Genetic diversity, population structure, linkage disequilibrium and GWAS for resistance to WSSV in Pacific white shrimp (Litopenaeus vannamei) using a 50K SNP chip

Medrano-Mendoza, Thania; García, Baltasar F.; Caballero-Zamora, Alejandra; Yáñez, José M.; Montoya‐Rodríguez, Leobardo; Quintana-Casares, Juan C.; Durán-Aguilar, Marina; Campos-Montes, Gabriel R.

doi:10.1016/j.aquaculture.2022.738835

Cited by 7 publications

(4 citation statements)

References 41 publications

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“…understanding on genetic variants controlling desirable characteristics and their implementation in breeding programs. In Pacific white shrimp (L. vannamei), GWAS has been instrumental in uncovering SNPs linked to various economically important traits, including resistance to white spot syndrome virus (WSSV) 102 , growth [131][132][133] , ammonia nitrogen tolerance 134 and sex-determining region 135,136 .…”

Section: Genome-wide Association Studies For Marker-assisted Selectio...mentioning

confidence: 99%

“…For instance, a study involving a WSSV-resistant line of L. vannamei identified two SNPs significantly associated with survival post-infection, which explained a low genetic variance for the trait, suggesting a polygenic nature of WSSV resistance and highlighting the potential of genomic selection for this trait 102 . Additionally, GWAS on body weight (BW) and growth traits has pinpointed SNPs within or near candidate genes such as deoxycytidylate deaminase, non-receptor protein tyrosine kinase, and class C scavenger receptor (LvSRC), protein kinase C delta type and ras-related protein Rap-2a, which are associated with significant phenotypic variance in growthrelated traits [131][132][133] .…”

Section: Genome-wide Association Studies For Marker-assisted Selectio...mentioning

confidence: 99%

“…Genome-wide association studies (GWAS) have significantly advanced aquaculture breeding and genetics by identifying genetic markers associated with key traits, thus facilitating a better understanding on genetic variants controlling desirable characteristics and their implementation in breeding programs. In Pacific white shrimp ( L. vannamei ), GWAS has been instrumental in uncovering SNPs linked to various economically important traits, including resistance to white spot syndrome virus (WSSV) 102 , growth 131-133 , ammonia nitrogen tolerance 134 and sex-determining region 135,136 .…”

Section: Future Directionsmentioning

confidence: 99%

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100 years domestication of penaeid shrimp and meta-analysis of breeding traits

Ren,

Yáñez,

Perez-Enriquez

et al. 2024

Preprint

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Penaeid shrimp farming plays a pivotal role in ensuring future food security and promoting economic sustainability. Compared to the extensive long history of domestication observed in terrestrial agriculture species, the domestication and selective breeding of penaeids are relatively recent endeavors. Selective breeding aimed at improving production traits holds significant promise for enhancing efficiency and reducing the environmental impact of shrimp farming, thereby contributing to its long-term sustainability. Assessing genotype-by-environment (G-by-E) interactions is essential in breeding programs to ensure that improved penaeid shrimp strains perform consistently across different production environments, with genomic selection proving more effective than sib-testing alone in mitigating environmental sensitivity. Genome editing tools like CRISPR/Cas9 offer significant potential to accelerate genetic gains in penaeid shrimp by enabling rapid introduction of desired genetic changes, with recent advancements showing promising results in achieving high transfection efficiency in shrimp embryos. Additionally, artificial intelligence and machine learning are being leveraged to streamline phenotyping and enhance decision-making in shrimp breeding and farming, improving efficiency and accuracy in managing traits and predicting disease outbreaks. Herein, we provide an overview and update on the domestication of penaeid shrimp, including the current status of domestication for principal farmed species, key milestones in domestication history, targeted breeding traits in selective breeding programs, the advantages of integrating genomeic selection for enhancing production traits, and future directions for selective breeding of penaeid shrimp.

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Section: Genome-wide Association Studies For Marker-assisted Selectio...mentioning

confidence: 99%

Section: Genome-wide Association Studies For Marker-assisted Selectio...mentioning

confidence: 99%

Section: Future Directionsmentioning

confidence: 99%

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100 years domestication of penaeid shrimp and meta-analysis of breeding traits

Ren,

Yáñez,

Perez-Enriquez

et al. 2024

Preprint

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“…Maceration or homogenisation of tissue samples for per os challenge can minimise the influence of heterogeneous viral particle distribution on dosage. [182][183][184] Additionally, implementing a starving period for experimental animals before per os challenge can increase shrimp receptivity to the inoculum feed, improving dose consistency. 57,159,185 Regardless of inoculation method, and the approach used and reported for normalisation of dosage, standardisation and reporting of dosage necessitates accurate quantification of viral copy number within the inoculum.…”

Section: Inoculum Concentration/dosementioning

confidence: 99%

Towards a ‘systems’ approach for viral challenge experiments in shrimp: Reporting guidelines for publication

Arbon,

Andrade Martinez,

Jerry

et al. 2023

Reviews in Aquaculture

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The success of contemporary disease management strategies in shrimp aquaculture, such as the ‘systems’ approach, is predicated on robust knowledge of the conditions and interactions between the host, pathogen and environment that promote disease. Pathogen challenge experiments (PCEs) are a power tool for investigating these conditions and interactions. However, absence of accurately reported experimental detail in published PCEs limits scientific transparency, reproducibility, and the potential for the research to make progressive advancements contributing to contemporary shrimp disease management strategies. This review identifies and discusses key factors relating to the host (shrimp), pathogen (virus), and environment that should be carefully considered during the design and publication of PCEs. We offer substantial evidence of their impact on viral disease outcomes, drawn from the existing body of literature, to supporting their consideration. The prevalence of reported experimental details for these factors across 186 viral PCEs in shrimp were evaluated. The review highlights a concerning paucity of experimental detail reported in published shrimp PCEs. We propose a checklist for the minimum reportable information in the publication of shrimp viral PCEs, hereafter referred to as the Shrimp PCE Reporting Guidelines (SPERG). The guidelines aim to enhance the transparency and standardisation of reporting in published PCEs, ensuring that key factors pertaining to the shrimp, pathogen, and environment are adequately considered and documented. Adoption of SPERG is envisaged to empower researchers, reviewers, and readers to assess the internal and external validity of PCEs, facilitating critical evaluation and improved utility of PCE findings for contemporary disease management.

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