Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments
Abstract
1. Introduction
2. Results
2.1. Sequencing Data Statistics and Population Structure Analysis
2.2. Statistical Analysis of Growth Data for GWAS and Heritability Assessment of Growth Traits
2.3. Screening of Growth-Associated SNPs in Hypertonic Environments
2.4. Candidate Gene Identification and Functional Annotation
2.5. Verification of Growth-Related SNPs
2.6. Joint Analysis of Significant SNP Peak and LD Block
2.7. Molecular Characterization and Expression Analysis of Shroom3 in Different Organizations
3. Discussion
4. Materials and Methods
4.1. Statement of Ethics
4.2. Management and Sample DNA Extraction
4.3. Sequencing Library Preparation, Genotyping, and Data Filtering
4.4. Population Genetic Structure and Linkage Disequilibrium Analysis
4.5. Assessment of Genetic Parameters for Growth Traits
4.6. Growth Trait GWAS
4.7. Annotation of Candidate Genes
4.8. Verification of Growth-Associated SNPs
4.9. LD Block Synthesis and Growth-Advantageous Genotype Statistics
4.10. Analysis of Candidate Gene Sequences and Expression Patterns Under Different Salinities
4.11. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | SNP | −Log (p Value) | Allele | Position |
---|---|---|---|---|
BH | 16:1462653 | 6.63270 | A/T | intergenic |
BT | 16:1462653 | 6.98889 | A/T | intergenic |
16:3192874 | 6.74434 | T/G | intergenic | |
16:3967223 | 6.50020 | A/T | Intronic (Dcp2) | |
16:3984271 | 6.89572 | C/T | Exonic (Psmb7) | |
16:4072454 | 6.77821 | T/A | Intronic (Mfsd14ba) | |
16:4116111 | 7.19193 | G/A | intronic (Shroom3) | |
16:4116118 | 6.89294 | A/T | intronic (Shroom3) | |
16:4120208 | 6.51879 | A/T | intronic (Shroom3) | |
16:4120214 | 7.20708 | A/T | intronic (Shroom3) | |
BW | 16:1964199 | 6.64524 | G/C | Intronic (Ralgps1) |
SNP | 16:4102436 | 16:4155322 | 16:4173817 | 16:4116285 | 16:4110656 | 16:4121717 | 16:4124047 |
---|---|---|---|---|---|---|---|
REF | G | T | A | T | C | A | T |
ALT | A | C | G | A | A | C | C |
D’ | 0.855 | 0.807 | 0.856 | 0.813 | 0.816 | 0.826 | 0.809 |
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Ding, M.; Tao, Y.; Hua, J.; Dong, Y.; Lu, S.; Qiang, J.; He, J. Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments. Int. J. Mol. Sci. 2025, 26, 1834. https://doi.org/10.3390/ijms26051834
Ding M, Tao Y, Hua J, Dong Y, Lu S, Qiang J, He J. Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments. International Journal of Molecular Sciences. 2025; 26(5):1834. https://doi.org/10.3390/ijms26051834
Chicago/Turabian StyleDing, Miaomiao, Yifan Tao, Jixiang Hua, Yalun Dong, Siqi Lu, Jun Qiang, and Jixiang He. 2025. "Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments" International Journal of Molecular Sciences 26, no. 5: 1834. https://doi.org/10.3390/ijms26051834
APA StyleDing, M., Tao, Y., Hua, J., Dong, Y., Lu, S., Qiang, J., & He, J. (2025). Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments. International Journal of Molecular Sciences, 26(5), 1834. https://doi.org/10.3390/ijms26051834