QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis
Abstract
:1. Introduction
2. Results
2.1. Genotyping and Genetic Marker Development
2.2. Construction of Linkage Maps
2.3. QTL Mapping of Disease-Related Traits
2.4. Functional Enrichment Analysis of Candidate Genes
2.5. Identification of Disease Resistance Gene Candidates
3. Discussion
4. Materials and Methods
4.1. Challenge Experiment and Sample Collection
4.2. Sequencing, Genotyping, and SNP Filtering
4.3. Genetic Map Construction and QTL Mapping
4.4. Gene Annotation and Enrichment Analysis
4.5. Analysis of Candidate Gene Expression Levels
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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Marker Type | Female Genotype | Male Genotype | SNP Number | After Segregation | Bin Marker Number | Percentage |
---|---|---|---|---|---|---|
hkxhk | hk | hk | 11,039 | 10,287 | 6112 | 22.60% |
nnxnp | nn | np | 18,052 | 15,912 | 6084 | 36.95% |
lmxll | lm | ll | 19,762 | 17,566 | 5840 | 40.45% |
Total | 48,853 | 43,765 | 18,036 | 100.00% |
Linkage | Marker Number | Length | Average Distance | Max Gap |
---|---|---|---|---|
LG1 | 1202 | 59.93 | 0.05 | 3.73 |
LG2 | 1255 | 75.23 | 0.06 | 4.98 |
LG3 | 1125 | 65.73 | 0.06 | 4.97 |
LG4 | 734 | 49.19 | 0.07 | 4.98 |
LG5 | 690 | 61.60 | 0.09 | 4.14 |
LG6 | 837 | 58.75 | 0.07 | 7.92 |
LG7 | 796 | 44.67 | 0.06 | 4.56 |
LG8 | 657 | 62.40 | 0.09 | 2.07 |
LG9 | 370 | 91.09 | 0.25 | 7.92 |
LG10 | 715 | 57.04 | 0.08 | 3.73 |
LG11 | 994 | 55.79 | 0.06 | 1.65 |
LG12 | 980 | 69.87 | 0.07 | 4.56 |
LG13 | 364 | 54.61 | 0.15 | 7.49 |
LG14 | 697 | 64.07 | 0.09 | 4.14 |
LG15 | 357 | 30.17 | 0.08 | 2.89 |
LG16 | 852 | 64.95 | 0.08 | 7.92 |
LG17 | 547 | 53.72 | 0.10 | 2.07 |
LG18 | 1017 | 75.33 | 0.07 | 8.77 |
LG19 | 865 | 60.77 | 0.07 | 4.56 |
LG20 | 309 | 43.81 | 0.14 | 3.72 |
LG21 | 871 | 60.76 | 0.07 | 4.14 |
LG22 | 621 | 59.53 | 0.10 | 5.40 |
LG23 | 716 | 53.54 | 0.07 | 11.79 |
LG24 | 164 | 23.17 | 0.14 | 4.97 |
Total | 17,735 | 1395.72 | 0.08 | — |
Group | Position | Peak Locus | Peak LOD | Expl (%) | Geno Number |
---|---|---|---|---|---|
9 | 22.37–24.02 | hk2455 | 3.71 | 11–13.3 | 47 |
9 | 29.39 | hk2465 | 3.16 | 11.4 | 1 |
9 | 30.22 | hk2470 | 3.19 | 11.5 | 1 |
9 | 30.63 | hk2461 | 3.03 | 11 | 0 |
21 | 2.48–3.31 | np5073 | 3.09 | 10.9–11.2 | 4 |
21 | 3.31 | hk5416 | 3.16 | 11.2–11.4 | 60 |
21 | 3.72 | np5077 | 3.27 | 11.4–11.8 | 9 |
21 | 4.55 | hk5428 | 3.03 | 11 | 1 |
21 | 4.55–6.2 | hk5440 | 3.33 | 10.9–12 | 28 |
21 | 6.2 | np5097 | 3.53 | 11.9–12.7 | 17 |
21 | 6.2 | np5099 | 3.53 | 12–12.7 | 22 |
21 | 10.33 | np5112 | 3.01 | 10.9 | 16 |
21 | 13.64–14.46 | lm5172 | 3.06 | 10.9–11.1 | 16 |
Gene | Gene_id | KEGG Pathway |
---|---|---|
chmp2a | A022229 | Endocytosis |
snf8 | A022226 | Endocytosis |
chmp6 | A022157 | Endocytosis |
chmp1a | A009223 | Endocytosis |
tat | A009234 | Phenylalanine, tyrosine and tryptophan biosynthesis; biosynthesis of amino acids; tyrosine metabolism |
asah2 | A022051 | Sphingolipid metabolism |
pten | A022010 | Inositol phosphate metabolism |
arg1 | A022064 | Arginine and proline metabolism; biosynthesis of amino acids |
heatr1 | A022065 | Ribosome biogenesis in eukaryotes |
map2k6 | A022132 | MAPK signaling pathway |
map3k14 | A022168 | MAPK signaling pathway; intestinal immune network for IgA production |
Gene | Primer | Primer Sequences (5′–3′) |
---|---|---|
chmp2a | chmp2a-F | CGCTCAAGTCCAACAACAGC |
chmp2a-R | TCGATGGCGTCGTTCATCAT | |
snf8 | snf8-F | CAGGACGTGAGCCAAGATGA |
snf8-R | CTCAGCCAGCTGCAGAACTA | |
chmp6 | chmp6-F | CAGATCGGTAACCTGGAGCG |
chmp6-R | TCGATGGACATCACCTCGTG | |
chmp1a | chmp1a-F | GAAGGTCAAGAAGGCGTTGC |
chmp1a-R | GGCGGTCTGGACTTTAGAGG | |
tat | tat-F | TCAACGAGCTGTCCACCATC |
tat-R | CGCTGAAGCAGGAAGACAGA | |
asah2 | asah2-F | CGAGTGGCACATTCCTCTGT |
asah2-R | GGCGACTTTGAAGACGTTGG | |
pten | Pten-F | TGTGCGGAACGACATTACGA |
Pten-R | TCCTCGCTCAACCACTTGTC | |
arg1 | arg1-F | GATCCGTCACACAGGTCTCC |
arg1-R | TAATCCTGCGGGTGGTTTCC | |
heatr1 | heatr1-F | CTCAGGCCGTTCAGGAAGTT |
heatr1-R | GTAGGTGGCGGCTTTGTAGT | |
map2k6 | map2k6-F | AGATGTGAAGCCCTCCAACG |
map2k6-R | AGCCTTTCTGGTTCGTCTCG | |
map3k14 | map3k14-F | TGCAGGGCGAATGTCTAAGG |
map3k14-R | GGAGCCACAGACAAGACTCC | |
β-actin | β-actin-F | CTCTGTCTGGATCGGAGGCT |
β-actin-R | GCTGAAGTTGTTGGGTGTTTG |
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Li, Q.; Zhu, J.; Liu, S.; Liu, H.; Zhang, T.; Ye, T.; Lou, B.; Liu, F. QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis. Int. J. Mol. Sci. 2024, 25, 10872. https://doi.org/10.3390/ijms252010872
Li Q, Zhu J, Liu S, Liu H, Zhang T, Ye T, Lou B, Liu F. QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis. International Journal of Molecular Sciences. 2024; 25(20):10872. https://doi.org/10.3390/ijms252010872
Chicago/Turabian StyleLi, Qian, Jiajie Zhu, Sifang Liu, Haowen Liu, Tianle Zhang, Ting Ye, Bao Lou, and Feng Liu. 2024. "QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis" International Journal of Molecular Sciences 25, no. 20: 10872. https://doi.org/10.3390/ijms252010872
APA StyleLi, Q., Zhu, J., Liu, S., Liu, H., Zhang, T., Ye, T., Lou, B., & Liu, F. (2024). QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis. International Journal of Molecular Sciences, 25(20), 10872. https://doi.org/10.3390/ijms252010872