEO
Project description:Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and de-domestication
| PRJEB104131 | ENA
Project description:Transposable elements (TEs) are mobile DNA sequences that can reshape genomes, yet their role in crop domestication and adaptation has not been systematically investigated. Here we show that TE-associated genetic variants drive heritable epigenetic changes underlying key domestication traits in foxtail millet (Setaria italica), a cereal domesticated from green millet within the past ~11,000 years. By analyzing DNA methylation, transcriptome, small RNA, and structural variation data across 60 wild and domesticated accessions of foxtail millet, we identify 76,815 differentially methylated regions (DMRs), which associated with extensive polymorphic TE insertions. The epigenomic variation enable the discovery of a polymorphic TE inventory linked to key domestication traits, including seed shattering, branching, and growth habit. Functional analyses reveal two DNA/PIF-Harbinger elements insertions in the 5’ UTR regions of pleiotropic gene SiGW3 modulate its expression and regulate the plant architecture, panicle morphology, and grain size. Our findings highlight that naturally occurring TE polymorphisms can generate epigenetic variations and contributing to phenotypic evolution during crop domestication, offering insights for crop improvement and adaptive breeding.
2026-09-17 | GSE347112 | GEO