Validation of single nucleotide polymorphism (SNP) markers from an immune Expressed Sequence Tag (EST) turbot, Scophthalmus maximus, database

Vera, Manuel; Álvarez‐Dios, José Antonio; Millán, Adrián; Pardo, Belén G.; Bouza, Carmen; Hermida, Miguel; Fernández, Carlos; Herrán, Roberto de la; Molina-Luzón, María Jesús; Martı́nez, Paulino

doi:10.1016/j.aquaculture.2011.01.038

Cited by 40 publications

(53 citation statements)

References 67 publications

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“…Among the 463 informative mapping markers ( Additional file 1: Table S1), 20 loci (4.3%), 18 microsatellites (4.6%) and two SNP (2.7%) showed null alleles in any of the eight diploid families (DF and QF1-7), in accordance with previous data [3,7]. Deviations from Mendelian expectations were detected at 27.5% loci (P < 0.05) mostly due to SNP (24.7% over 91 tests, P < 0.05) than to microsatellites (10.8% over 916 tests, P < 0.05) as previously reported in turbot [7,25]. As suggested [36], the existence of paralogous genes due to the teleost gene duplication probably interferes with SNP genotyping, hence the higher proportion of Mendelian deviations observed.…”

Section: Resultssupporting

confidence: 89%

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

et al. 2012

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BackgroundThe turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies.ResultsA consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups.ConclusionsThe new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.

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Section: Resultssupporting

confidence: 89%

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

et al. 2012

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“…Among these 25,511 SNPs, 18,214 were finally retained after filtering loci by: (i) consistent deviations from Mendelian segregation (5,866 loci: P < 0.01 in at least two families and representing more than 20% of the informative families); (ii) very low minimum allele frequency in the parental population (< 0.015) suggestive of genotyping errors (991 SNPs); and (iii) extreme deviations from HWE suggesting either paralogous genes (364 loci) or high null allele frequency (91 loci) (Supplementary Table S1). This set of 18,214 SNPs represented a frequency of one SNP every 163 bp in the reduced portion of the genome sequenced with 2b-RAD, a frequency slightly lower than that reported in other studies in turbot, 55 , 56 and a density of one SNP every 31,130 bp in the whole turbot genome (567 Mb 34 ). The average proportion of genotyping errors (Mendelian inconsistencies in families) of our 2b-RAD genotyping approach was 0.68% throughout all families in the filtered SNP dataset.…”

Section: Resultsmentioning

confidence: 56%

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Maroso¹,

Hermida

Millán³

et al. 2018

DNA Research

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Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

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“…For the two assays combined, 34.61% of the SNPs were located in the 3′ untranslated regions (UTRs), while 50.85% of the SNPs were in coding regions. Further analysis of functional changes revealed that 69 of the total SNPs were synonymous and 50 were non-synonymous, of which the latter accounted for over 20% of the SNPs developed in this study and could be considered as functionally important changes in the corresponding proteins [50]. …”

Section: Resultsmentioning

confidence: 99%

Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Merwe

Blaauw

Plessis

et al. 2013

IJMS

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Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and single nucleotide (SNPs). Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%–69% conversion rate (percentage polymorphic markers) with a global genotyping success rate of 76%–85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174) were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50) located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.

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Validation of single nucleotide polymorphism (SNP) markers from an immune Expressed Sequence Tag (EST) turbot, Scophthalmus maximus, database

Cited by 40 publications

References 67 publications

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

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