Abstract
BackgroundThe silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters.ResultsA total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes.ConclusionsThis high-density SNP genetic map is the first comprehensive linkage map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-810) contains supplementary material, which is available to authorized users.
Highlights
The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought “South Sea” pearls
Following robust linkage map construction, this study evaluates heterochiasmy between the sexes, extent of linkage disequilibrium (LD) across the genome, and the localization of important biomineralization genes
The map length of the P. maxima linkage groups ranged from 48.3 cM to 75.6 cM and exhibited a negative correlation with the number of markers mapped per linkage group (Table 1)
Summary
The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought “South Sea” pearls. The construction of a high-density genetic linkage map for P. maxima is essential for unravelling the genomic architecture of complex pearl quality traits, and provides indispensable information on the genome structure of pearl oysters. The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species that, along with P. margaritifera, produces almost 50% of marketed pearls worldwide by value [1]. Promising developments in livestock genomics are opening up opportunities, allowing genomic information to be incorporated into breeding programs in order to increase the rate of genetic gain for complex commercial traits in oyster. The current impediment to the implementation of genomic approaches in mollusc breeding programs, is a significant lack of genomic resources such as genome-wide molecular markers, genomic maps and genome sequences [2,5,6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
