Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora

Shi Wang,Lingling Zhang,Eli Meyer,Mikhail V Matz

doi:10.1186/gb-2009-10-11-r126

Shi Wang, Lingling Zhang + Show 2 more

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https://doi.org/10.1186/gb-2009-10-11-r126

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Journal: Genome Biology	Publication Date: Jan 1, 2009
Citations: 150	License type: cc-by

Affiliation: The University of Texas at Austin

Abstract

A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.

Highlights

Worldwide, coral reefs are in decline due to a range of anthropogenic disturbances, and are under threat from global climate change
single nucleotide polymorphism (SNP) marker development For SNP marker development, we designed PCR primers for 1,033 candidate SNPs, which were previously identified in the A. millepora larval transcriptome by 454-FLX sequencing [11]
Longer amplicons greatly diminish the precision of high-resolution melting (HRM) SNP analysis, so most of these intron-containing amplicons were discarded

Summary

Introduction

Coral reefs are in decline due to a range of anthropogenic disturbances, and are under threat from global climate change. Nothing is currently known about the genetic factors that might determine whether corals adapt to the changing climate or continue to decline. Quantitative genetics studies aiming to identify the adaptively important genomic loci will require a high-resolution genetic linkage map. We have recently demonstrated that the coral Acropora millepora shows considerable genetically determined variation in thermal tolerance and responsiveness of the larvae to the settlement cue, which may be the raw evolutionary material for future local thermal adaptation or modification of the larval dispersal strategy in response to ongoing climate change [4]. Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes, and are the preferred genetic markers for a variety of applications such as high-resolution linkage mapping, QTL mapping of complex traits, and for combining these results with population genomics, which is arguably the most powerful way of detecting and understanding the process of natural adaptation [10]. Since the detected SNPs reside in or immediately next to the protein-coding sequences ('gene-based SNPs'), they are useful for QTL mapping and population genomics studies because they have the potential for quickly identifying causal genes underlying complex traits [12,13]

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Conclusion