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Title:	SNP-based linkage map construction for Acacia auriculiformis x A. mangium hybrids via transcriptome sequencing
Authors:	Wong Melissa (P48211)
Supervisor:	Wickneswari Ratnam, Prof. Dr.
Keywords:	Earleaf acacia
Issue Date:	28-Feb-2013
Description:	Acacia auriculiformis x A. mangium hybrid (2n=26) is an emerging forest tree for pulpwood production in Southeast Asia due to its high growth rate, good fibre properties, disease resistance and high adaptability to various environments. There is a need to increase the productivity of forest plantation by selection of superior trees through breeding programmes. Marker Assisted Selection (MAS) is a promising approach that enables the identification of genes controlling wood and pulp properties. The aim of this study was to construct linkage maps for two Acacia hybrid F1 mapping populations, namely Wood Density (WD) and Fibre length (FL) populations. Transcriptome sequencing that was performed separately for four parents on an Illumina GAII machine using total RNA pooled from young stem and inner bark tissues produced a total of 20,913,146 paired-end reads of 48-51 nucleotides long after filtering. De novo transcriptome assembly using SOAPdenovo yielded a total of 124,582 contigs with total length of 58,123,842 bp. A total of 43,286 putative Single Nucleotide Polymorphisms (SNPs) were detected from 7,839 contigs using Bowtie and Samtools. To evaluate the in silico SNPs detection approach, 96 SNPs were tested on 96 samples using Illumina GoldenGate Assay and a conversion rate of 37.5% was obtained. The SNP detection approach was further improved by increasing filtering stringency and a total of 768 SNPs were selected based on two-way pseudo-testcross strategy, even genome coverage and increased assay successful rate. SNP genotyping using Illumina GoldenGate Assay that was carried out on 173 and 182 progenies from FL and WD populations respectively gave an overall conversion rate of 57.4% where 32.9% out of these polymorphic SNPs were transferable to FL population. A total of 123 and 83 progenies from WD and FL population respectively were used in linkage analysis. Four linkage maps were constructed for each parent using Joinmap. For WD population, 239 and 163 markers were mapped to paternal and maternal map where 13 linkage groups ranging from 22.9 cM to 156.6 cM were identified. The total lengths of WD paternal and maternal maps were 1086.7 cM and 822.3 cM with an average marker interval of 4.5 and 5.0 cM respectively. For FL population, 78 male and 45 female markers were mapped, and total lengths of 484.8 cM and 235.4 cM spanning 10 and 7 linkage groups in male and female parents respectively were obtained. Although the markers mapped in FL population were fewer as expected, the order of most markers agreed with the order in WD population. The ordering of anchor loci between parental maps are consistent suggesting both species shared high similarity in genome organization. Comparative genomics study revealed that significant amount of gene conservation and coliearity between Acacia and Medicago truncatula. These sequence-based linkage maps have provided important insights in genome organization and duplication of Acacia.,Ph.D
Pages:	243
Call Number:	QH445.2.W644 2013
Publisher:	UKM, Bangi
Appears in Collections:	Faculty of Science and Technology / Fakulti Sains dan Teknologi

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