Linkage Mapping in Aquaculture Species

Danzmann, Roy G.; Gharbi, Karim

doi:10.1002/9780470277560.ch10

Cited by 16 publications

(15 citation statements)

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“…LINKMFEX version 2.4 [30] was used to calculate the recombination fraction, number of co-informative meiotic events (N) and the number of recombinations (r) for all mapped locus intervals for the maternal and paternal lines of each family separately. The Zmax score (LOD) was calculated for the mother and father in each family, and combined across all mothers and fathers respectively using methods outlined in Ott [33].…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2013

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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.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2013

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“…A genetic linkage map of the kelp grouper was produced based on microsatellite markers . Several studies on growth-related quantitative traits (QTLs) have been carried out recently on fishes such as the rainbow trout, Nile tilapia, Arctic char (Salvelinus alpinus) (Danzmann and Ghabi 2007), Atlantic salmon (Baranski et al 2010), barramundi (Lates calcarifer) , and turbot (Scophthalmus maximus) (Molano et al 2011).…”

Section: Introductionmentioning

confidence: 99%

“…In the recent decades, several genetic linkage maps of fin fish have been constructed using genetic markers, such as those for rainbow trout (Oncorhynchus mykiss), using simple sequence repeats (SSRs); Atlantic salmon (Salmo salar) using amplified fragment length polymorphisms (AFLPs) and SSRs; brown trout (Salmo trutta, AFLPs and SSRs); Nile tilapia (Oreochromis niloticus, AFLPs and SSRs); channel catfish (Ictalurus punctatus, AFLPs and SSRs), Japanese flounder (Paralichthys olivaceus, AFLPs and SSRs); ayu (Plecoglossus altivelis, AFLPs and SSRs; and yellowail (Seriola quinqueradiata, SSRs) (Danzmann and Ghabi 2007). A genetic linkage map of the kelp grouper was produced based on microsatellite markers .…”

Section: Introductionmentioning

confidence: 99%

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

et al. 2016

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To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F 1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using nonparametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1 % of the genomewide significance and accounted for 14.6-18.9 and 14.7-18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.

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“…INKAGE maps are powerful research tools for mapping quantitative trait loci (QTL) to complement marker-assisted selection in many species, including aquaculture species (Lander and Botstein 1989;Sakamoto et al 2000;Fishman et al 2001;Nichols et al 2003;Hubert and Hedgecock 2004;Moen et al 2004Moen et al , 2008Chistiakov et al 2005;Lee et al 2005;Gharbi et al 2006;Liu et al 2006;Sekino et al 2006;Phillips et al 2007;Sekino and Hara 2007; for a recent review, see Danzmann and Gharbi 2007). However, marker density for all aquacultured species is still low.…”

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confidence: 99%

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

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Linkage Mapping in Aquaculture Species

Cited by 16 publications

References 59 publications

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

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

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

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