Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management

There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore (“Bonito del Norte con Eusko Label”) and Bay of Biscay anchovy (“Anchoa del Cantábrico”) are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling

MOESM1 of Genomic selection signatures in sheep from the Western Pyrenees

Additional file 1. Details of the in silico simulation study that was carried out to determine the appropriate window size to be used for GWSS analysis

MOESM3 of Genomic selection signatures in sheep from the Western Pyrenees

Additional file 3. Raw data for Z(FSTp): raw data for pooled fixation index (Z(FSTp)) for each analyzed window in each comparison (SAS vs. LAS, SAS vs. LAN, and LAS vs. LAN)

Thrombotic Antiphospholipid Syndrome Shows Strong Haplotypic Association with <i>SH2B3-ATXN2</i> Locus

<div><p>Background</p><p>Thrombotic antiphospholipid syndrome is defined as a complex form of thrombophilia that is developed by a fraction of antiphospholipid antibody (aPLA) carriers. Little is known about the genetic risk factors involved in thrombosis development among aPLA carriers.</p><p>Methods</p><p>To identify new loci conferring susceptibility to thrombotic antiphospholipid syndrome, a two-stage genotyping strategy was performed. In stage one, 19,000 CNV loci were genotyped in 14 thrombotic aPLA+ patients and 14 healthy controls by array-CGH. In stage two, significant CNV loci were fine-mapped in a larger cohort (85 thrombotic aPLA+, 100 non-thrombotic aPLA+ and 569 healthy controls).</p><p>Results</p><p>Array-CGH and fine-mapping analysis led to the identification of 12q24.12 locus as a new susceptibility locus for thrombotic APS. Within this region, a <i>TAC</i> risk haplotype comprising one SNP in <i>SH2B3</i> gene (rs3184504) and two SNPs in <i>ATXN2</i> gene (rs10774625 and rs653178) exhibited the strongest association with thrombotic antiphospholipid syndrome (p-value = 5,9 × 10⁻⁴ OR 95% CI 1.84 (1.32–2.55)).</p><p>Conclusion</p><p>The presence of a <i>TAC</i> risk haplotype in <i>ATXN2-SH2B3</i> locus may contribute to increased thrombotic risk in aPLA carriers.</p></div

SNP selection in 12q24.12 candidate susceptibility region.

a<p>CNV, copy number variant detected by array-CGH.</p

Candidate susceptibility regions with positive results in array-CGH and published GWA studies.

a<p>DGV, Database genomic variants.</p

MOESM2 of Genomic selection signatures in sheep from the Western Pyrenees

Additional file 2. Raw data for Z(Hp) and Z(Dp): raw data for pooled heterozygosity (Z(Hp)) and pooled Tajima’s D (Z(Dp)) for each analyzed window in each sequenced pool (SAS, LAS, and LAN)

Characteristics of individuals included in the study.

<p>Characteristics of individuals included in the study.</p

Significant allelic associations detected and odds ratios of SNPs.

*<p>In the aPLA+/th+ <i>vs.</i> aPLA+/th- analysis the aPLA+/th- are considered as controls for the purpose of MAF.</p

Overview of study design.

<p>Overview of study design.</p