- Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network. - Background: Oyster is rich in glycogen and free amino acids and is called “ the milk of sea. - Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. - Oyster is rich in taurine (50 μmol/g wet weight), amino acids (45–57% of dry weight), and glycogen (20–40% of the dry weight),. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - 1 Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong, China Full list of author information is available at the end of the article Meng et al. - How- ever, reduced genome representation sequencing can genotype only a fraction of the genome. - In the present study, we aimed to understand the main genetic effects of nutrient traits and genetic networks underlying phenotypic correlation in oysters. - In the present study, we collected 427 individuals from different geographical populations (Fig. - In the present study, 42 other individuals col- lected from different countries, including Canada, Japan, and Korea, were further used for whole genome resequen- cing. - The accuracy of the identified SNPs was more than 96.5 and 98.2% according to SNP chip array and Sanger sequencing verification [33].. - In the present study, the neighbor-join- ing tree (NJ) suggested that three populations from Canada, Japan, and Korea were different from the indi- viduals in China (Additional file 10: Figure S1). - The LD decay and PCA analyses of the 427 oysters collected. - Additional file 5: Table S5). - 2a), which were mainly discussed in the following parts. - Among these loci, 111 SNPs distributed in the gene region and 57 in the intergenic region. - These 288 individuals were one-year old and were cultured in the same environment, which were used for phenotype and genotype detection. - We have conducted the candidate genes analysis within 100 kb of the leading SNPs on scaffold and 426. - There are 21 genes located within 100 kb of the leading SNPs in these regions based on our gen- ome sequence (Additional file 17: Figure S8). - of the phenotypic variation (Fig. - Also, we have identified a total of 19 SNPs in the CDS region of this gene and four haplotypes based on this non- synonymous SNPs (Fig. - These clustered SNPs were distributed in the following regions: 134,231 to 148,283 bp in scaffold618 (chromosome to 63,179 bp in scaffold535 (chromosome to 51,456 bp in scaffold1610 (chromosome 7), and 242, 446 to 243,557 bp in scaffold142 (chromosome 3) (Fig. - In the present study, 12 significant SNP signals were identified for taurine content (Fig. - In the present study, the polymorphism of these two genes induced their differential expression patterns, which might affect the shell formation process in oyster. - However, further studies should be conducted to analyze this genes function in the amino acids’ metabolism process.. - To elucidate the genetic basis of the correlation among dif- ferent traits, we analyzed the association networks using by a previously reported method [31] based on the LD analysis. - The negative log 10 -transformed P-values from a genome-wide scan are plotted against position on each of the 10 chromosomes. - c The 0.1-Mb region on each side of the peak SNP in scaffold389, and the position of peak SNP is indicated by a vertical red line with the red triangle. - One group of the connected SALs located on scaf- fold340 and scaffold426 regions, which regulated the content of glycogen, protein, Asp, Ser, Leu, and Thr. - Be- sides, the SAL on scaffold1243 plays important roles in the regulation of glycogen, protein, and Asp content, whereas, that on scaffold1597 regulates glycogen and Cys content.. - To verify the ef- fects of these three regions in the association network, we analyzed different genotypes with leading SNP loci in scaffold340, scaffold426, and scaffold1243 (Fig. - b, c The upper panel indicates the 0.1-Mb region on each side of the peak SNP in scaffold426 and scaffold340, and the position of peak SNP is indicated by a vertical red line with the red triangle. - The bottom panel shows the annotated genes of the 100-kb region. - For the F 1. - individuals in different families were cultured in the same marine environments and have the same male par- ent, their differences will reflect the genetic differenti- ation of their female parents. - 4 Genome-wide association study of Met and Tau with 427 individuals. - The negative log10-transformed P-values from the genome-wide scan are plotted against position in each of the 10 chromosomes. - c, f The 0.1-Mb region on each side of the peak SNP in scaffold618 (c) and scaffold801 (f), the position of peak SNP is indicated by a vertical red line with red triangle. - The bottom panel shows the annotated genes of the 100-kb region and the LD analysis of pairwise SNP loci in the 100 kb-region on both sides of the leading SNP obtained by GWAS (P <. - d The candidate genes for Met content with one non-synonymous mutation in the coding region. - However, it must be illustrated that the sampling methods from different sites has the potential to introduce genetic heterogeneity, including local adaptation and genetic ori- gin, leading to a non-causative marker being a better de- scriptor of the phenotype than a causative one [50].. - Besides, LD decay re- vealed that oyster was one of the most diverse spe- cies with considerably rapid decay of LD when assessed at the genome-wide scale. - c The number of oysters distributed among different genotypes of the peak SNPs in scaffold340, scaffold426, and scaffold1243. - In the present study, we first conducted GWAS analysis with resequencing data and found the genome wide SNP loci associated with glycogen contents in molluscan. - We found that CYP17A1 contained a non-synonymous SNP lo- cated in the enzyme active center and exhibited high ex- pressions in individuals with higher glycogen content.. - CYP17A1 is a single gene-encoded protein that mediates 17α-hydroxylase and promotes gluconeogenesis by acti- vating the transcriptional activity of the gluconeogenesis metabolism process in mammals [55]. - In the present study, higher expression of gluconeogenesis genes (PEPCK and G6Pase) were also observed, which further indicated the stronger gluconeogenesis capacity of indi- viduals with higher glycogen content. - In previous studies, the mutations in CYP17A1 may result in the complete or partial loss of catalytic activities, inducing phenotypic variation in several species [56]. - In the present study, according to the multiple alignment and three-dimensional protein structural modeling analysis, the non-synonymous SNP loci is located at a turn in β- sheet and formed the substrate-binding pocket. - how- ever the specific SAL will be used for breeding of the specific trait.. - These 427 families were cultured in the same environment for approximately 1 year, and then 30 F 1 individuals from each family line were col- lected and used for phenotype measurement [11]. - Genome-wide association study. - genome SNPs, were used as fixed effects in the mixed model to correct stratification. - 0.1 in the population were used in the GWAS. - These juvenile oysters were sam- pled in the wild and then reared under common condi- tions. - Functional analysis of candidate genes in the GWAS associated loci. - gigas, we analyzed the SNP types located in the candidate region. - We focused on the genes with associated non-synonymous SNPs sig- nificantly associated with the traits in the GWAS and those that could induce changes in amino acids.. - The qRT-PCR was carried out in triplicate with a reaction mixture of total volume 20 μ L containing 10 μ L of SYBR Green 2X Supermix (Takara), 1 μ L of 1:100 diluted cDNA, 0.4 μ L each of the forward and reverse primers, 0.4 μ L of ROX Dye II, and 7.8 μ L of DEPC H 2 O. - The analysis was based on the Ct values of the PCR products. - Melting curve analysis of the products was performed at the end of each PCR amplification. - The Δ Ct of each sample was then sub- tracted from the Δ Ct of the calibrator, and this differ- ence is called the ΔΔ Ct value. - The expression level of the target genes was then calculated as 2 - ΔΔ Ct. - Additional file 2: Table S2 Summary of the results of whole-genome resequencing. - They were cultured in the same environment for approximately one year, and then 30 individuals in each family line were collected and used for phenotype measurement. - (DOCX 692 kb) Additional file 14: Figure S5 Genome-wide analysis of glycogen, protein, and amino acids components. - The left panel shows the Manhattan plots of the MLM model. - The right panel shows the Quantile-quantile plot of the MLM model. - (DOCX 2787 kb) Additional file 15: Figure S6 Pairwise LD analysis of the 100 kb-region on both sides of the leading SNP of glycogen and protein. - The upper panel shows the GWAS results of the 100 kb-region on both sides of the leading SNP of the trait, whereas, the panel below shows the pairwise LD analysis of the SNPs (P <. - included in the region. - Additional file 16: Figure S7 Pairwise LD analysis of the 100 kb-region on both sides of the leading SNP of amino acids. - Second part presents 0.1-Mb region on each side of the peak SNP, the position of which is indicated by a vertical red line with red triangle. - Bottom of each panel shows the annotated genes of the 200-kb region. - If the significant SNP was located in the gene, the gene name is highlighted in red bold font, and the coding region of the gene is indicated by black vertical lines. - Additional file 19: Figure S10 Genome-wide association study of Asp (A), His (B), Leu (C), Cys (D), and Met (E) content. - The negative log10-transformed P-values from the genome-wide scan are plotted against position on each of the 10 chromosomes. - Second part exhibits the 0.1-Mb region on each side of the peak SNP and its position is indicated by a vertical red line with red triangle. - The bottom of each panel shows the annotated genes of the 200-kb region. - If the significant SNP was located in the gene, the gene name is highlighted in red bold font and the coding region of the gene was indicated by black vertical lines. - GWAS: Genome wide association analysis. - The authors thank all members of the laboratory for valuable discussions.. - JM, CYL, TW and LL participated in oyster collection and acquisition of the resequencing data. - All authors read and approved the final version of the manuscript.. - The funding body didn ’ t participate in the design of the study, collection, analysis and interpretation of data or in writing the manuscript.. - The Whole genome resequencing and transcriptomes data sets were deposited in the Sequence Read Archive (SRA) database under the accession numbers PRJNA394055.. - The State of the World Fisheries and Aquaculture: FAO Fisheries and Aquaculture Department. - Seasonal variation in reproductive activity and biochemical composition of flat oyster (Ostrea edulis) in the Homa lagoon, Izmir Bay, Turkey. - Quantitative trait locus analysis of stage- specific inbreeding depression in the Pacific oyster Crassostrea gigas.. - Genome-wide association studies of 14 agronomic traits in rice landraces. - A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. - Combining two-stage testing and interval mapping strategies to detect QTL for resistance to bonamiosis in the European flat oyster Ostrea edulis. - QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas). - Mapping QTL controlling growth and body size in the Pacific oyster. - Candidate gene polymorphisms and their association with glycogen content in the Pacific oyster Crassostrea gigas. - Divergence and plasticity shape adaptive potential of the Pacific oyster. - Linkage disequilibrium patterns of the human genome across populations.. - Sequencing-based genome-wide association study in rice. - Genome-wide association studies for complex traits:. - Association and functional analyses revealed that PPP1R3B plays an important role in the regulation of glycogen content in the Pacific oyster Crassostrea gigas
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