The trees for this experiment were planted in a breeding gardern in Guangzhou under natural condition. In 2008, the seeds of E. urophylla from 24 different sources were introduced into southern China through Commonwealth Scientific and Industrial Research Organisation (CSIRO), which comprised seed from 197 mother trees throughout the species’ entire natural distribution range. Among them, Thailand and Africa population belonged to cultivated species (Table S1). The minimum distance between individual trees was at least 50 m to avoid sampling close relatives. A map of the geographical locations of the 19 populations was created using software GenGis 2.5.037 (http://kiwi.cs.dal.ca/GenGIS/Main_Page) and free raster map data from Natural Earth (http://www.naturalearthdata.com/) (Fig. 1 and Table S1). Seeds were sown in a commercial nursery and were planted at the Experimental Farm of the Guangdong Academy of Forestry in Guangzhou District, Guangdong, China. The experimental site (23°22'N, 112°45'E, 45 m elevation) had a humid climate with an average annual rainfall of 1,400 mm and an average slope gradient of less than 25°. The population was planted in 2008 using 2m×3m spacing with 59 replications, and using a randomized complete block design with each family with one tree in each block. In the present study, 332 unrelated individuals included one or two originating from a different mother tree were used to assess genetic diversity and population structure that representing the entire geographic distribution of E. urophylla.
Extracted molecule
genomic DNA
Extraction protocol
Leaf tissue was collected at April, 2015. Total genomic DNA was extracted from 50 mg fresh individual plant leaves using a Plant Genomic DNA kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.
Label
cy3 and cy5
Label protocol
Standard Illumina protocol
Hybridization protocol
Standard Illumina protocol
Scan protocol
SNP genotypes were called using GenomeStudio (Illumina Inc., San Diego,CA, USA) following standard genotyping and quality control procedures with no manual editing of clusters.
Description
SAMPLE 291
Data processing
The DNA samples were genotyped with the Eucalyptus EuCHIP60K chip, based on the Illumina Infinium technology being a total of 64,639 markers.
Genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multi-species single nucleotide polymorphism chip analysis
