Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Cloning and Characterization of Tg-LAP3
2.3. Analysis of Nucleotide and Amino Acid Sequences
2.4. Gene Expression Analysis of Tg-LAP3
2.5. Association Analysis of SNPs with Growth Trait in T. granosa
2.6. Statistical Analysis
3. Results
3.1. Gene Structure and Characterization of Tg-LAP3
3.2. Analysis of the Deduced Amino Acid Sequence of Tg-LAP3
3.3. Quantitative Expression Analysis of Tg-LAP3
3.4. Association Analysis of SNPs with Growth Traits
4. Discussion
4.1. Tg-LAP3 Gene and Amino Acid Sequence Features
4.2. Quantitative Expression Analysis of Tg-LAP3
4.3. Association Analysis between SNPs of Tg-LAP3 Gene and Growth Traits
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer Name | Sequence from 5′ to 3′ | Information of Primer |
---|---|---|
Tg-LAP3-GSP1 | CCCCCTGACCTTCCAGCGTTACCAATGT | 5’-RACE |
Tg-LAP3-GSP2 | AAACAGGTGACAGAATGTGGAGAATGCC | 3’-RACE |
Tg-LN1-F | TAAGCGACTCAAAATGGCAG | Cloning of intron 1 |
Tg-LN1-R | TGTTCATCAAATTTTTGTGC | |
Tg-LN2-F | GCACAAAAATTTGATGAACA | Cloning of intron 2 |
Tg-LN2-R | ATCCTTCACCTTGCTTTCCC | |
Tg-LN3/4-F | ACCCGAGTATTTTATGGATT | Cloning of intron 3 and 4 |
Tg-LN3/4-R | GTTATTACCTATCTGCTACA | |
Tg-LN5-F | TTGTTATCTCAGTTTGTGTA | Cloning of intron 5 |
Tg-LN5-R | CTGTGGAGTAAGTTTATTTG | |
Tg-LN6-F | TTGTTATCTCAGTTTGTGTA | Cloning of intron 6 |
Tg-LN6-R | TGTGAACCTTGAGCAACTGA | |
Tg-LN7-F | TTATCAGTTGCTCAAGGTTC | Cloning of intron 7 |
Tg-LN7-R | AACAGCAAACAGTGTCCCAG | |
Tg-LN8-F | CAGTCAAACCTGGTGATGTA | Cloning of intron 8 |
Tg-LN8-R | TCAGGGTTCAGTTCAGATAG | |
Tg-LN9-F | ACAGGTTGACAATACAGATG | Cloning of intron 9 |
Tg-LN9-R | CCAGCCTGTTGTAAGGTATT | |
Tg-LN10-F | ATTGATGTTGCTCTTGGCTC | Cloning of intron 10 |
Tg-LN10-R | TGACCTTCCAGCGTTACCAA | |
Tg-LN11-F | ACATTGGTAACGCTGGAAGG | Cloning of intron 11 |
Tg-LN11-R | AGCTAGATAAGGAATTTCTG | |
Tg-LN12-F | ATAAAAACTGGTTACATCTA | Cloning of intron 12 |
Tg-LN12-R | TTAGTTGTCTATTGTATGTC | |
GSP1 | TCCACTAAATGGGGTTTTCTAATAAC | Cloning of proximal promoter sequence |
GSP2 | TGGGGGCTGCCATTTTGAGTCGCTTACA | |
GSP3 | TTACTCTACTCCACTTCACTCCAAAT | |
GW-F | GAAGTGGAGTAGAGTAATGC | Verification of proximal promoter sequence |
GW-R | TTGGGAGGTCCTGGTTCTTG | |
SNP-F1 | TGTTCTGCTAAGCTGGGT | HRM primer |
SNP-R1 | CACAGGAATGCTAACGCT | |
SNP-F2 | AGTTACAAGTTAGGGGAC | HRM primer |
SNP-R2 | ACATTTTCGTCTGATTAG | |
SNP-F3 | GTTTTTATTATTTGTGAC | HRM primer |
SNP-R3 | AAGTTATCAGGTTACATT | |
LAP3-real-F | GATGTTGCTCTTGGCTCAGG | qRT-PCR |
LAP3-real-R | TCCCGTATTGTTATTTTTCGTCACT | |
18S rRNA-real-F | CGTGCTCGTCCACCTTGGAG | qRT-PCR |
18S rRNA-real-R | GAACTCGTCGAGCTGCATCTTG |
Intron Name | Starting Postion(bp) | Length (bp) | Characteristy |
---|---|---|---|
Tg-LN1 | 111 | 615 | GT-AG |
Tg-LN2 | 233 | 1040 | GT-AG |
Tg-LN3 | 394 | 540 | GT-AG |
Tg-LN4 | 463 | 864 | GT-AG |
Tg-LN5 | 575 | 1042 | GT-AG |
Tg-LN6 | 737 | 1127 | GT-AG |
Tg-LN7 | 899 | 581 | GT-AG |
Tg-LN8 | 1113 | 1105 | GT-AG |
Tg-LN9 | 1216 | 1853 | GT-AG |
Tg-LN10 | 1296 | 1567 | GC-AG |
Tg-LN11 | 1446 | 378 | GT-AG |
Tg-LN12 | 1540 | 1345 | GT-AG |
Common Name | Species | GenBank No. | Size (aa) | Identity (%) |
---|---|---|---|---|
Blood clam | Tegillarca granosa | AFP57676 | 530 | - |
Yesso scallop | Mizuhopecten yessoensis | XP_021371955 | 529 | 73.4 |
Eastern oyster | Crassostrea virginica | XP_022345091 | 529 | 70.7 |
Razor clam | Sinonovacula constricta | MF687490 | 519 | 70.4 |
Pacific oyster | Crassostrea gigas | ACJ05337 | 529 | 71.7 |
Hard clam | Meretrix meretrix | KU678388 | 417 | 58.0 |
Golden apple snail | Pomacea canaliculata | XP_025095362 | 523 | 69.2 |
Sea hare | Aplysia californica | XP_012937771 | 527 | 64.4 |
Freshwater snail | Biomphalaria glabrata | XP_013075022 | 497 | 62.2 |
Sea squirt | Ciona intestinalis | XP_00213156 | 529 | 55.2 |
Sea cucumber | Apostichopus japonicas | PIK48812 | 547 | 59.8 |
Sea urchin | Strongylocentrotus purpuratus | XP_030841514 | 527 | 66.1 |
Amphioxus | Branchiostoma belcheri | XP_019624998 | 531 | 63.5 |
Channel catfish | Ictalurus punctatus | XP_017316877 | 518 | 62.4 |
Zebrafish | Danio rerio | CAM13051 | 517 | 62.3 |
Half-smooth tongue sole | Cynoglossus semilaevis | XP_008315686 | 520 | 61.4 |
Western clawed frog | Xenopus tropicalis | AAH84523 | 520 | 60.8 |
African clawed frog | Xenopus laevis | NP_001084691 | 495 | 61.6 |
Human | Homo sapiens | CAG33409 | 519 | 61.6 |
Chimpanzees | Pan troglodytes | JAA04696 | 519 | 61.6 |
Mouse | Mus musculus | CAJ18509 | 519 | 61.4 |
Locus | Genotype | Number | Frequency (%) | Body Weight (g) | Shell Length (mm) | Shell Width (mm) | Shell Height (mm) |
---|---|---|---|---|---|---|---|
g.-488A > G | AA | 6 | 10.34 | 8.51 ± 1.91 | 28.37 ± 2.36 | 21.96 ± 1.82 | 19.61 ± 1.45 |
AG | 28 | 48.28 | 9.16 ± 2.36 | 29.35 ± 2.68 | 22.37 ± 2.12 | 19.93 ± 1.65 | |
GG | 24 | 41.34 | 9.74 ± 2.75 | 29.86 ± 2.60 | 22.97 ± 2.00 | 20.14 ± 1.54 | |
g.-1123C > T | CC | 30 | 49.18 | 8.17 ± 2.45 | 27.88 ± 2.88 | 21.72 ± 2.21 | 19.23 ± 1.78 |
CT | 26 | 42.62 | 9.42 ± 1.84 | 29.71 ± 1.98 | 22.60 ± 1.45 | 20.16 ± 1.29 | |
TT | 5 | 8.20 | 8.83 ± 1.88 | 29.20 ± 2.21 | 22.22 ± 1.76 | 19.84 ± 1.68 | |
g.-1304C > A | CC | 39 | 72.22 | 7.78 ± 1.75 | 27.66 ± 2.36 | 21.21 ± 1.66 | 19.11 ± 1.38 |
CA | 13 | 22.22 | 9.64 ± 2.23 | 29.75 ± 2.46 | 22.89 ± 2.07 | 20.09 ± 1.55 | |
AA | 3 | 5.56 | 9.66 ± 0.46 | 30.48 ± 0.99 | 22.95 ± 0.38 | 20.26 ± 0.65 |
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Yao, H.; Ren, F.; Bao, Y.; Dong, Y.; Lin, Z. Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa. Fishes 2021, 6, 54. https://doi.org/10.3390/fishes6040054
Yao H, Ren F, Bao Y, Dong Y, Lin Z. Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa. Fishes. 2021; 6(4):54. https://doi.org/10.3390/fishes6040054
Chicago/Turabian StyleYao, Hanhan, Fuzhen Ren, Yongbo Bao, Yinghui Dong, and Zhihua Lin. 2021. "Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa" Fishes 6, no. 4: 54. https://doi.org/10.3390/fishes6040054