Effects of Polymorphisms in Pepsinogen (PEP), Amylase (AMY) and Trypsin (TRY) Genes on Food Habit Domestication Traits in Mandarin Fish
Abstract
:1. Introduction
2. Results
2.1. Genetic Polymorphism of PEP, AMY and TRY Gene
2.2. Analysis of Genotype Frequencies, Allele Frequencies and Genetic Diversity Parameter at Each SNPs in PEP and TRY Gene
2.3. Associations of Genotypes and Diplotypes with Food Habit Domestication Traits
3. Discussion
4. Experimental Section
4.1. Fish and DNA Samples
4.2. SNP Discovery
4.3. Genotyping of SNPs
4.4. Statistical Analysis
5. Conclusions
PEP T2477C | |||||||||
---|---|---|---|---|---|---|---|---|---|
Groups | Sample size | Genotype frequencies | Allelic frequencies | HWE | PIC | He | |||
CC | CT | TT | C | T | |||||
Feeders | 120 | 0.0000(0) | 0.2167(26) | 0.7833(94) | 0.1083 | 0.8917 | X2 = 1.6970 | 0.1745 | 0.1940 |
p = 0.1927 | |||||||||
Nonfeeders | 120 | 0.0000(0) | 0.2917(35) | 0.7083(85) | 0.1458 | 0.8542 | X2 = 3.3862 | 0.2181 | 0.2502 |
p = 0.0657 | |||||||||
PEPC2528T | |||||||||
Groups | Sample size | Genotype frequencies | Allelic frequencies | HWE | PIC | He | |||
CC | CT | TT | C | T | |||||
Feeders | 120 | 0.6667(80) | 0.2750(33) | 0.0583(7) | 0.8042 | 0.1958 | X2 = 2.0823 | 0.2653 | 0.3163 |
p = 0.1490 | |||||||||
Nonfeeders | 120 | 0.5583(67) | 0.3417(41) | 0.1000(12) | 0.7292 | 0.2708 | X2 = 2.3333 | 0.3169 | 0.3966 |
p = 0.1266 | |||||||||
TRYG648A | |||||||||
Groups | Sample size | Genotype frequencies | Allelic frequencies | HWE | PIC | He | |||
AA | AG | GG | A | G | |||||
Feeders | 120 | 0.2250(27) | 0.4750(57) | 0.3000(36) | 0.4625 | 0.5375 | X2 = 0.2859 | 0.3734 | 0.4993 |
p = 0.5928 | |||||||||
Nonfeeders | 120 | 0.2083(25) | 0.5333(64) | 0.2583(31) | 0.4750 | 0.5250 | X2 = 0.5095 | 0.3744 | 0.5008 |
p = 0.4754 |
Diplotype | SNPs site | Frequency | ||
---|---|---|---|---|
T2477C | C2528T | feeders | nonfeeders | |
Dip1 | CT | CC | 0.1525 | 0.1709 |
Dip2 | CT | CT | 0.0508 | 0.1026 |
Dip3 | TT | CC | 0.5254 | 0.4017 |
Dip4 | TT | CT | 0.2288 | 0.2479 |
Dip5 | TT | TT | 0.0424 | 0.0769 |
Diplotype | Feeders | Nonfeeders | p Value |
---|---|---|---|
Dip1 | 80 | 20 | 0.000 |
Non-Dip1 | 38 | 97 | |
Dip2 | 6 | 12 | 0.136 |
Non-Dip2 | 112 | 105 | |
Dip3 | 62 | 47 | 0.057 |
Non-Dip3 | 56 | 70 | |
Dip4 | 27 | 29 | 0.732 |
Non-Dip4 | 91 | 88 | |
Dip5 | 45 | 9 | 0.000 |
Non-Dip5 | 73 | 108 |
Primer pair name | Primer sequence | Annealing Temperature (°C) | Amplified region |
---|---|---|---|
PEP-01F | TTACCAGTTAGCACCTTCAGCATG | 59 | 5′ flanking-Intron 1 |
PEP-01R | TTGAGCCTGTACTCCTCCCATAGA | ||
PEP-02F | AAAAGGCAATGTAGCCGAACG | 57 | Exon 2-Exon 4 |
PEP-02R | TGTCATATCCAAGGTAGCCAGTCA | ||
PEP-03F | AGGCAAGAGCAGCACCTACAGAAA | 55 | Exon 4-Intron 6 |
PEP-03R | TGCAAGCCACAACCTGACCATT | ||
PEP-04F | TGGTGTTGACCCCAACCACTACTA | 58 | Exon 6-Exon 9 |
PEP-04R | ATAATTACAGTAGCACTG | ||
AMY-01F | GTTGCTGCTGAATCCTTG | 57 | 5′ flanking-Intron 2 |
AMY-01R | GGTAGATGCAGGATTGTA | ||
AMY-02F | CTGTGTTGTTGCTCAGA | 57 | Exon 2-Exon 4 |
AMY-02R | TGAGCTGAAGCCACTAA | ||
AMY-03F | GAGTGGATGCCTGCAAG | 60 | Exon 4-Exon 5 |
AMY-03R | CAGTGACCCTTCCCAGATG | ||
AMY-04F | GTGCAGTTAATCTAACCCAT | 58 | Exon 5-Exon 6 |
AMY-04R | ATCTTGTAGAGCCTGGAAT | ||
AMY-05F | CAACCACGACAACCAGAGAG | 57 | Exon 6-Exon 9 |
AMY-05R | CACCTGTTTCCTTCCTTC | ||
TRY-01F | TTGTTCTGCACCACATCC | 59 | 5′ flanking |
TRY-01R | GTGGTGTGCCATGATGC | ||
TRY-02F | TAGAGAGTTGTCAGTCAATGC | 59 | 5′ flanking-Exon 1 |
TRY-02R | AGGAACTTACAGGCTGCA | ||
TRY-03F | GTACGCTCAGTAGGTG | 55 | Exon 1-Exon 5 |
TRY-03R | CAGGAGTTGTAGTTGCAGACC |
Gene | SNPs locus | Genotyping primer | |
---|---|---|---|
PEP | T2477C | forward | AGTGTTGTGACCTTCGGTGG |
C2528T | reverse | ACTCGTCTTTCTTGGCGCTT | |
TRY | G648A | forward | TAAGGTCATCCGTCACCCCA |
reverse | CATACCCCGACGTGTACCAA |
Acknowledgments
Conflicts of Interest
References
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Yi, T.; Sun, J.; Liang, X.; He, S.; Li, L.; Wen, Z.; Shen, D. Effects of Polymorphisms in Pepsinogen (PEP), Amylase (AMY) and Trypsin (TRY) Genes on Food Habit Domestication Traits in Mandarin Fish. Int. J. Mol. Sci. 2013, 14, 21504-21512. https://doi.org/10.3390/ijms141121504
Yi T, Sun J, Liang X, He S, Li L, Wen Z, Shen D. Effects of Polymorphisms in Pepsinogen (PEP), Amylase (AMY) and Trypsin (TRY) Genes on Food Habit Domestication Traits in Mandarin Fish. International Journal of Molecular Sciences. 2013; 14(11):21504-21512. https://doi.org/10.3390/ijms141121504
Chicago/Turabian StyleYi, Tilin, Jian Sun, Xufang Liang, Shan He, Ling Li, Zhengyong Wen, and Dan Shen. 2013. "Effects of Polymorphisms in Pepsinogen (PEP), Amylase (AMY) and Trypsin (TRY) Genes on Food Habit Domestication Traits in Mandarin Fish" International Journal of Molecular Sciences 14, no. 11: 21504-21512. https://doi.org/10.3390/ijms141121504