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

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.

Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

“…The sex-average linkage map for Pinctada maxima was constructed from 887 SNPs, with an average spacing of 2.0 cM, using 335 individuals that belonged to eight families. Genotyping was performed using Illumina 3 k iSelect custom arrays [11]. The sex-average linkage map coverage, Coa, observed here was 97.24%, which is similar to the linkage map of Chlamys farreri (99.5%, constructed by a 2b-restriction site-associated DNA method, using two parents and 96 progeny) [46].…”

“…In comparisons of high resolution genetic linkage maps, those with more markers may result in a longer genome length. The consensus map of Chlamys farreri (1551.9 cM, with 3806 markers) [46] is longer than linkage maps of P. fucata , in this study, and Pinctada maxima [11]. The RAD-seq method was available for high-resolution linkage map construction of P. fucata and this research has provided foundation materials for the utility of RAD-seq in non-model animals.…”

“…The sex-average linkage map for P. fucata consists of 1373 markers, with an average spacing of 1.4 cM. It is denser than the linkage maps for Pinctada martensii and Pinctada maxima [11], [12]. Linkage maps have been constructed for Pinctada martensii using amplified fragment length polymorphism and microsatellite markers from an F1 family of two parents and 78 progeny [12].…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Genetic linkage maps were constructed also for some other species important for aquaculture, as gilthead sea bream, Sparus aurata (Tsigenopoulos et al, 2014); Asian seabass, Lates calcarifer Sun et al, 2017); mandarin fish, Siniperca chuatsi ; turbot, Scophthalmus maximus (Wang et al, 2015b); Japanese flounder, Paralichthys olivaceus (Castaño-Sánchez et al, 2010;Shao et al, 2015); large yellow croaker, Larimichthys crocea (Ao et al, 2015); black tiger shrimp, Penaeus monodon (Baranski et al, 2014); Pacific white shrimp, L. annamei (Du et al, 2010); Pacific abalone, Haliotis discus hannai (Qi et al, 2010); South African abalone, Haliotis midae (Vervalle et al, 2013) and silver-lipped pearl oyster, Pinctada maxima (Jones et al, 2013). Linkage maps of commercial fish and shellfish have been listed in other review papers (Wenne et al, 2007;Yue, 2014;Abdelrahman et al, 2017).…”

Recombination in the eggs and sperm in a simultaneously hermaphroditic vertebrate

“…Yet as pointed out in the Introduction, the vast majority of studies in non-model organisms do not provide information about heterochiasmy along LGs, and hermaphroditic animals are no exception. The ones that do generally indicate higher recombination rates in females close to the centromeres in a variety of animal groups as molluscs [23,25], fishes [42][43][44], and mammals (including humans [8]). Here again there are exceptions, but the broad picture suggests that it might be quite common among animals and possibly driven by female meiotic drive.…”