Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fish Sampling
2.2. DNA Extraction
2.3. SNP Prediction and Sequence Annotation
2.4. SNP Validation and Genotyping
2.5. Genetic Analysis
3. Results
3.1. SNP Identification and Annotation
3.2. Genetic Diversity of Closed Colony and Wild Samples
3.3. Genetic Structure Analysis of Closed Colony
3.4. Differences in the Results of the SNP and SSR Marker Analyses in the Same Samples
4. Discussion
4.1. Characteristics of SNP Markers in Rare Minnow
4.2. Relationship between Heterozygosity of Genetic Markers and Population History
4.3. Stability Maintenance of the Genetic Structure in a Closed Colony
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Loci | Wild | F1 | F3 | ||||||
Ne | Ho | He | Ne | Ho | He | Ne | Ho | He | |
Seq3 | 1.3846 | 0.3333 | 0.3030 | 1.8672 | 0.5333 | 0.4723 | 1.8967 | 0.2333 | 0.4808 |
Seq10-1 | 1.8000 | 0.6667 | 0.4848 | 1.6423 | 0.2667 | 0.3977 | 1.8000 | 0.3333 | 0.4520 |
Seq11-1 | 1.3846 | 0.3333 | 0.3030 | 1.3006 | 0.2667 | 0.2350 | 1.3423 | 0.2333 | 0.2593 |
Seq12 | 1.3846 | 0.3333 | 0.3030 | 1.2195 | 0.2000 | 0.1831 | 1.3006 | 0.2000 | 0.2350 |
Seq13-1 | 1.6000 | 0.1667 | 0.4091 | 1.5139 | 0.3667 | 0.3452 | 1.5139 | 0.3000 | 0.3452 |
Seq15-1 | 1.9459 | 0.5000 | 0.5303 | 1.9978 | 0.3667 | 0.5079 | 2.0000 | 0.4667 | 0.5085 |
Seq18-2 | 1.6000 | 0.5000 | 0.4091 | 1.8672 | 0.4667 | 0.4723 | 1.9912 | 0.5333 | 0.5062 |
Seq26-1 | 1.9459 | 0.5000 | 0.5303 | 1.8672 | 0.3333 | 0.4723 | 1.8967 | 0.5000 | 0.4808 |
Seq26-2 | 2.8800 | 0.5000 | 0.7121 | 2.8302 | 0.8000 | 0.6576 | 2.9412 | 0.6000 | 0.6712 |
Seq28 | 2.0000 | 0.6667 | 0.5455 | 1.7630 | 0.5667 | 0.4401 | 1.4706 | 0.3333 | 0.3254 |
Seq29 | 1.6000 | 0.5000 | 0.4091 | 1.8672 | 0.5333 | 0.4723 | 1.8000 | 0.5333 | 0.4520 |
Seq30 | 1.9459 | 0.1667 | 0.5303 | 1.6423 | 0.3333 | 0.3977 | 1.6838 | 0.3000 | 0.4130 |
Seq31-1 | 1.9459 | 0.5000 | 0.5303 | 1.9459 | 0.6333 | 0.4944 | 1.9802 | 0.5667 | 0.5034 |
Seq31-5 | 1.9459 | 0.5000 | 0.5303 | 1.9802 | 0.6333 | 0.5034 | 1.9802 | 0.5667 | 0.5034 |
Seq38-1 | 1.9459 | 0.1667 | 0.5303 | 1.8000 | 0.5333 | 0.4520 | 1.8967 | 0.5667 | 0.4808 |
Seq39-2 | 2.0000 | 0.6667 | 0.5455 | 1.8967 | 0.4333 | 0.4808 | 1.9651 | 0.8000 | 0.4994 |
Seq42-2 | 1.9459 | 0.5000 | 0.5303 | 1.9978 | 0.6333 | 0.5079 | 1.9651 | 0.6000 | 0.4994 |
Seq49 | 1.8000 | 0.3333 | 0.4848 | 1.8349 | 0.5667 | 0.4627 | 1.8967 | 0.5667 | 0.4808 |
Seq51-1 | 1.8000 | 0.3333 | 0.4848 | 1.9459 | 0.5000 | 0.4944 | 1.8967 | 0.5000 | 0.4808 |
Seq53-2 | 1.6000 | 0.5000 | 0.4091 | 1.7630 | 0.5000 | 0.4401 | 1.9459 | 0.7667 | 0.4944 |
Mean | 1.8228 | 0.4333 | 0.4758 | 1.8271 | 0.4733 | 0.4445 | 1.8582 | 0.4750 | 0.4536 |
St. | 0.3295 | 0.1567 | 0.1010 | 0.3203 | 0.1516 | 0.1008 | 0.3373 | 0.1713 | 0.0981 |
Loci | F4 | F5 | F10 | ||||||
Ne | Ho | He | Ne | Ho | He | Ne | Ho | He | |
Seq3 | 1.9978 | 0.5000 | 0.5079 | 1.9912 | 0.5333 | 0.5062 | 1.8824 | 0.4375 | 0.4762 |
Seq10-1 | 1.7630 | 0.5000 | 0.4401 | 1.3006 | 0.2000 | 0.2350 | 1.7167 | 0.4062 | 0.4241 |
Seq11-1 | 1.5571 | 0.4667 | 0.3638 | 1.5139 | 0.3667 | 0.3452 | 1.7534 | 0.3750 | 0.4365 |
Seq12 | 1.4274 | 0.3667 | 0.3045 | 1.3846 | 0.2667 | 0.2825 | 1.4787 | 0.4062 | 0.3289 |
Seq13-1 | 1.7241 | 0.4667 | 0.4271 | 1.6838 | 0.3667 | 0.4130 | 1.7886 | 0.4062 | 0.4479 |
Seq15-1 | 1.9459 | 0.5000 | 0.4944 | 1.9978 | 0.5667 | 0.5079 | 1.7167 | 0.4688 | 0.4241 |
Seq18-2 | 1.9651 | 0.4667 | 0.4994 | 1.8672 | 0.5333 | 0.4723 | 1.9922 | 0.3125 | 0.5060 |
Seq26-1 | 1.8349 | 0.2333 | 0.4627 | 1.8672 | 0.5333 | 0.4723 | 1.7167 | 0.4688 | 0.4241 |
Seq26-2 | 2.9364 | 0.5667 | 0.6706 | 2.8986 | 0.7333 | 0.6661 | 2.5222 | 0.5312 | 0.6131 |
Seq28 | 1.7630 | 0.3667 | 0.4401 | 1.6423 | 0.4000 | 0.3977 | 1.9523 | 0.4688 | 0.4955 |
Seq29 | 1.7241 | 0.3333 | 0.4271 | 1.6838 | 0.3667 | 0.4130 | 1.9523 | 0.4688 | 0.4955 |
Seq30 | 1.6838 | 0.3000 | 0.4130 | 1.6838 | 0.4333 | 0.4130 | 1.4787 | 0.3438 | 0.3289 |
Seq31-1 | 1.9459 | 0.5000 | 0.4944 | 1.9651 | 0.6000 | 0.4994 | 1.8534 | 0.5312 | 0.4678 |
Seq31-5 | 1.9802 | 0.5667 | 0.5034 | 1.9978 | 0.5667 | 0.5079 | 1.9087 | 0.5938 | 0.4836 |
Seq38-1 | 1.8000 | 0.4667 | 0.4520 | 1.7630 | 0.5667 | 0.4401 | 1.7534 | 0.4375 | 0.4365 |
Seq39-2 | 1.8349 | 0.4333 | 0.4627 | 1.8967 | 0.5667 | 0.4808 | 1.8221 | 0.6250 | 0.4583 |
Seq42-2 | 1.9912 | 0.7333 | 0.5062 | 2.0000 | 0.6667 | 0.5085 | 1.7534 | 0.4375 | 0.4365 |
Seq49 | 1.8000 | 0.4667 | 0.4520 | 1.7241 | 0.5333 | 0.4271 | 1.7534 | 0.4375 | 0.4365 |
Seq51-1 | 1.9802 | 0.5667 | 0.5034 | 1.9231 | 0.5333 | 0.4881 | 1.8534 | 0.4062 | 0.4678 |
Seq53-2 | 1.8349 | 0.4333 | 0.4627 | 1.8349 | 0.6333 | 0.4627 | 1.7167 | 0.5312 | 0.4241 |
Mean | 1.8745 | 0.4617 | 0.4644 | 1.8310 | 0.4983 | 0.4469 | 1.8183 | 0.4547 | 0.4506 |
St. | 0.2920 | 0.1094 | 0.0706 | 0.3229 | 0.1348 | 0.0913 | 0.2135 | 0.0782 | 0.0603 |
Loci | Wild | F1 | F3 | F4 | F5 | F10 |
---|---|---|---|---|---|---|
Seq3 | 0.7389 | 0.4705 | 0.0041 | 0.9309 | 0.7653 | 0.6398 |
Seq10-1 | 0.3006 | 0.0637 | 0.1419 | 0.4459 | 0.3863 | 0.8076 |
Seq11-1 | 0.7389 | 0.4339 | 0.5632 | 0.1103 | 0.7246 | 0.4155 |
Seq12 | 0.7389 | 0.5814 | 0.3863 | 0.2442 | 0.7481 | 0.1685 |
Seq13-1 | 0.0852 | 0.7246 | 0.4582 | 0.6036 | 0.5287 | 0.5913 |
Seq15-1 | 0.8774 | 0.1213 | 0.6469 | 0.9492 | 0.5193 | 0.5426 |
Seq18-2 | 0.5186 | 0.9467 | 0.7653 | 0.7146 | 0.4705 | 0.0280 |
Seq26-1 | 0.8774 | 0.1002 | 0.8235 | 0.0056 | 0.4705 | 0.5426 |
Seq26-2 | 0.3165 | 0.1124 | 0.1419 | 0.1725 | 0.8575 | 0.5707 |
Seq28 | 0.5510 | 0.1072 | 0.8901 | 0.3499 | 0.9745 | 0.7559 |
Seq29 | 0.5186 | 0.4705 | 0.3138 | 0.2181 | 0.5287 | 0.7559 |
Seq30 | 0.0641 | 0.3623 | 0.1244 | 0.1244 | 0.7821 | 0.7911 |
Seq31-1 | 0.8774 | 0.1169 | 0.4836 | 0.9492 | 0.2617 | 0.4340 |
Seq31-5 | 0.8774 | 0.1503 | 0.4836 | 0.4836 | 0.5193 | 0.1899 |
Seq38-1 | 0.0641 | 0.3138 | 0.3187 | 0.8557 | 0.1072 | 0.9895 |
Seq39-2 | 0.5510 | 0.5816 | 0.0008 | 0.7226 | 0.3187 | 0.0360 |
Seq42-2 | 0.8774 | 0.1689 | 0.2617 | 0.0124 | 0.0831 | 0.9895 |
Seq49 | 0.3884 | 0.2091 | 0.3187 | 0.8557 | 0.1631 | 0.9895 |
Seq51-1 | 0.3884 | 0.9492 | 0.8235 | 0.4836 | 0.6055 | 0.4485 |
Seq53-2 | 0.5186 | 0.4459 | 0.0021 | 0.7226 | 0.0393 | 0.1439 |
mean | 0.5434 | 0.3715 | 0.3976 | 0.4977 | 0.4927 | 0.5415 |
Std | 0.2741 | 0.2701 | 0.2794 | 0.3203 | 0.2632 | 0.3014 |
Loci | FIS | FIT | FST |
---|---|---|---|
Seq3 | 0.0689 | 0.1021 | 0.0356 |
Seq10-1 | 0.1099 | 0.1331 | 0.026 |
Seq11-1 | −0.0591 | −0.0327 | 0.0249 |
Seq12 | −0.0972 | −0.0861 | 0.0101 |
Seq13-1 | 0.0204 | 0.0305 | 0.0103 |
Seq15-1 | 0.014 | 0.0514 | 0.0379 |
Seq18-2 | 0.0428 | 0.075 | 0.0337 |
Seq26-1 | 0.0903 | 0.0939 | 0.0039 |
Seq26-2 | −0.0021 | 0.0082 | 0.0103 |
Seq28 | −0.0344 | −0.0086 | 0.025 |
Seq29 | −0.0057 | 0.0053 | 0.0109 |
Seq30 | 0.1152 | 0.1196 | 0.005 |
Seq31-1 | −0.1705 | −0.166 | 0.0038 |
Seq31-5 | −0.1896 | −0.1853 | 0.0036 |
Seq38-1 | −0.1559 | −0.1526 | 0.0029 |
Seq39-2 | −0.22 | −0.2148 | 0.0043 |
Seq42-2 | −0.27 | −0.2366 | 0.0263 |
Seq49 | −0.157 | −0.1526 | 0.0038 |
Seq51-1 | −0.0467 | −0.0427 | 0.0039 |
Seq53-2 | −0.2752 | −0.2659 | 0.0073 |
Mean | −0.0631 | −0.0476 | 0.0146 |
Generation | F1 | F3 | F4 | F5 | F10 |
---|---|---|---|---|---|
F1 | **** | 0.0034 | 0.0058 | 0.0077 | 0.015 |
F3 | 0.0054 | **** | 0.0055 | 0.0066 | 0.0163 |
F4 | 0.0025 | 0.0091 | **** | 0.0032 | 0.0126 |
F5 | 0.0122 | 0.0106 | 0.0052 | **** | 0.0153 |
F10 | 0.0242 | 0.027 | 0.0211 | 0.0249 | **** |
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Cai, L.; Hou, M.; Xu, C.; Xia, Z.; Wang, J. Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony. Diversity 2020, 12, 483. https://doi.org/10.3390/d12120483
Cai L, Hou M, Xu C, Xia Z, Wang J. Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony. Diversity. 2020; 12(12):483. https://doi.org/10.3390/d12120483
Chicago/Turabian StyleCai, Lei, Miaomiao Hou, Chunsen Xu, Zhijun Xia, and Jianwei Wang. 2020. "Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony" Diversity 12, no. 12: 483. https://doi.org/10.3390/d12120483