Pearl Quality Traits Research Articles

A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection

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.

Evidence of donor effect on cultured pearl quality from a duplicated grafting experiment onPinctada margaritiferausing wild donors

Producing high quality cultured black pearls from Pinctada margaritifera is one of the major challenges for the oyster industry in French Polynesia. In order to assess donor effect on cultured pearl quality, wild Pinctada margaritifera originating from the Tuamotu Archipelago were used in a duplicated grafting experiment. After 12 months of culture, nucleus retention was assessed and seven pearl quality traits recorded on the 454 cultured pearls harvested from the experiment. The traits scored were nacre thickness and pearl weight, surface defects, lustre, grade, and the components: 1) darkness of cultured pearl colour, and 2) visual perception of class (bodycolor and/or overtone). Our results demonstrate for the first time that individual wild donors of implanted mantle grafts significantly affect these seven quality traits in P. margaritifera cultured pearls. This finding was repeated in two series of grafts made by different professional grafters. The wild donors could be ranked from best (e.g., the donor whose grafts produced the cultured pearl with the maximum lustre) to the worst. Moreover, we showed strong correlations between: 1) cultured pearl nacre thickness and grade, with grade A showing the greatest nacre thickness on average compared with grade D and rejects; and 2) nacre thickness/cultured pearl weight and components (darkness and visual colour categories), with the palest cultured pearls (i.e. white cultured pearls) being the smallest (lowest nacre thickness and weight). Thus, one way of enhancing P. margaritifera foundation stocks for a selective breeding program could be to select the best donors, using appropriate molecular tools. Generation of selected donor lines from these stocks through hatchery production would be one way to increase the quality of cultured pearl farming of P. margaritifera in French Polynesia.

Donor-oyster derived heritability estimates and the effect of genotype × environment interaction on the production of pearl quality traits in the silver-lip pearl oyster, Pinctada maxima

The silver-lip pearl oyster, Pinctada maxima, produces the largest and most valuable pearls in the world. Despite the importance of this species very little is known about genetic parameters of commercially important pearl traits. As an initial step towards developing a selective breeding program, site selection effects, donor oyster derived genetic parameters and genotype by environment (G×E)interactions were estimated for pearl quality traits of P. maxima, originating from three populations (Aru, Bali, West Papua), reared at two commercial grow-out locations in Indonesia (Bali and Lombok). Microsatellite-based DNA parentage analyses were used to assign oysters to families and population of origin. Six pearl traits that are together the major determinants of pearl value (pearl weight (g), size (mm), shape, colour, complexion and lustre) were recorded at harvest. Pearls produced at the Lombok site were bigger and more valuable compared to pearls produced at the Bali site (P<0.05). G×E interactions were present for size (rg=−0.22), colour (rg=0.28), weight (rg=0.38), shape (rg=0.56) and lustre (rg=0.59) due to re-ranking of relative family performances at the two sites, although there were large standard errors associated with these estimates. Complexion was the only trait that showed little evidence for re-ranking (rg=0.85). Donor related-heritability estimates for size (h2=0.13), lustre (h2=0.14), weight (h2=0.15), colour (h2=0.15) and shape (h2=0.06) were low, while for complexion estimates were moderate (h2=0.25). A positive and high genetic correlation was found between pearl size and weight (rg=0.99), shape and complexion (rg=0.65) and shape and colour (rg=0.62); however, interestingly pearl weight was negatively genetically correlated with shape (rg=−0.46), complexion (rg=−0.11), colour (rg=−0.03) and lustre (rg=−0.15). Given the complex relationship amongst pearl quality traits and the likelihood for G×E interaction effects care should be executed when designing breeding objectives for the genetic improvement of these traits in P. maxima.

Xenografts and pearl production in two pearl oyster species, P. maxima and P. margaritifera: Effect on pearl quality and a key to understanding genetic contribution

Mantle xenografts between two Pinctada pearl oyster species, P. maxima (silver-lip pearl oyster) and P. margaritifera (black-lip pearl oyster), were used to examine their influence on pearl quality and to further our understanding of the respective contribution host and donor oysters have in pearl formation. Here, host oysters were implanted with mantle tissue originating from either the same species (allograft) or the other species (xenograft) and pearl formation allowed to proceed for 14 months, where after pearls were harvested and nuclei retention and pearl quality traits (nacre deposition/weight, shape, colour, complexion and lustre) recorded. Results showed that xenografts did not significantly affect pearl sac formation and subsequent nuclei retention ( χ 2 = 5.64, df = 3, P > 0.05), but did influence pearl colour, complexion, shape, nacre deposition and nacre weight ( P < 0.05). Nacre deposition and weight were found to be higher in xenografts comprising of a P. maxima donor and P. margaritifera host, than in the reciprocal xenograft and allografts. Pearl colour and complexion were also strongly influenced by the donor oyster species used as xenografts, with P. maxima host oysters implanted with mantle from P. margaritifera producing generally black colour based pearls. Conversely, P. margaritifera hosts implanted with P. maxima mantle produced silver colour based pearls. This study demonstrates the potential of xenografts as a means to improve pearl quality traits such as pearl size, and highlights the role that donor oysters have in the realisation of pearl growth, colour and surface complexion.

Progress towards a selective breeding program for silver- or gold-lip pearl oysters Pinctada maxima in Indonesia

James Cook University and Atlas Pacific Limited recently embarked on a collaborative research project aimed at establishing a selective breeding program for the silveror gold-lip pearl oyster, Pinctada maxima in Indonesia. The initial phase of the project, estimated to last 4 years, will focus on developing the molecular tools and acquiring the fundamental genetic information essential to the instigation of a future selective breeding program for this species. Specific objectives of the project are to (1) screen genetic diversity and performance of available wild populations to identify superior founder stocks as a base for future selection, (2) to estimate heritability of pearl growth and quality traits, (3) to determine if genotype by environment interactions may significantly influence pearl quality and (4) to develop a microsatellite DNA pedigree marker suite to enable retention of pedigree information during early developmental stages prior to the feasible application of physical tags. The scope of the project will be outlined and results to date presented.