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Series GSE145072 Query DataSets for GSE145072
Status Public on Jan 31, 2023
Title Genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multi-species single nucleotide polymorphism chip analysis
Organism Eucalyptus urophylla
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary 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.
Overall design In total, 382 samples were analyzed without replicates or control or/and reference samples.
Contributor(s) Yang H, Yang X, Xu F, Liao H, Pan W, Zhang W, Xu B, Zhu B, Wang Y, Chen X
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Submission date Feb 10, 2020
Last update date Feb 02, 2023
Contact name Huixiao Yang
Phone 15989204715
Organization name Guangdong Academy of Forestry
Street address No 233 1st Guangshan Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510520
Country China
Platforms (1)
GPL28143 Illumina EUChip60k SNP array
Samples (382)
GSM4305753 Leaves_natural_rep1
GSM4305754 Leaves_natural_rep2
GSM4305755 Leaves_natural_rep3
BioProject PRJNA607094

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE145072_Matrix_signal_intensities.txt.gz 3.1 Mb (ftp)(http) TXT
GSE145072_RAW.tar 422.0 Mb (http)(custom) TAR (of IDAT)
GSE145072_RAW.tar.gz 423.8 Mb (ftp)(http) TAR
Processed data included within Sample table

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