Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna ( Thunnus albacares )

Pecoraro, Carlo; Babbucci, Massimiliano; Villamor, Adriana; Franch, Rafaella; Papetti, Chiara; Leroy, Bruno; Ortega‐García, Sofia; Muir, Jeff; Rooker, Jay R.; Arocha, Freddy; Murua, Hilário; Zudaire, Iker; Chassot, Emmanuel; Bodin, Nathalie; Tinti, Fausto; Bargelloni, Luca; Cariani, Alessia

doi:10.1016/j.margen.2015.12.002

Cited by 50 publications

(38 citation statements)

References 26 publications

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“…Our analysis suggested the absence of significant genetic structure in both T. albacares and S. brasiliensis. For T. albacares, our results are in accordance with previous reports carried out with microsatellites and SNPs that could not find significant population structure within oceanic basins likely related to its high migration capacity (Ely et al, 2005;Pecoraro et al, 2016a). Grewe et al (2015) suggested the existence of differentiation in this species within the Pacific Ocean using 215 SNPs potentially under selection, but no differentiation was found at the remaining 5054 presumably neutral loci.…”

Section: Genetic Diversity and Structuresupporting

confidence: 92%

SNP identification and validation on genomic DNA for studying genetic diversity in Thunnus albacares and Scomberomorus brasiliensis by combining RADseq and long read high throughput sequencing

et al. 2018

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A combination of a RADseq method (ddRAD) with long read high throughput sequencing (Roche 454) was tuned up in order to identify and validate a set of SNPs useful for gene diversity analysis in two important South American commercial tuna (Thunnus albacares and Scomberomorus brasiliensis). A total of 11 and 21 individuals of T. albacares and S. brasiliensis, respectively, were used for SNP identification. DNA was individually digested with two restriction enzymes (SbfI and SphI) and fragments between 300 and 600 bp selected. Combinatorial barcoding was used to identify individuals by including short sequences (5-7 bp) in the adaptors of each restriction site (P1 and P2). After adaptor ligation, samples were pooled and size-selected, amplified by PCR, and sequenced on a 454 GS-Junior sequencer. A total of 180,779 reads were produced with an average length and coverage of 287 bp and 26x, respectively. Sets of 60 and 79 SNPs were in silico selected for T. albacares and S. brasiliensis, respectively, and were tested and validated in 74 and 66 individuals, respectively, on a MassARRAY platform. A total of 36 and 47 SNPs were polymorphic and useful for population analysis. A preliminary study on two distant Brazilian populations of both species (∼3000 km) with these SNPs suggested the absence of significant structure among local populations of both species. Our results demonstrate the possibility of combining ddRAD with long read high throughput sequencing for marker development in species with scarce genomic resources.

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Section: Genetic Diversity and Structuresupporting

confidence: 92%

SNP identification and validation on genomic DNA for studying genetic diversity in Thunnus albacares and Scomberomorus brasiliensis by combining RADseq and long read high throughput sequencing

et al. 2018

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“…A total of 892 2b-RAD libraries (67 parents and 825 juveniles) were constructed by following the protocol reported by Wang et al (2012), with some modifications (Pecoraro et al 2016). Template DNA for each individual (500 ng) was digested in 6 μl reaction volume using 1 U AlfI (Thermo Fisher Scientific) at 37° for 1 hr, followed by enzyme heat inactivation at 65° for 20 min.…”

Section: Methodsmentioning

confidence: 99%

“…Quality and adapters trimming of sequenced reads were performed by running a customized script (Pauletto et al 2016; Pecoraro et al 2016), obtaining 34-bp long fragments. SNP calling was performed using STACKS v1.23 (Catchen et al 2013).…”

Section: Methodsmentioning

confidence: 99%

Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

Palaiokostas

Ferraresso

Franch

et al. 2016

G3 Genes|Genomes|Genetics

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Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 × 105 CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11–0.36) and 0.28 (95% highest density interval: 0.17–0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r = 0.38–0.46) outperformed the traditional BLUP approach based on pedigree records (r = 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species.

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“…To assess the robustness of the method, two libraries were replicated (Technical replicates, TRs) for two individuals42. A total of 200 ng of gDNA from each sample were digested with 2 U CspC I (New England Biolabs, NEB, Ipswich, Massachusetts, USA) for 1 h at 37 °C.…”

Section: Methodsmentioning

confidence: 99%

“…Different settings were tested on the TRs dataset to fine tune the STACKS pipeline parameters and to assess the consistency of the results as in ref. 42. To construct stacks and catalogue loci, a minimum coverage of 10X was used for parental samples45.…”

Section: Methodsmentioning

confidence: 99%

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

Babbucci

Ferraresso

Pauletto

et al. 2016

Sci Rep

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Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the “nervous system development” as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity.

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Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna ( Thunnus albacares )

Cited by 50 publications

References 26 publications

SNP identification and validation on genomic DNA for studying genetic diversity in Thunnus albacares and Scomberomorus brasiliensis by combining RADseq and long read high throughput sequencing

SNP identification and validation on genomic DNA for studying genetic diversity in Thunnus albacares and Scomberomorus brasiliensis by combining RADseq and long read high throughput sequencing

Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

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