Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture

Abstract It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecula...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2022-07, Vol.50 (W1), p.W66-W74
Main Authors: Zeng, Qifan, Zhao, Baojun, Wang, Hao, Wang, Mengqiu, Teng, Mingxuan, Hu, Jingjie, Bao, Zhenmin, Wang, Yangfan
Format: Article
Language:English
Subjects:
Animals
Aquaculture - methods
Breeding
DNA Shuffling
Genotype
Internet
Phenotype
Polymorphism, Single Nucleotide
Software
Web Server Issue
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http://mgb.qnlm.ac. Graphical Abstract Graphical Abstract AMBP is designed for genetic data exploration and breeding strategy development of aquaculture species. It integrates functions of genotype imputation, population characterizing, genomic selection and mating.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkac424