Ontology highlight
ABSTRACT:
PROVIDER: PRJNA694021 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. High levels of genetic diversity were observed throughout the 19 E. urophylla populations based on genome-wide SNP data (HE=0.2677 to 0.3487). Analysis with STRUCTURE software, Principal component analysis (PCA) and a neighbor-joining (NJ) tree indicated that E. urophylla populations could be divided into three groups, and moderate and weak population structure was observed with pairwise genetic differentiation (FST) values ranging from −0.09 to 0.074. The low genetic diversity and shallow genetic differentiation found within the 19 populations may be a consequence of their pollination system and seed dispersal mechanism. In addition, 55 core germplasms of E. urophylla were constructed according to the genetic marker data. The genome-wide SNPs we identified will provide a valuable resource for further genetic improvement and effective use of the germplasm resources.
2023-01-31 | GSE145072 | GEO
Project description:Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-10-20 | E-GEOD-3479 | biostudies-arrayexpress
Project description:Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-10-20 | GSE3479 | GEO
Project description:The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.
2019-10-07 | GSE127968 | GEO
Project description:Population genetic structure of the Ashkenazi Jewish population
| PRJNA130941 | ENA
Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.
2019-12-31 | GSE74100 | GEO