Dataset Information

Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails.

ABSTRACT: In agriculture, diversifying production implies picking up, in the wild biodiversity, species or populations that can be domesticated and fruitfully produced. Two alternative approaches are available to highlight wild candidate(s) with high suitability for aquaculture: the single-trait (i.e. considering a single phenotypic trait and, thus, a single biological function) and multi-trait (i.e. considering multiple phenotypic traits involved in several biological functions) approaches. Although the former is the traditional and the simplest method, the latter could be theoretically more efficient. However, an explicit comparison of advantages and pitfalls between these approaches is lacking to date in aquaculture. Here, we compared the two approaches to identify best candidate(s) between four wild allopatric populations of Perca fluviatilis in standardised aquaculture conditions. Our results showed that the single-trait approach can (1) miss key divergences between populations and (2) highlight different best candidate(s) depending on the trait considered. In contrast, the multi-trait approach allowed identifying the population with the highest domestication potential thanks to several congruent lines of evidence. Nevertheless, such an integrative assessment is achieved with a far more time-consuming and expensive study. Therefore, improvements and rationalisations will be needed to make the multi-trait approach a promising way in the aquaculture development.

SUBMITTER: Toomey L

PROVIDER: S-EPMC7360571 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails.

Toomey Lola L Lecocq Thomas T Bokor Zoltán Z Espinat Laurent L Ferincz Árpád Á Goulon Chloé C Vesala Sami S Baratçabal Margot M Barry Mamadou-Diouhe MD Gouret Mélanie M Gouron Camille C Staszny Ádám Á Mauduit Emilie E Mean Vicheka V Muller Iris I Schlick Nicolas N Speder Kévin K Thumerel Romain R Piatti Clémentine C Pasquet Alain A Fontaine Pascal P

Scientific reports 20200714 1

In agriculture, diversifying production implies picking up, in the wild biodiversity, species or populations that can be domesticated and fruitfully produced. Two alternative approaches are available to highlight wild candidate(s) with high suitability for aquaculture: the single-trait (i.e. considering a single phenotypic trait and, thus, a single biological function) and multi-trait (i.e. considering multiple phenotypic traits involved in several biological functions) approaches. Although the ...[more]

PMID: 32665568

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Project description:Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRNA rather than protein levels. Many variants remain without annotation. To address this problem, we measured the steady state abundance of 441 human signaling and transcription factor proteins from 68 Yoruba HapMap lymphoblastoid cell lines to identify novel relationships between inter-individual protein levels, genetic variants, and sensitivity to chemotherapeutic agents. Proteins were measured using micro-western and reverse phase protein arrays from three independent cell line thaws to permit mixed effect modeling of protein biological replicates. We observed enrichment of protein quantitative trait loci (pQTLs) for cellular sensitivity to two commonly used chemotherapeutics: cisplatin and paclitaxel. We functionally validated the target protein of a genome-wide significant trans-pQTL for its relevance in paclitaxel-induced apoptosis. GWAS overlap results of drug-induced apoptosis and cytotoxicity for paclitaxel and cisplatin revealed unique SNPs associated with the pharmacologic traits (at p<0.001). Interestingly, GWAS SNPs from various regions of the genome implicated the same target protein (p<0.0001) that correlated with drug induced cytotoxicity or apoptosis (p ≤ 0.05). Two genes were functionally validated for association with drug response using siRNA: SMC1A with cisplatin response and ZNF569 with paclitaxel response. This work allows pharmacogenomic discovery to progress from the transcriptome to the proteome and offers potential for identification of new therapeutic targets. This approach, linking targeted proteomic data to variation in pharmacologic response, can be generalized to other studies evaluating genotype-phenotype relationships and provide insight into chemotherapeutic mechanisms.

Dataset Information

Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails.

Publications

Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails.

Similar Datasets

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