Genomic analysis of a Nile tilapia strain selected for salinity tolerance shows signatures of selection and hybridization with blue tilapia (Oreochromis aureus)

Yu, Xiaofei; Setyawan, Priadi; Bastiaansen, J.W.M.; Liu, Langqing; Imron, Imron; Groenen, M.A.M.; Komen, Hans; Megens, Hendrik‐Jan

doi:10.1016/j.aquaculture.2022.738527

Cited by 16 publications

(12 citation statements)

References 58 publications

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“…In the Sukamandi hybrid strain, 33 salinity‐tolerance genes were inherited from blue tilapia. Among them, five genes ( slc12a10.1 , zgc : 153039 , slc9a2 , slc25a24 and cdh1 ) were under strong positive selection 134 . Results of this study not only contribute to our understanding of the evolution of salinity‐tolerance in fish, but also provide an interesting model for gene introgressing in farmed fish species through hybridization 135 .…”

Section: Status Of Breeding Salinity‐tolerant Tilapiamentioning

confidence: 74%

“…A study using RNA‐seq in the gills of hybrid tilapia ( O. mossambicus female × O. urolepis hornorum male) under salinity stress identified DEGs, such as kinase ( CaM kinase ) II ( camk2 ), aquaporin‐1 ( aqp1 ), sodium bicarbonate cotransporter ( slc4a4/nbc1 ), chloride channel 2 ( clcn2 ) and sodium/potassium/chloride transporter ( slc12a2/nkcc1 ) 133 . Eight genes for salinity‐tolerance, including caprin1a (cell cycle associated protein 1), nucb2a (nucleobindin 2), abcb10 (ATP‐binding cassette, sub‐family B), slc12a10.1 (solute carrier family 12 member 10, tandem duplicate 1), cacna1ab (calcium channel, voltage‐dependent, P/Q type, alpha 1A subunit, b), ulk2 (unc‐51 like autophagy activating kinase 2), slc25a24 (solute carrier family 25 member 24) and cdh1 (cadherin 1), were identified using genome‐wide scans in a Nile tilapia strain selected for salinity tolerance 134 . In the Sukamandi hybrid strain, 33 salinity‐tolerance genes were inherited from blue tilapia.…”

Section: Status Of Breeding Salinity‐tolerant Tilapiamentioning

confidence: 99%

“…(cell cycle associated protein 1), nucb2a (nucleobindin 2), abcb10 (ATPbinding cassette, sub-family B), slc12a10.1 (solute carrier family 12 member 10, tandem duplicate 1), cacna1ab (calcium channel, voltagedependent, P/Q type, alpha 1A subunit, b), ulk2 (unc-51 like autophagy activating kinase 2), slc25a24 (solute carrier family 25 member 24) and cdh1 (cadherin 1), were identified using genome-wide scans in a Nile tilapia strain selected for salinity tolerance. 134 In the Sukamandi hybrid strain, 33 salinity-tolerance genes were inherited from blue tilapia.…”

Section: Genes Associated With Salinity Tolerance and Genome Sequence...mentioning

confidence: 99%

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Status of conventional and molecular breeding of salinity‐tolerant tilapia

Yue

Xia

2023

Reviews in Aquaculture

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Aquaculture is an important sector for ensuring global food security. Due to the scarcity of freshwater available for expanding aquaculture, the development of omnivorous fish species and varieties that can tolerate high salinity will enhance fish production. Some tilapia species are good candidates for aquaculture in brackish and seawater because they can grow in high salinity. Among tilapia species, Oreochromis mossambicus, Oreochromis aureus, Oreochromis spilurus, Oreochromis urolepis hornorum, Sarotherodon galilaeus and Coptodon zillii are the most salinity‐tolerant. Hybrids derived from salinity‐tolerant tilapia species are tolerant to a certain level of salinity. They have been used in aquaculture production in brackish water and full seawater. Conventional selective breeding has been applied to increase the growth rate of salinity‐tolerant tilapias. However, their growth rate is lower than that of the freshwater Oreochromis niloticus. Recently, many genomic resources and tools have been developed for salinity‐tolerant tilapia. Quantitative trait locus (QTL) mapping and genome‐wide association studies (GWAS) for important economic traits, including salinity tolerance and other desired traits, have been carried out and applied in molecular breeding for superior salinity‐tolerant tilapia lines. In this review, we systematically analysed tilapia species that can be cultured in brackish and saltwater. We summarized previous works in conventional breeding and molecular breeding for salinity‐tolerant tilapia. We pointed out a few known and potential challenges in the selective breeding and culture of salinity‐tolerant tilapia. Due to the rapid advances in molecular and other disruptive technologies, we are optimistic that novel breeding approaches will significantly increase the production salinity‐tolerant tilapia.

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Section: Status Of Breeding Salinity‐tolerant Tilapiamentioning

confidence: 74%

Section: Status Of Breeding Salinity‐tolerant Tilapiamentioning

confidence: 99%

Section: Genes Associated With Salinity Tolerance and Genome Sequence...mentioning

confidence: 99%

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Status of conventional and molecular breeding of salinity‐tolerant tilapia

Yue

Xia

2023

Reviews in Aquaculture

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“…Enrichment analysis of these genes revealed associations with growth, immune system, reproduction, behaviour, adaptation to environmental conditions and nervous system. In a more recent study performed using whole‐genome sequences from 20 individuals from the Sukamandi Indonesian strain, several selection signatures were found, revealing eight potential genes related to salinity tolerance (cell cycle‐associated protein 1a, caprin1a ; nucleobindin 2; ATP binding cassette subfamily; solute carrier family 12 member 1; calcium channel; unc‐51 like autophagy activating kinase; solute carrier and cadherin‐1, cdh1 ) 217 . The authors also found that the Sukamandi strain is approximately 10% derived from blue tilapia ( O .…”

Section: Signatures Of Domestication and Selectionmentioning

confidence: 99%

Genome‐wide association and genomic selection in aquaculture

Yáñez

Barría

López

et al. 2022

Reviews in Aquaculture

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Recent advancements in genomic technologies have led to the discovery and application of DNA-markers [e.g. single nucleotide polymorphisms (SNPs)] for the genetic improvement of several aquaculture species. The identification of specific genomic regions associated with economically important traits, using, for example, genome-wide association studies (GWAS), has allowed the discovery and incorporation of markers linked to quantitative trait loci (QTL) into aquaculture breeding programs through marker-assisted selection (MAS). However, most of the traits of economic relevance are expected to be controlled by many QTLs, each one explaining only a small proportion of the genetic variation. For traits under polygenic control, prediction of the genetic merit of animals based on the sum of effects at positions across the entire genome (i.e. genomic estimated breeding values, GEBV, which are used for what has become known as genomic selection), has been demonstrated to speed the rate of genetic gain for several traits in aquaculture breeding. The aim of this review was to provide an overview of the development and application of genomic technologies in uncovering the genetic basis of complex traits and accelerating the genetic progress in aquaculture species, as well as providing future perspectives about the deployment of novel molecular technologies for selective breeding in coming years.

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“…Numerous studies have been carried out over the last ten years to detect signatures of selection in farmed fish species (Channel Catfish: Sun et al, 2014; Atlantic salmon: Mäkinen et al, 2015; Gutierrez et al, 2016; Liu et al, 2016; Pritchard et al, 2018; López et al, 2019; Carp: Su et al, 2018; Nile Tilapia: Hong et al, 2015; Cádiz et al 2020; Yu et al, 2022; Rainbow trout: Cádiz et al, 2021; Coho salmon : López et al, 2021; Australasian snapper: Baesjou & Wellenreuther, 2021; Brown trout: Magris et al, 2022) in order to identify genomic regions involved in recent adaptation or domestication processes (Smith & Haigh, 1974; Pennings & Hermisson, 2006). In this study, we were interested in farmed rainbow trout populations as it is one of the oldest farmed fish and the analysis of genes under either positive or balancing subsequent selection in.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

Paul

Restoux

Phocas

2022

Preprint

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Evolutionary processes leave footprints across the genome over time. Highly homozygous regions may correspond to positive selection of favourable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed 176 genomes coming from 20 sequenced US fish and 156 fish from three different French lines that were genotyped using a HD Axiom Trout Genotyping 665K SNP Array. Using methods based on either Run of Homozygosity or Extended Haplotype Homozygosity, we detected selection signals in four domesticated rainbow trout populations. Nine genomic regions composed of 253 genes, mainly located on chromosome 2 but also on chromosomes 12, 15, 16, and 20, were identified under positive selection in all four populations. In addition, four heterozygous regions containing 29 genes putatively under balancing selection were also shared by the four populations and located on chromosomes 10, 13, and 19. Whatever the homozygous or heterozygous nature of the region, we always found some genes highly conserved among vertebrates due to their critical roles in cellular and nuclear organisation, embryonic development or immunity. We identify new promising candidate genes involved in rainbow trout fitness, as well as genes already detected under positive selection in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, emilin-3). These findings represent a genome-wide map of signatures of selection common over rainbow trout populations, which is the foundation to understand the processes in action and to identify what kind of diversity should be preserved, or conversely avoided in breeding programs, in order to maintain or improve essential biological functions in domesticated rainbow trout populations.

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Genomic analysis of a Nile tilapia strain selected for salinity tolerance shows signatures of selection and hybridization with blue tilapia (Oreochromis aureus)

Cited by 16 publications

References 58 publications

Status of conventional and molecular breeding of salinity‐tolerant tilapia

Status of conventional and molecular breeding of salinity‐tolerant tilapia

Genome‐wide association and genomic selection in aquaculture

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

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