A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Barría, Agustín; Trinh, Trong Quoc; Mahmuddin, Mahirah; Peñaloza, Carolina; Papadopoulou, Athina; Gervais, Ophélie; Chadag, V.; Benzie, John A. H.; Houston, Ross D.

doi:10.1038/s41437-021-00447-4

Cited by 34 publications

(17 citation statements)

References 85 publications

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“…QTL mapping in tilapia has been conducted in relation to economic traits, including ammonia-nitrogen tolerance ( Zhu et al, 2021 ), body traits ( Yoshida & Yáñez, 2021 ), salt tolerance ( Jiang et al, 2019 ), body color ( Li et al, 2019 ), and tilapia lake virus resistance ( Barría et al, 2021 ). QTL mapping for sex has also been explored in tilapia previously.…”

Section: Discussionmentioning

confidence: 99%

First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

Zhu¹,

Lin²,

Ai³

et al. 2022

Zoological Research

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Red tilapia ( Oreochromis spp . ) is one of the most popular fish in China due to its bright red appearance, fast growth rate, and strong adaptability. Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia. In this research, the genetic architecture for sex from four mapping populations ( n =1 090) of red tilapia was analyzed by quantitative trait loci (QTL)-seq, linkage-based QTL mapping, and linkage disequilibrium (LD)-based genome-wide association studies. Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1 (22.4–23.9 Mb) and ChrLG23 (32.0–35.9 Mb), respectively. The QTL on ChrLG1 was detected in family 1 (FAM1), FAM2, and FAM4, and the other QTL on ChrLG23 was detected in FAM3 and FAM4. Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection. Interestingly, three ( lpp , sox14 , and amh ) of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males, while the remaining genes were more highly expressed in females. Seven genes ( scly , ube3a , lpp , gpr17 , oca2 , cog4 , and atp10a ) were significantly differentially expressed between the male and female groups. Furthermore, LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia. Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.

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Section: Discussionmentioning

confidence: 99%

First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

Zhu¹,

Lin²,

Ai³

et al. 2022

Zoological Research

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“…Field or natural outbreak data can provide very valuable phenotypes for disease resistance, as the fish are exposed to realistic commercial conditions. In various fish species resistance measured after an natural disease outbreak has been successfully used to estimate genetic parameters (Bangera et al, 2014; Barría et al, 2020; Lillehammer et al, 2013) and detect QTL associated with resistance (Barría et al, 2021; Fraslin et al, 2018; Houston et al, 2008). However, they also have disadvantages such as being unpredictable and the uncertainty of which specific pathogens are responsible for the observed disease or mortality.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association and genomic prediction of resistance to Flavobacterium columnare in a farmed rainbow trout population

Fraslin

Koskinen

Nousianen

et al. 2022

Preprint

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Columnaris disease is an emerging disease affecting farmed rainbow trout (Oncorhynchus mykiss) globally. In aquaculture breeding, genomic selection has been increasingly used to improve traits that are difficult to measure on candidate fish (such as disease resistance traits). Following a natural outbreak of columnaris disease, 3,054 exposed fish and their 81 parents (33 dams and 48 sires) were genotyped with the 57K SNP Axiom ™ trout genotyping array. Genetic parameters of host resistance (measured as a binary survival trait) were estimated, a genome wide association study was performed, and the accuracy of pedigree-based and genomic prediction was estimated. After quality controls, 2,874 challenged fish (1,403 dead fish and 1,471 alive fish) and 78 parents genotyped for 27,907 SNPs remained. Pedigree based heritability was estimated to be 0.18 and 0.35 on the observed and underlying scale, respectively. Genomic heritability was estimated to be 0.21 and 0.43 on the observed and underlying scale, respectively. A quantitative trait loci (QTL) was detected on chromosome Omy3, significant at the genome-wide level, along with several suggestive QTLs on two other chromosomes. The additive effect on mortality proportion of the peak SNP from Omy3 was estimated to be 0.11 (0.018; se). Pedigree-based prediction accuracy was 0.59, and the use of genomic evaluation increased the prediction accuracy by at least 13.6%. Using the second iteration of a weighted genomic-based evaluation increased the prediction accuracy by 18.6% compared to the pedigree-based model. These results suggest that resistance is a suitable target trait for genetic improvement by selective breeding, and genomic selection may be a useful approach to speed up this process.

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“…With few exceptions ( Houston et al, 2008 ; Moen et al, 2009 ; Boison et al, 2019 ; Sinclair-Waters et al, 2020 ; Barria et al, 2021 ), commercially important traits in aquaculture are underpinned by a polygenic genetic architecture ( Tsai et al, 2015 ; Barría et al, 2018 ; Gutierrez et al, 2018 ; Palaiokostas et al, 2018 ; Mohamed et al, 2019 ; Aslam et al, 2020 ; Lu et al, 2020 ). This genetic architecture is also typical of FE traits in several breeding populations of livestock ( Yuan et al, 2015 ; Higgins et al, 2018 ; Fu et al, 2020 ; Marchesi et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a wide variety of genomic tools have been developed for Nile tilapia (reviewed in Yáñez et al, 2020 ). These genomic tools have facilitated studies to unravel the relationships among improved strains ( Hamilton et al, 2020 ), to detect regions associated with important traits ( Cáceres et al, 2019 ; Yoshida et al, 2019 ; Taslima et al, 2020 ; Barria et al, 2021 ), and to assess the accuracy of prediction of breeding values using genomic selection (GS) models, compared with pedigree-based models ( Yoshida et al, 2019 ; Joshi et al, 2020 ). However, there is a lack of studies targeting identification of genomic regions associated with FE traits (i.e.…”

Section: Introductionmentioning

confidence: 99%

Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

et al. 2021

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Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; −0.60 and −0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.

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A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Cited by 34 publications

References 85 publications

First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

Genome-wide association and genomic prediction of resistance to Flavobacterium columnare in a farmed rainbow trout population

Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

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