Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)

Neto, Rafael Vilhena Reis; Yoshida, Grazyella Massako; Lhorente, Jean Paul; Yáñez, José M.

doi:10.1007/s00438-018-1518-2

Cited by 50 publications

(28 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The use of genomic information can help in the identification of QTLs controlling complex traits which are economically important for aquaculture purposes, such as growthrelated traits. Previous studies have identified loci and candidate genes associated with growth-related traits in aquaculture species [19,22,23,25,36,37]. However, similar to what we found when using stGWAS ( Supplementary Figure 1), few or no markers surpassed the genome-wide significance threshold or represented a small proportion of genetic variance in GWAS.…”

Section: Discussionsupporting

confidence: 82%

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Yoshida¹,

Yáñez²

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

show abstract

Section: Discussionsupporting

confidence: 82%

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Yoshida¹,

Yáñez²

2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…To identify the regions of the genome associated with the traits analyzed, we identified windows of 20 adjacent SNPs where 1% or more of the phenotypic variance was explained, similar to Neto et al (2019) 66 . The cumulative percentage of variance explained for each trait was visualized using a Manhattan plot in R 67 .…”

Section: Methodsmentioning

confidence: 99%

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

Cáceres

Barría

Christensen

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…A major quantitative trait locus (QTL) for resistance against IPN has been identified (Houston et al 2008) and successfully implemented at a commercial level in European (Moen et al 2015) and Chilean stocks. Yoshida et al (2017a) andNeto et al (2019) have also identified several genomic regions and candidate genes associated with body weight in Chilean Atlantic salmon and rainbow trout populations, as it has been shown in previous studies (Gutierrez et al 2015;Tsai et al 2015;Gonzalez-Pena et al 2016). Thus, the opportunities for MAS are still likely to be limited compared to GS in aquaculture because having few markers explaining a large proportions of variation is rare in most commercially important traits (i.e.…”

Section: Incorporation Of Genomicsmentioning

confidence: 83%

Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

Lhorente

Araneda

Neira

et al. 2019

Reviews in Aquaculture

View full text Add to dashboard Cite

Genetic improvement is key to the development of a more efficient aquaculture industry. By 2010, there were 104 breeding programmes for aquaculture species in the world, most of them for fish species. Usually, the breeding goals include traits such as growth rate, disease resistance, maturation and carcass quality. Resistance to specific pathogens has been one of the main objectives of research and development in the genetic improvement programmes of salmonids in Chile and worldwide. In Chile, trait selection has been conducted through the application of selection indexes. New technologies like next generation sequencing and genotyping have helped disentangle the genetic basis and enhance genetic evaluation methods of economically important traits. This work aims to review the advances in genetic improvement for salmon and trout aquaculture with emphasis on the Chilean experience. We focus on the implementation of breeding programmes in the country, definition of breeding objectives, results on genetic parameters and response to selection and incorporation of genomics. Future challenges and opportunities regarding genotype‐by‐environment interactions, climate change and research and development, plus the demonstration of the economic benefit of breeding programmes are also addressed.

show abstract

Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)

Cited by 50 publications

References 67 publications

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

Contact Info

Product

Resources

About