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Open Access Highly Accessed Research article

Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

Melissa ML Wong1, Charles H Cannon23 and Ratnam Wickneswari1*

Author Affiliations

1 School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia

2 Ecological Evolution Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Menglun, Mengla, Yunnan, 666303, P. R. China

3 Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA

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BMC Genomics 2012, 13:726  doi:10.1186/1471-2164-13-726

Published: 24 December 2012

Additional files

Additional file 1:

Clustering profiles of 29 SNPs in 96-plex and 384-plex genotyping. This Word document file contains a table showing the clustering profiles of 29 SNPs. The clustering profiles in 96-plex and 384-plex genotyping are shown side-by-side to indicate the reproducibility of Illumina GoldenGate Assay.

Format: DOCX Size: 1.6MB Download file

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Additional file 2:

Clustering profiles of SNPs from 50 genes in 768 SNPs genotyping. This Word document file contains a table showing the clustering profiles of 50 genes. The clustering profiles of the two SNPs from the same gene are shown side-by-side.

Format: DOCX Size: 2.7MB Download file

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Additional file 3:

Python scripts used in SNP detection. This compressed file in tar.gz format contains six Python scripts used in SNP detection. The title of each script is the same as the title that appeared in the text.

Format: GZ Size: 4KB Download file

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Additional file 4:

Reference sequences used in SNP detection. This compressed file in tar.gz format contains a FASTA file of AArefseq (AArefseq_merge.fa).

Format: GZ Size: 2.7MB Download file

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Additional file 5:

A SNP summary of 96 SNPs validation and 768 SNPs genotyping. This Excel file contains three sheets, namely “96plex”, “aaOPA3” and “amOPA3”. Each sheet contains SNP information of dbSNP id, SNP contig and position, design score, SNP score, homologous genes in Mt3.5, assay success, polymorphism, mapping population, minor allele frequency in A. auriculiformis and A. mangium natural germplasms. Description of each column can be found on the right in sheet “96plex”.

Format: XLS Size: 185KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data