First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus)

Wu, Lina; Yang, Yang; Li, Bijun; Huang, Wenhua; Wang, Xi; Liu, Xiaochun; Meng, Zining; Xia, Jian‐Bai

doi:10.1007/s10126-019-09916-8

Cited by 35 publications

(20 citation statements)

References 68 publications

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“…2021). However, the 100 candidate SNPs explain similar phenotypic variation (4.4%) to those in other fish studies (0.1–19.0 %; Wu et al . 2019; Gong et al .…”

Section: Discussionsupporting

confidence: 76%

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Wellenreuther

Sandoval‐Castillo

Beheregaray

2021

Preprint

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Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality SNPs and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the SNPs were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation SNPs and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programmes and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.

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“…2021). However, the 100 candidate SNPs explain similar phenotypic variation (4.4%) to those in other fish studies (0.1–19.0 %; Wu et al . 2019; Gong et al .…”

Section: Discussionsupporting

confidence: 76%

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Wellenreuther

Sandoval‐Castillo

Beheregaray

2021

Preprint

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“…The remaining seven individuals were eliminated for inconsistence between the assignment of two molecular marker panels, while five of them showed fairly different genotype from all of the candidate parents in most loci. Besides this, we also compared the results of parentage analysis with our previous GWAS research using the same family [ 35 ]—which conducted family clustering based on identical by descent (IBD) using Plink—so as to further confirm the accuracy of parentage allocation, and found it completely consistent except for the five individuals described above. One likely explanation was that there might be individuals accidently introduced from other families during the fish culturing period.…”

Section: Discussionmentioning

confidence: 95%

“…The giant grouper samples in this study were described in our previous work [ 35 ]. Briefly, the broodstock were derived from the South China Sea area adjacent to Hainan province, and were then transferred to the Oceans Farms Hatchery of Fisheries Research Institute of Fujian in 2014.…”

Section: Methodsmentioning

confidence: 99%

“…GBS was similar to restriction site-associated DNA sequencing (RAD-seq) but more cost-effective and less complicated [ 30 ], so that it is tailored for large-scale genotyping applications such as marker-assisted selection (MAS) and QTL mapping, if available reference genome information was provided [ 11 ]. Indeed, low-coverage GBS has been successfully used for genetic parameter estimation [ 32 ], genomic selection [ 33 ], QTL mapping [ 34 ] and genome-wide association studies (GWAS) [ 35 ] in aquaculture. It has been proposed that GBS data is one of the best options for cost-effective SNP discovery and parentage analysis [ 36 ].…”

Section: Introductionmentioning

confidence: 99%

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng

Yang

Wang

et al. 2021

Genes

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Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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“…The genes located on the up-and down-stream 500 Kb distance of the associated genomic region of body weight and umbrella diameter were detected 14,50…”

Section: Genome-wide Association Analysismentioning

confidence: 99%

Combined QTL and GWAS Analysis to Identify the Growth-Related Gene in Rhopilema Esculentum with the Help of 2b-RAD Sequencing

Chen

Tian

et al. 2021

Preprint

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R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the high-resolution genetic map and growth-related molecular markers still lack, hindering the process of the genetic breeding of R. esculentum. Therefore, we firstly used the 2b-RAD method to sequence 152 R. esculentum specimens, identified 9100 single nucleotide polymorphism (SNP) markers and constructed a high-resolution genetic map with a marker interval of 0.58 cM, covering 98.68% of the genome. Then, we separately detected four and three quantitative trait loci (QTLs) associated with umbrella diameter and body weight based on the linkage map, which is located on linkage group (LG) 4, 13, 14 and 15. Finally, 27 genes were found both associated with umbrella diameter and body weight of R. esculentum by genome-wide association study (GWAS), in which one gene named RE13670 containing calcium-binding EGF-like domain may play an important role in controlling the growth. This study will be beneficial for underlying the growth mechanism of R. esculentum and also provide background knowledge for guiding its genetic breeding.

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First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus)

Cited by 35 publications

References 68 publications

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Combined QTL and GWAS Analysis to Identify the Growth-Related Gene in Rhopilema Esculentum with the Help of 2b-RAD Sequencing

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