Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

Kon, Tetsuo; Pei, Liyi; Ichikawa, Ryota; Chen, Chunyan; Wang, Ping; Takemura, Ikuyo; Ye, Yingying; Yan, Xiaojun; Guo, Baoying; Li, Weiye; Lauden, Hagai Nsobi; Tabata, Hiromasa; Pan, Hao; Omori, Yoshihiro; Ogura, Atsushi; Jiang, Lihua

doi:10.1038/s41598-021-90645-1

Cited by 24 publications

(14 citation statements)

References 29 publications

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“…So far, it has been extensively applied in a large number of plants and animals, such as maize ( Zea mays ssp. mays L.) (Wang et al, 2020 ), rice ( Oryza sativa L.) (Yano et al, 2016 ), chicken ( Gallus gallus ) (Rubin et al, 2010 ), sheep ( Ovis aries ) (Li et al, 2020 ), Atlantic salmon ( Salmo salar ) (Bertolotti et al, 2020 ), large yellow croaker ( Larimichthys crocea ) (Kon et al, 2021 ), and black tiger shrimp ( Penaeus monodon ) (Wong et al, 2020 ). In the present study, in order to profile genome signatures of selection in Pacific oyster, we performed whole‐genome resequencing of 20 oysters from two fast‐growing strains and 20 oysters from their corresponding wild populations.…”

Section: Introductionmentioning

confidence: 99%

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Tian

et al. 2021

Evolutionary Applications

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The Pacific oyster, Crassostrea gigas , is an important aquaculture shellfish around the world with great economic and ecological value. Selective breeding programs have been carried out globally to improve production and performance traits, while genomic signatures of artificial selection remain largely unexplored. In China, we performed selective breeding of C . gigas for over a decade, leading to production of several fast‐growing strains. In the present study, we conducted whole‐genome resequencing of 20 oysters from two fast‐growing strains that have been successively selected for 10 generations, and 20 oysters from the two corresponding wild populations. Sequencing depth of >10× was achieved for each sample, leading to identification of over 12.20 million SNPs. The population structures investigated with three independent methods (principal component analysis, phylogenetic tree, and structure) suggested distinct patterns among selected and wild oyster populations. Assessment of the linkage disequilibrium (LD) decay clearly indicated the changes in genetic diversity during selection. Fixation index ( F st ) combined with cross‐population composite likelihood ratio (XP‐CLR) allowed for identification of 768 and 664 selective sweeps (encompassing 1042 and 872 genes) tightly linked to selection in the two fast‐growing strains. KEGG enrichment and functional analyses revealed that 33 genes are important for growth regulation, which act as key components of various signaling pathways with close connection and further take part in regulating the process of cell cycle. This work provides valuable information for the understanding of genomic signatures for long‐term selective breeding and will also be important for growth study and genome‐assisted breeding of the Pacific oyster in the future.

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Section: Introductionmentioning

confidence: 99%

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Tian

et al. 2021

Evolutionary Applications

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“…As geographical stock delimitation based on morphology is often inconsistent with analysis results based on molecular data, determining the accurate genetic structure is of particular concern. A series of studies based on molecular markers have been conducted since the last decade in wild and cultured populations of large yellow croaker, but these studies were limited in terms of their success in determining population structure and phylogeography due, for instance, to sampling only part of the distribution area (Wang et al, 2012(Wang et al, , 2014Kon et al, 2021), small sample size in one group (Wang et al, 2013;Han et al, 2015); or collecting cultured populations from only a few farms (Huang et al, 2012;Wang et al, 2012;Kon et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Yuan

Lin

et al. 2021

Front. Mar. Sci.

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The large yellow croaker, Larimichthys crocea, was once the most abundant and economically important marine fish in China. Thus far, it has also been the most successful mariculture fish species in China. However, its wild stock severely declined in the 1970s because of overexploitation, and therefore hatchery release has been carried out for stock enhancement since 2000. As a migratory fish, large yellow croaker was divided into three geographical stocks according to ambiguous morphological and biological characteristics in early documents. To investigate the identity of wild large yellow croaker populations and assess the influence of hatchery supplementation on wild populations, a total of 2,785 cultured individuals and 591 wild individuals were collected from 91 hatcheries and six wild populations along the coast of mainland China and analyzed using two mitochondrial genes [cytochrome oxidase I (COI) and cytochrome b (Cyt b)] and one nuclear gene (RyR3). The higher haplotype diversity and moderate nucleotide diversity of wild large yellow croaker indicated that overexploitation, which caused a sharp decrease in biomass, did not lead to a loss of genetic diversity. According to phylogenetic construction and network analysis, the absence of a significant population structure pattern revealed a single panmictic population of wild large yellow croaker with exception of a population collected from the Sansha Bay, which showed high genetic relatedness to the cultured population, suggesting significant genetic effects resulting from stock enhancement. Overall, our study suggests no genetic differentiation in the entire wild population of large yellow croaker, which means that we have great flexibility in mixing and matching farmed and wild populations. However, since the result showed that domestication, the relaxation of purifying selection, increased genetic loads, and maladapted farmed fish will be at a selective disadvantage when cultured juveniles are released in the wild, the effectiveness of stock enhancement and the negative impact of hatchery-wild fish hybridization on the wild population must be carefully evaluated in future.

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“…Previous studies have identified selection signatures in several aquaculture fish species, including large yellow croaker ( Kon et al, 2021 ), Amur ide ( Wang et al, 2021a ), Atlantic salmon ( Gutierrez et al, 2016 ; López et al, 2019 ), Nile tilapia ( Cádiz et al, 2020 ; Nayfa et al, 2020 ), and brown trout ( Lemopoulos et al, 2018 ). To date, however, genomic selection signatures of the largemouth bass have not been reported.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (<i>Micropterus</i> <i>salmoides</i>)

Sun

Zhang

Dong

et al. 2023

Zoological Research

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Largemouth bass ( Micropterus salmoides ) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10 ), early development ( klf9 , sp4 , and sp8 ), and immune traits ( pkn2 , sept2 , bcl6 , and ripk2 ). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

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Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

Cited by 24 publications

References 29 publications

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (<i>Micropterus</i> <i>salmoides</i>)

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