Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing

Zhou, Zhixiong; Han, Kunhuang; Wu, Yidi; Bai, Haili; Ke, Qiaozhen; Pu, Fei; Wang, Yilei; Xu, Peng

doi:10.1007/s10126-019-09910-0

Cited by 49 publications

(29 citation statements)

References 72 publications

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“…The sample numbers of every location are shown in Table 1. After eugenol anesthesia, white muscles were collected and used for DNA extraction (Zhou et al 2019). Total DNA extracted from muscle was used to construct a library.…”

Section: Sampling and Sequencingmentioning

confidence: 99%

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

Gong¹,

Chen²,

Li³

et al. 2020

Zoologia

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The whole mitochondrial genome of Lateolabrax maculatus (Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity of L. maculatus were 0.998 and 0.00169, respectively. Pairwise FST values between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history of L. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation of L. maculatus.

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Section: Sampling and Sequencingmentioning

confidence: 99%

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

Gong¹,

Chen²,

Li³

et al. 2020

Zoologia

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“…2013), potentially affecting multiple growth traits. Concordantly, FGF18 has also been associated with differences in growth of the large yellow croaker, Larimichthys crocea (Zhou et al . 2019).…”

Section: Discussionmentioning

confidence: 87%

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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“…For example, csad plays an important role in synthesizing taurine which is a rate-limiting enzyme affecting growth rate in parrotfishes (79), rainbow trout (80), and Japanese flounder (81). Second, glcci1 is associated with the body depth/length ratio in the large yellow croaker (82). Third, ino80c is associated with measures of body size in the Nile tilapia (83).…”

Section: Genome-wide Association Mapping Of Fitnessmentioning

confidence: 99%

Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

Patton

Richards

Gould

et al. 2021

Preprint

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Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. Empirical fitness landscapes have now been estimated for numerous systems, from phage to proteins to finches. However, the nature of adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically distinct pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. Here, we leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, visualize the first genotypic fitness networks in a vertebrate system, and infer the contributions of different sources of genetic variation to the accessibility of the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures, including six associated genes that were differentially expressed between specialists, and one gene (protein-lysine methyltransferase: METTL21E) misexpressed in hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that only introgressed and de novo variants, not standing genetic variation, increased the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo variants provided key connections in adaptive walks necessary for crossing fitness valleys and triggering the evolution of novelty during adaptive radiation.

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Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing

Cited by 49 publications

References 72 publications

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

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

Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

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