Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq)
Abstract
:1. Introduction
2. Results
2.1. Sequencing and Genotyping
2.2. Genetic Linkage Map
2.3. Growth Trait–Associated Quantitative Trait Loci (QTL) and Related Genes
3. Discussion
4. Materials and Methods
4.1. Sample Preparation
4.2. ddRAD Library Construction and Sequencing
4.3. SNP (Single-Nucleotide Polymorphism) Calling and Genotyping
4.4. High-Density Genetic Map Construction
4.5. QTL Mapping
4.6. Identification of the Genes on Growth Traits Associated QTLs
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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QTL | Trait | Genetic Position(cM) | Logarithm of Odds (LOD) | R2 (%) |
---|---|---|---|---|
qLG1 | BW | 30.8–31.0 | 3.3 | 19.6 |
qLG2 | BL | 29.8–30.2 | 3.3 | 21 |
qLG5_1 | BW | 15.1–15.6 | 4.7 | 24.3 |
qLG5_2 | BW | 17.0–17.5 | 3.1 | 17.1 |
qLG5_3 | BW | 17.0–17.5 | 2.8 | 16.5 |
qLG5_4 | BW | 17.8–18.0 | 2.9 | 15.8 |
qLG5_5 | BW | 18.7–19.4 | 3.2 | 19.1 |
qLG5_6 | BW | 18.7–19.4 | 4.2 | 24.6 |
qLG5_7 | BW | 19.9–20.2 | 3.5 | 20.8 |
qLG5_8 | BW | 20.4–20.8 | 3.4 | 20 |
qLG5_9 | BW | 27.4–27.9 | 2.6 | 21.5 |
qLG5_10 | BW | 27.4–27.9 | 2.8 | 24.5 |
qLG5_11 | BW | 28.1–28.3 | 2.8 | 28.3 |
qLG5_12 | BW | 29.4–29.7 | 2.7 | 14.6 |
qLG5_13 | BW | 29.4–29.7 | 3 | 29.1 |
qLG5_14 | BW | 32.2–32.4 | 3.2 | 17.6 |
qLG5_15 | BW | 33.0–33.3 | 2.9 | 15.6 |
qLG5_16 | BL | 15.1–15.4 | 4.4 | 23.3 |
qLG5_17 | BL | 17.0–17.1 | 2.6 | 14.5 |
qLG5_18 | BL | 19.2–19.3 | 3.8 | 20.5 |
qLG5_19 | BL | 19.9–20.2 | 3.4 | 20.3 |
qLG5_20 | BL | 19.9–20.2 | 3.8 | 22.2 |
qLG5_21 | BL | 20.4–20.8 | 3.5 | 20.8 |
qLG7_1 | BW | 14.4–14.5 | 2.8 | 16.8 |
qLG7_2 | BL | 14.4–14.5 | 2.6 | 15.1 |
qLG21 | BL | 16.0–16.5 | 2.9 | 15.5 |
qLG24 | BW | 48.8–49.0 | 2.6 | 14.4 |
QTL | Gene ID | Gene Description | Gene Symbol | Physical Position |
---|---|---|---|---|
qLG1 | Eco_gene_10012941 | fasciculation and elongation protein ζ-2-like | fez2 | scaffold416 |
qLG2 | Eco_gene_10013595 | Dol-P-Man: Man(5)GlcNAc(2)-PP-Dolα-1,3-mannosyltransferase | alg3 | scaffold438 |
Eco_gene_10013597 | endothelin converting enzyme 2 | ece2 | scaffold438 | |
qLG5_1 | Eco_gene_10014238 | armadillo repeat gene deleted in velocardiofacial syndrome | arvcf | scaffold468 |
qLG5_3 | Eco_gene_10004531 | solute carrier family 27 (fatty acid transporter), member 4 | slc27a4 | scaffold1517 |
Eco_gene_10005552 | tyrosine-protein kinase SgK223 | sgk223 | scaffold1706 | |
qLG5_4 | Eco_gene_10002069 | calcium/calmodulin-dependent protein kinase 2 | camk2 | scaffold1180 |
qLG5_5 | Eco_gene_10005555 | proline-rich coiled-coil 2B | prrc2b | scaffold1706 |
Eco_gene_10000893 | melanin-concentrating hormone receptor 1 | mchr1 | scaffold1067 | |
qLG5_19 | Eco_gene_10005043 | sarcosine dehydrogenase | sardh | scaffold1600 |
qLG5_8 | Eco_gene_10018102 | pregnancy-associated plasma protein A | pappa | scaffold675 |
qLG5_9 | Eco_gene_10014809 | spleen tyrosine kinase | syk | scaffold491 |
qLG5_11 | Eco_gene_10002109 | telomerase reverse transcriptase | tert | scaffold1187 |
qLG5_12 | Eco_gene_10005999 | WD repeat-containing protein 91-like | wdrcp91 | scaffold1804 |
Eco_gene_10000470 | ftz transcription factor 1 | ftz-f1 | scaffold1023 | |
qLG7 | Eco_gene_10021611 | multidrug and toxin extrusion protein 1-like | mate1 | scaffold919 |
qLG21 | Eco_gene_10003094 | neurogenic locus notch homolog protein 1-like | notch1 | scaffold130 |
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Yu, H.; You, X.; Li, J.; Liu, H.; Meng, Z.; Xiao, L.; Zhang, H.; Lin, H.-R.; Zhang, Y.; Shi, Q. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq). Int. J. Mol. Sci. 2016, 17, 501. https://doi.org/10.3390/ijms17040501
Yu H, You X, Li J, Liu H, Meng Z, Xiao L, Zhang H, Lin H-R, Zhang Y, Shi Q. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq). International Journal of Molecular Sciences. 2016; 17(4):501. https://doi.org/10.3390/ijms17040501
Chicago/Turabian StyleYu, Hui, Xinxin You, Jia Li, Hankui Liu, Zining Meng, Ling Xiao, Haifa Zhang, Hao-Ran Lin, Yong Zhang, and Qiong Shi. 2016. "Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq)" International Journal of Molecular Sciences 17, no. 4: 501. https://doi.org/10.3390/ijms17040501