Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis)
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Simple Sequence Repeats Mining in the Genome of Himalayan Griffon
2.2. Feather Sampling and DNA Extraction
2.3. SSR Primer Design
2.4. Sample Selection and PCR Amplification
2.5. Capillary Electrophoresis and Data Analysis
3. Results
3.1. Characteristic of Microsatellite Loci in the Genome of G. himalayensis
3.2. Design and Evaluation of SSR Primers
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Motif | Number of SSRs | Proportion (%) | Average Length (bp) | Average Mismatches | Counts/Mbp |
---|---|---|---|---|---|
Mononucleotide | 128,024 | 53.18 | 20.98 | 0.21 | 107.52 |
Dinucleotide | 16,534 | 6.87 | 22.91 | 0.38 | 13.89 |
Trinucleotide | 25,186 | 10.46 | 23.67 | 0.56 | 21.15 |
Tetranucleotide | 31,514 | 13.09 | 19.93 | 0.28 | 26.47 |
Pentanucleotide | 32,804 | 13.63 | 23.97 | 0.31 | 27.55 |
Hexanucleotide | 6679 | 2.77 | 29.85 | 0.69 | 5.61 |
Marker ID | Repeat | * Primer Sequences (5′ → 3′) | Alleles | Size (bp) | PIC # | Heterozygosity | |
---|---|---|---|---|---|---|---|
Expected (He) | Observed (Ho) | ||||||
FHYSSR008 | (aggag)13 | F -tatttccaggtgcagggacc R -tccctctctcatgtcccagg | 8 | 161–206 | 0.817 | 0.836 | 0.5 |
FHYSSR009 | (ccggc)4 | F -ctcgtttgctgatgcctgc R -cccaccacgttacctgagc | 5 | 168–188 | 0.717 | 0.758 | 0.75 |
FHYSSR012 | (cctct)5 | F -gacagctctggatcagctcc R -ctgtcaacaaaacccgtccc | 3 | 174–184 | 0.427 | 0.477 | 0.625 |
FHYSSR016 | (ggctc)4 | F -ggtcagttgtccgcgatcc R -gaggaaccgacccaaccc | 4 | 143–174 | 0.53 | 0.609 | 0.75 |
FHYSSR017 | (gccga)8 | F -ggtctgtgcaccctgagg R -atgcaaggagaggggaggg | 4 | 230–250 | 0.458 | 0.492 | 0.375 |
FHYSSR024 | (gtttg)13 | F -atccaggtttgtcttgggcg R -tgctggctgcttatttcaagc | 4 | 205–222 | 0.644 | 0.695 | 0.625 |
FHYSSR037 | (tg)8 | F -gttaaggactctgatgctgatgc R -acattagacgtgcagcgacc | 3 | 147–152 | 0.294 | 0.32 | 0.375 |
FHYSSR043 | (ca)10 | F -ggtgaccacgtcttactcgg R -gctgtgcaccttgtctttcc | 3 | 177–183 | 0.294 | 0.32 | 0.375 |
FHYSSR044 | (at)11 | F -acaatttcaaggctgcaatgc R -gtctccttcagcatccctcc | 3 | 206–212 | 0.428 | 0.508 | 0.125 |
FHYSSR045 | (tg)12 | F -tcaggatccaacacagtgagc R -ctccctagtgcatcacgtgg | 4 | 187–193 | 0.458 | 0.492 | 0.375 |
FHYSSR046 | (tc)7 | F -cgcctaccctaccccacc R -tgtgcaagtgattaagggattgg | 2 | 168–170 | 0.258 | 0.305 | 0.125 |
FHYSSR048 | (tat)5 | F -cgtttcctgttcacacaagcc R -tgcttaaaacactggacacgc | 2 | 179–188 | 0.375 | 0.5 | 0.25 |
FHYSSR059 | (gct)5 | F -gttcctcagaccgtctctgg R -atgtcagaagctcacctgcg | 3 | 180–189 | 0.521 | 0.586 | 0.5 |
FHYSSR063 | (gag)8 | F -gaaaggttccccggaccg R -ctgcccaagtcctccagc | 2 | 178–181 | 0.384 | 0.43 | 0.375 |
FHYSSR066 | (ttc)9 | F -cagttgttgctgatcgctgg R -gtcctcttctgcagggtgc | 2 | 181–184 | 0.371 | 0.492 | 0.625 |
FHYSSR074 | (act)6 | F -ccccttcttaccttagtgacttcc R -cgactcatagctcttctagtggg | 3 | 183–189 | 0.503 | 0.594 | 0.75 |
FHYSSR095 | (tttg)5 | F -tctggcattgtataccgggc R -tgtcccaaaggtcctttcagg | 2 | 149–153 | 0.337 | 0.43 | 0.375 |
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Guo, W.; Ke, D.; Wang, C.; Fan, H. Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis). Animals 2025, 15, 1438. https://doi.org/10.3390/ani15101438
Guo W, Ke D, Wang C, Fan H. Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis). Animals. 2025; 15(10):1438. https://doi.org/10.3390/ani15101438
Chicago/Turabian StyleGuo, Weibin, Dianhua Ke, Changcao Wang, and Haiying Fan. 2025. "Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis)" Animals 15, no. 10: 1438. https://doi.org/10.3390/ani15101438
APA StyleGuo, W., Ke, D., Wang, C., & Fan, H. (2025). Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis). Animals, 15(10), 1438. https://doi.org/10.3390/ani15101438