Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction and SNP Genotyping
2.3. Quality Control of Data
2.4. Calculation of Inbreeding Coefficient
2.5. Detection of ROH Islands
3. Results
3.1. Runs of Homozygosity Analysis
3.2. Genomic Inbreeding Coefficients
3.3. Gene Annotation
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Populations | Statistics | ROH Length Category (Mb) | |||||
---|---|---|---|---|---|---|---|
1+ | 2+ | 4+ | 8+ | 16+ | |||
POP1 n = 95 | Number of ROHs per animal | Mean | 40.3 | 6.9 | 3.2 | 2.4 | 2.1 |
SD | 6.8 | 3.0 | 2.7 | 1.9 | 1.2 | ||
Min | 26 | 1 | 0 | 0 | 0 | ||
Max | 58 | 15 | 12 | 8 | 5 | ||
Length of ROHs per animal (Mb) | Mean | 51.4 | 18.7 | 17.2 | 26.2 | 41.4 | |
SD | 8.9 | 8.3 | 15.1 | 21.4 | 25.0 | ||
Min | 31.2 | 2.2 | 0 | 0 | 0 | ||
Max | 74.4 | 41.8 | 68.8 | 96.5 | 101.5 | ||
POP2 n = 115 | Number of ROHs per animal | Mean | 42.2 | 8.0 | 3.9 | 3.2 | 1.6 |
SD | 11.0 | 5.0 | 3.4 | 3.0 | 1.1 | ||
Min | 17 | 1 | 0 | 0 | 0 | ||
Max | 102 | 30 | 16 | 14 | 5 | ||
Length of ROHs per animal (Mb) | Mean | 54.1 | 21.5 | 21.4 | 35.3 | 31.8 | |
SD | 14.6 | 14.1 | 19.3 | 33.1 | 22.5 | ||
Min | 22.5 | 2.1 | 0 | 0 | 0 | ||
Max | 133.5 | 85.2 | 85.6 | 143.7 | 100.2 | ||
POP3 n = 71 | Number of ROHs per animal | Mean | 40.7 | 6.4 | 2.3 | 1.8 | 1.1 |
SD | 8.5 | 3.5 | 1.7 | 1.1 | 0.4 | ||
Min | 24 | 1 | 0 | 0 | 0 | ||
Max | 83 | 23 | 7 | 4 | 2 | ||
Length of ROHs per animal (Mb) | Mean | 52.5 | 17.3 | 12.5 | 19.6 | 19.9 | |
SD | 11.5 | 9.2 | 9.3 | 14.7 | 5.7 | ||
Min | 30.3 | 2.3 | 0 | 0 | 0 | ||
Max | 112 | 58.6 | 38.5 | 53.6 | 33.8 |
Population | FROH > 1 Mb | FROH > 2 Mb | FROH > 4 Mb | FROH > 8 Mb | FROH > 16 Mb |
---|---|---|---|---|---|
Pop1 | 0.042 | 0.021 | 0.016 | 0.017 | 0.017 |
Pop2 | 0.047 | 0.025 | 0.019 | 0.020 | 0.013 |
Pop3 | 0.036 | 0.014 | 0.009 | 0.010 | 0.008 |
CHR | nSNP | Start, Mb | End, Mb | Candidate Genes |
---|---|---|---|---|
1 | 78 | 130.47 | 135.69 | TIAM1 |
2 | 36 | 218.8 | 219.93 | BMPR2 |
3 | 20 | 182.28 | 183.49 | MYBPC1 |
4 | 24 | 42.18 | 43.2 | CACNA2D1 |
6 | 21 | 78.04 | 79.31 | CLOCK |
6 | 33 | 33.61 | 35 | BMPR1B |
13 | 19 | 50.59 | 51.89 | BMP2 |
13 | 204 | 0.12 | 8.87 | TASP1 |
17 | 87 | 60.65 | 64.98 | KDM2B |
23 | 28 | 41.93 | 43.98 | MYOM1 |
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Amandykova, M.; Akhatayeva, Z.; Kozhakhmet, A.; Kapassuly, T.; Orazymbetova, Z.; Yergali, K.; Khamzin, K.; Iskakov, K.; Dossybayev, K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed. Genes 2023, 14, 1988. https://doi.org/10.3390/genes14111988
Amandykova M, Akhatayeva Z, Kozhakhmet A, Kapassuly T, Orazymbetova Z, Yergali K, Khamzin K, Iskakov K, Dossybayev K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed. Genes. 2023; 14(11):1988. https://doi.org/10.3390/genes14111988
Chicago/Turabian StyleAmandykova, Makpal, Zhanerke Akhatayeva, Altynay Kozhakhmet, Tilek Kapassuly, Zarina Orazymbetova, Kanagat Yergali, Kadyrzhan Khamzin, Kairat Iskakov, and Kairat Dossybayev. 2023. "Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed" Genes 14, no. 11: 1988. https://doi.org/10.3390/genes14111988
APA StyleAmandykova, M., Akhatayeva, Z., Kozhakhmet, A., Kapassuly, T., Orazymbetova, Z., Yergali, K., Khamzin, K., Iskakov, K., & Dossybayev, K. (2023). Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed. Genes, 14(11), 1988. https://doi.org/10.3390/genes14111988