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

Zeng, Qifan; Zhao, Baojun; Wang, Hao; Wang, Mengqiu; Teng, Mingxuan; Hu, Jiang; Bao, Zhenmin; Wang, Yangfan

doi:10.1093/nar/gkac424

Cited by 11 publications

(6 citation statements)

References 37 publications

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“…Some mussels are important economic species, for instance, Mytilus chilensis , Mytilus. edulis, Mytilus coruscus, Perna viridis [ 11 , 12 ] . According to the Fishery and Aquaculture Statistics 2018 reported by Food and Agriculture Organization, the total production of M. chilensis (major species) in 2018 was 365,595 tonnes.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

et al. 2022

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Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.

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Section: Introductionmentioning

confidence: 99%

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

et al. 2022

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“…It has been proven to a cost-effective approach that greatly increase the density of genotypes to WGS level data and is widely used in the genetic studies to boost power such as in GWAS and GP. To date, several genotype imputation haplotype reference panels have been developed for animal [ 46 ], plant [ 47 ], and aquaculture species [ 48 ]. With the aid of genotype imputation, exploration of the combining admixed population into single reference population or improving the genomic prediction accuracy of combined populations is feasible and convenient in animals, such as in cattle and pig [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Zhuang

Qiu

et al. 2023

J Animal Sci Biotechnol

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Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs. Results We produced WGS data (18,695,907 SNPs and 2,106,902 INDELs exceed quality control) from 1,469 sequenced Duroc × (Landrace × Yorkshire) pigs and developed a reference panel for meat quality including meat color score, marbling score, L* (lightness), a* (redness), and b* (yellowness) of genomic prediction. The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population. Using different marker density panels derived from WGS data, accuracy differed substantially among meat quality traits, varied from 0.08 to 0.47. Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39% to 75%. We optimized the marker density and found medium- and high-density marker panels are beneficial for the estimation of heritability for meat quality. Moreover, we conducted genotype imputation from 50K chip to WGS level in the same population and found average concordance rate to exceed 95% and r2 = 0.81. Conclusions Overall, estimation of heritability for meat quality traits can benefit from the use of WGS data. This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

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“…Comprehensive human genotype imputation panels and platforms, such as 1000 Genomes Project (37) and NyuWa in China (38), have been provided. For agricultural animals, universal reference panels have been released for cattle (13,39,40), pigs (35,41), and aquatic animals (42). The Animal Impute DB version 2 provides genotype imputation services for 20 animal species, but the sample size of chickens (n=509) was limited and insufficiently representative (14).…”

Section: Discussionmentioning

confidence: 99%

Integrated Global Chicken Reference Panel From 13,187 Chicken Genomes

Zhu,

Wang,

et al. 2023

Preprint

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Chickens are a crucial source of protein for humans and a popular model animal for bird research. Despite the emergence of imputation as a reliable genotyping strategy for large populations, the lack of a high-quality chicken reference panel has hindered progress in chicken genome research. To address this issue, here we introduce the first phase of the 100 K Global Chicken Reference Panel Project (100 K GCRPP). The project includes 13,187 samples and provides services for varied applications on its website (http://farmrefpanel.com/GCRP/). Currently, two panels are available: a Comprehensive Mix Panel (CMP) for domestication diversity research and a Commercial Breed Panel (CBP) for breeding broilers specifically. Evaluation of genotype imputation quality showed that CMP had the highest imputation accuracy compared to imputation using existing chicken panel in animal SNPAtlas, whereas CBP performed stably in the imputation of commercial populations. Additionally, we found that genome-wide association studies using GCRP-imputed data, whether on simulated or real phenotypes, exhibited greater statistical power. In conclusion, our study indicates that the GCRP effectively fills the gap in high-quality reference panels for chickens, providing an effective imputation platform for future genetic and breeding research.

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

Cited by 11 publications

References 37 publications

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Integrated Global Chicken Reference Panel From 13,187 Chicken Genomes

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