Population Genomics and Application for Growth Improvement of Domesticated Asian Seabass Lates calcarifer from Thailand
Abstract
:1. Introduction
2. Materials and Methods
2.1. Stock Maintenance and Rearing
2.2. Estimation of EBVs for Growth
2.3. DNA Extraction
2.4. SLAF-Sequencing
2.5. Population Genomics Data Analysis
3. Results
3.1. EBVs for Growth of L. calcarifer G0
3.2. SLAF-Seq Library Preparation and Processing
3.3. Intrapopulation Diversity of Domesticated L. calcarifer
3.4. Phylogenetic Analysis and PCA
3.5. Relatedness Between HEBV and LEBV Populations of Domesticated L. calcarifer
3.6. Selective Sweep, GO, and KEGG Enrichment Analysis
3.7. Genetic Distance and Population Admixture Analysis
4. Discussion
4.1. Population Genomic Studies of Domesticated L. calcarifer
4.2. Genetic Differentiation of HEBV and LEBV Populations
4.3. Selective Sweep Analysis Implied Different Performance of Fast- and Slow-Growing L. calcarifer
4.4. Application of Population Admixture Analysis for Genetic Improvement of L. calcarifer
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
SLAF-Seq | Specific Locus Amplified Fragment Sequencing (SLAF-Seq) |
HEBVs | High estimated breeding values |
LEBVs | Low estimated breeding values |
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Parameter | HEBVs | LEBVs | Parent |
---|---|---|---|
Total reads | 1,706,574–24,836,624 (5,380,913.85) | 1,802,730–23,074,886 (5,170,992.62) | 1,704,794–29,396,770 (5,106,726.10) |
Q30 (%) | 90.52–97.09 (95.76) | 89.49–96.95 (95.54) | 88.17–97.01 (95.59) |
GC (%) | 32.1–42.7 (40.41) | 34.77–42.96 (38.74) | 31.38–43.16 (40.68) |
Total depth | 674,159–11,042,360 (2,322,203.03) | 809,377–10,621,017 (2,224,944.23) | 772,403–13,495,035 (2,117,953.73) |
Average depth | 5.3671–85.2515 (14.51) | 5.7312–72.7642 (15.8) | 5.0578–53.9756 (12.78) |
Mapped (%) | 96.91–99.8 (99.49) | 98.81–99.8 (99.52) | 95.53–99.84 (99.47) |
Properly mapped (%) | 84.15–97.62 (89.31) | 83.75–98.85 (89.21) | 83.89–98.75 (90.86) |
SLAF number | 42,827–263,201 (162,972.89) | 63,899–250,664 (131,852.73) | 32,906–251,003 (161,807.99) |
Chromosome ID | SLAF Number | Polymorphic SLAF |
---|---|---|
1 | 15,327 | 10,308 |
2 | 18,867 | 13,022 |
3 | 14,122 | 9825 |
4 | 15,526 | 10,970 |
5 | 17,332 | 11,869 |
6 | 17,375 | 11,640 |
7_1 | 14,088 | 9919 |
7_2 | 8477 | 6002 |
8 | 15,872 | 11,071 |
9 | 13,833 | 9575 |
10 | 16,906 | 11,689 |
11 | 14,142 | 9957 |
12 | 16,918 | 10,826 |
13 | 17,046 | 12,171 |
14 | 8118 | 5645 |
15 | 18,876 | 13,175 |
16_LG22 | 15,294 | 10,305 |
17 | 16,844 | 11,503 |
18 | 11,649 | 8280 |
19 | 15,098 | 9270 |
20 | 14,805 | 10,445 |
21 | 17,633 | 12,211 |
23 | 11,076 | 7715 |
24 | 11,924 | 7999 |
Parameters/Group | HEBVs | LEBVs | Parent |
---|---|---|---|
Average MAF | 0.220 | 0.167 | 0.217 |
No. of polymorphic markers | 221,949 | 214,420 | 206,202 |
Observed no. of allele (Ao) | 1.000–2.000 (1.984) | 1.000–2.000 (1.951) | 1.000–2.000 (1.914) |
Expected no. of allele (Ae) | 1.000–2.000 (1.497) | 1.000–2.000 (1.363) | 1.000–2.000 (1.455) |
Observed heterozygosity (Ho) | 0.008–0.992 (0.224) | 0.007–0.986 (0.178) | 0.038–1.000 (0.184) |
Expected heterozygosity (He) | 0.007–0.500 (0.308) | 0.007–0.500 (0.246) | 0.038–0.500 (0.305) |
PIC | 0.007–0.375 (0.251) | 0.007–0.375 (0.205) | 0.037–0.375 (0.249) |
Nei diversity index | 0.008–0.505 (0.309) | 0.007–0.505 (0.247) | 0.038–0.667 (0.317) |
Shannon Wiener index | 0.025–0.693(0.472) | 0.023–0.693(0.392) | 0.095–0.693 (0.470) |
Value | Count | Percentage |
---|---|---|
−0.6–−0.4 | 2570 | 5.489 |
−0.4–−0.2 | 1505 | 3.215 |
−0.2–0.0 | 28,063 | 59.941 |
0.0–0.2 | 7367 | 15.735 |
0.2–0.4 | 4542 | 9.701 |
0.4–0.6 | 2184 | 4.665 |
0.6–0.8 | 220 | 0.470 |
0.8–1.0 | 114 | 0.243 |
1.0–1.2 | 126.5 | 0.270 |
1.2–1.4 | 89 | 0.190 |
1.4–1.6 | 10 | 0.021 |
1.6–1.8 | 1.5 | 0.003 |
1.8–2.0 | 5.5 | 0.012 |
2.0–2.2 | 8.5 | 0.018 |
2.2–2.4 | 7.5 | 0.016 |
2.4–2.6 | 4.5 | 0.010 |
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Khamnamtong, B.; Chaimongkol, A.; Prasertlux, S.; Janpoom, S.; Chaimongkol, J.; Tang, S.; Ittarat, W.; Songsangjinda, P.; Sakamoto, T.; Sae-Lim, P.; et al. Population Genomics and Application for Growth Improvement of Domesticated Asian Seabass Lates calcarifer from Thailand. Diversity 2025, 17, 383. https://doi.org/10.3390/d17060383
Khamnamtong B, Chaimongkol A, Prasertlux S, Janpoom S, Chaimongkol J, Tang S, Ittarat W, Songsangjinda P, Sakamoto T, Sae-Lim P, et al. Population Genomics and Application for Growth Improvement of Domesticated Asian Seabass Lates calcarifer from Thailand. Diversity. 2025; 17(6):383. https://doi.org/10.3390/d17060383
Chicago/Turabian StyleKhamnamtong, Bavornlak, Atra Chaimongkol, Sirikan Prasertlux, Sirithorn Janpoom, Jutaporn Chaimongkol, Sureerat Tang, Wanwipa Ittarat, Putth Songsangjinda, Takashi Sakamoto, Panya Sae-Lim, and et al. 2025. "Population Genomics and Application for Growth Improvement of Domesticated Asian Seabass Lates calcarifer from Thailand" Diversity 17, no. 6: 383. https://doi.org/10.3390/d17060383
APA StyleKhamnamtong, B., Chaimongkol, A., Prasertlux, S., Janpoom, S., Chaimongkol, J., Tang, S., Ittarat, W., Songsangjinda, P., Sakamoto, T., Sae-Lim, P., & Klinbunga, S. (2025). Population Genomics and Application for Growth Improvement of Domesticated Asian Seabass Lates calcarifer from Thailand. Diversity, 17(6), 383. https://doi.org/10.3390/d17060383