Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Isolation and Characterization of Cross-Amplification Microsatellite Loci
2.2. General Discussion of Results
2.2.1. Isolation Strategies for Polymorphic Microsatellite
2.2.2. Genetic Diversity of the Three Procapra Species
3. Experimental Section
3.1. Sample Collection and Genomic DNA Extraction
3.2. Isolation of Microsatellite Markers
3.2.1. Cross-Amplification of Microsatellite Loci from Related Species
3.2.2. Construction of Enriched Genomic Library
3.3. Polymorphisms Assessment
4. Conclusions
Acknowledgments
- Conflict of InterestThe authors declare no conflict of interest in this study.
References
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Locus | Repeat motif | Primer sequences (5′–3′) | Size range (bp) | Tm (°C) | Source |
---|---|---|---|---|---|
AC1 # | (AC)14 | F: TTGGCAGGTGGATTATTTAC R: TGGTTGTCAATGGAAGGAA | 171–199 | 50 | This study |
AC29 # | (AC)14 | F: AGGACGGCACTTAAACTTATG R: TATCATTGTCAGGCTTCTCT | 169–198 | 50 | This study |
AC35 # | (AC)12GAAGTATA T(AC)4 | F: TGGACAGAAGAGCGTAATG R: TCCTTGTGGCTGAGTAGTA | 210–222 | 50 | This study |
AC77 # | (GT)13 | F: CACAGTCTCTTCTCATAATGC R: CGGATTCTTTACCTCATACAC | 147–161 | 50 | This study |
AC91 # | (AC)14 | F: TTGGTCGTACTGACTGGTA R: GGAGTGACTGAGGACAGA | 176–200 | 50 | This study |
AC170 # | (AC)19 | F: TCTCAAGAGGCAGGTCAG R: GATTCCTTTGGCTCCTAGAAG | 230–260 | 50 | This study |
AC230 # | (AC)16ATATGC (AC)6 | F: TGGCTGAGCAACTAAGAG R: GGGAAATACTTGGGTAACAG | 152–168 | 50 | This study |
AC244 # | (AC)6 (GT)14 (T)5G(T)9C(T)9 | F: GGGATAGCAGAGAGTCAGA R: GGAAGGAACAATTAGGAGTATG | 332–350 | 50 | This study |
AC299 # | (AC)5T(AC)8 | F: CGGTGTTCATATAACAGATTCC R: GGTTGCTCAGTGGTCTCA | 159–189 | 50 | This study |
Aam9 † | (GT)15 | F: ATGTGGGAGACTTGATGATG R: AAGACTGGAGACTGGGATTATC | 205–227 | 52 | [44] |
HDZ8 † | (AC)14 | F: GACAAACACTCAGAAGGCAAAG R: GGTGGCAGGACTGAGCAAG | 132–166 | 50 | [45] |
HDZ496 † | (AC)15 | F: GTTTTTCCAGATGGTATTTTCCTC R: GTATTCGGCTGAAGGGACC | 228–250 | 48 | [45] |
MAF23 † | (GT)20 | F: GTGGAGGAATCTTGACTTGTGATAG R: GGCTATAGTCCATGGAGTCGCAG | 124–160 | 50 | [46] |
VH34 † | (AC)17 | F: TCGTAAGAGTGGACACAACTGAGCG R: CGCAGTATTTAGTCCTTTTAATAATGGC | 81–101 | 50 | [46] |
BM4505 † | (ACAT)4(AC)11 | F: TTATCTTGGCTTCTGGGTGC R: ATCTTCACTTGGGATGCAGG | 240–258 | 48 | [47] |
AF5 ‡ | (CA)18 | F: GTGGGAAGAGATAGAGGAAGC R: GAGCCACAAGGCACAGCCAAC | 135–157 | 51 | [43] |
BM1225 ‡ | (CT)13TA(CA)18 | F: TTTCTCAACAGAGGTGTCCAC R: ACCCCTATCACCATGCTCTG | 231–275 | 50 | [43] |
CSSM43 ‡ | (CA)15AT(CT)5 | F: AAAACTCTGGGAACTTGAAAACTA R: GTTACAAATTTAAGAGACAGAGTT | 246–268 | 48 | [43] |
RT1 ‡ | (GT)22 | F: TGCCTTCTTTCATCCAACAA R: CATCTTCCCATCCTCTTTAC | 195–233 | 50 | [43] |
TEXAN-15 ‡ | (CT)9TT(CT)5GCAG ATA(CA)20 | F: TCGCAAACAGTCAGAGACCACTC R: TGGATGAGAAAGAAGAGCAGAGTTG | 203–227 | 50 | [43] |
Locus | No. of samples | No. of alleles | HO | HE | PIC | PHW | Null allele frequency |
---|---|---|---|---|---|---|---|
AC1 | 16 | 6 | 0.500 | 0.772 | 0.709 | 0.010 | 0.209 |
AC29 | 16 | 6 | 0.375 | 0.667 | 0.695 | 0.004 | 0.276 |
AC35 | 16 | 5 | 0.438 | 0.627 | 0.557 | 0.003 | 0.212 |
AC77 | 16 | 6 | 0.000 | 0.807 | 0.748 | 0.000 * | 1.000 |
AC91 | 16 | 8 | 0.625 | 0.851 | 0.801 | 0.004 | 0.145 |
AC170 | 16 | 13 | 1.000 | 0.923 | 0.885 | 0.000 * | −0.057 |
AC230 | 16 | 7 | 0.688 | 0.815 | 0.757 | 0.013 | 0.064 |
AC244 | 16 | 6 | 0.625 | 0.593 | 0.546 | 0.836 | −0.091 |
AC299 | 16 | 9 | 0.813 | 0.859 | 0.814 | 0.038 | 0.014 |
Aam9 | 16 | 7 | 0.813 | 0.829 | 0.776 | 0.252 | −0.008 |
HDZ8 | 16 | 13 | 0.938 | 0.925 | 0.888 | 0.003 | −0.026 |
HDZ496 | 16 | 11 | 0.875 | 0.905 | 0.865 | 0.077 | 0.005 |
MAF23 | 16 | 12 | 0.875 | 0.897 | 0.857 | 0.052 | −0.003 |
VH34 | 16 | 8 | 0.625 | 0.857 | 0.810 | 0.002 | * 0.145 |
BM4505 | 16 | 4 | 0.563 | 0.599 | 0.531 | 0.379 | 0.020 |
AF5 | 16 | 8 | 0.750 | 0.869 | 0.823 | 0.096 | 0.064 |
BM1225 | 16 | 11 | 0.688 | 0.919 | 0.881 | 0.000 * | 0.123 |
CSSM43 | 16 | 3 | 0.938 | 0.643 | 0.552 | 0.029 | −0.223 |
RT1 | 16 | 8 | 0.500 | 0.859 | 0.810 | 0.001 * | 0.242 |
TEXAN-15 | 16 | 9 | 0.625 | 0.871 | 0.825 | 0.000 * | 0.157 |
Locus | No. of samples | No. of alleles | HO | HE | PIC | PHW | Null allele frequency |
---|---|---|---|---|---|---|---|
AC1 | 22 | 12 | 0.864 | 0.904 | 0.872 | 0.010 | 0.009 |
AC29 | 22 | 14 | 0.909 | 0.927 | 0.898 | 0.573 | −0.003 |
AC35 | 22 | 5 | 0.682 | 0.723 | 0.653 | 0.646 | 0.022 |
AC77 | 22 | 5 | 0.500 | 0.661 | 0.610 | 0.150 | 0.133 |
AC91 | 22 | 10 | 0.818 | 0.881 | 0.845 | 0.026 | 0.025 |
AC170 | 22 | 12 | 0.864 | 0.921 | 0.891 | 0.001 * | 0.020 |
AC230 | 22 | 10 | 0.773 | 0.870 | 0.833 | 0.201 | 0.052 |
AC244 | 22 | 15 | 0.818 | 0.914 | 0.884 | 0.119 | 0.044 |
AC299 | 22 | 11 | 0.818 | 0.825 | 0.791 | 0.273 | 0.001 |
Aam9 | 22 | 12 | 0.682 | 0.883 | 0.850 | 0.037 | 0.120 |
HDZ8 | 22 | 12 | 0.818 | 0.793 | 0.759 | 0.610 | −0.058 |
HDZ496 | 22 | 9 | 0.636 | 0.819 | 0.775 | 0.057 | 0.112 |
MAF23 | 22 | 14 | 0.955 | 0.928 | 0.900 | 0.018 | −0.028 |
VH34 | 22 | 10 | 0.727 | 0.764 | 0.726 | 0.521 | 0.020 |
BM4505 | 22 | 4 | 0.500 | 0.602 | 0.542 | 0.075 | 0.063 |
AF5 | 22 | 14 | 0.955 | 0.886 | 0.856 | 0.814 | −0.053 |
BM1225 | 22 | 20 | 0.818 | 0.935 | 0.907 | 0.008 | 0.056 |
CSSM43 | 22 | 8 | 0.864 | 0.804 | 0.754 | 0.981 | −0.048 |
RT1 | 22 | 13 | 0.909 | 0.892 | 0.860 | 0.465 | −0.024 |
TEXAN-15 | 22 | 11 | 0.773 | 0.884 | 0.850 | 0.091 | 0.063 |
Locus | No. of samples | No. of alleles | HO | HE | PIC | PHW | Null allele frequency |
---|---|---|---|---|---|---|---|
AC1 | 15 | 5 | 0.600 | 0.543 | 0.496 | 0.895 | −0.079 |
AC29 | 15 | 5 | 0.933 | 0.786 | 0.721 | 0.470 | −0.112 |
AC35 | 15 | 3 | 0.800 | 0.570 | 0.456 | 0.093 | −0.200 |
AC77 | 15 | 5 | 0.333 | 0.816 | 0.755 | 0.000 * | 0.400 |
AC91 | 15 | 4 | 0.667 | 0.559 | 0.491 | 1.000 | −0.116 |
AC170 | 15 | 5 | 0.733 | 0.793 | 0.728 | 0.101 | 0.025 |
AC230 | 15 | 5 | 0.733 | 0.763 | 0.690 | 0.278 | −0.002 |
AC244 | 15 | 4 | 0.333 | 0.715 | 0.635 | 0.000 * | 0.368 |
AC299 | 15 | 5 | 0.467 | 0.749 | 0.686 | 0.005 | 0.231 |
Aam9 | 15 | 5 | 0.333 | 0.578 | 0.545 | 0.009 | 0.282 |
HDZ8 | 15 | 5 | 0.333 | 0.412 | 0.381 | 0.192 | 0.059 |
HDZ496 | 15 | 4 | 0.600 | 0.524 | 0.432 | 0.000 * | −0.103 |
MAF23 | 15 | 6 | 0.533 | 0.683 | 0.626 | 0.023 | 0.138 |
VH34 | 15 | 6 | 0.800 | 0.749 | 0.686 | 0.921 | −0.041 |
BM4505 | 15 | 4 | 0.800 | 0.733 | 0.656 | 0.215 | −0.071 |
AF5 | 15 | 3 | 0.267 | 0.301 | 0.271 | 0.009 | 0.105 |
BM1225 | 15 | 7 | 0.667 | 0.809 | 0.750 | 0.000 * | 0.079 |
CSSM43 | 15 | 5 | 0.467 | 0.759 | 0.686 | 0.013 | 0.231 |
RT1 | 15 | 5 | 0.600 | 0.575 | 0.520 | 0.104 | −0.026 |
TEAXAN-15 | 15 | 4 | 0.867 | 0.671 | 0.586 | 0.252 | −0.150 |
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Chen, J.; Li, C.; Yang, J.; Luo, Z.; Tang, S.; Li, F.; Li, C.; Liu, B.; Jiang, Z. Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae). Int. J. Mol. Sci. 2012, 13, 8805-8818. https://doi.org/10.3390/ijms13078805
Chen J, Li C, Yang J, Luo Z, Tang S, Li F, Li C, Liu B, Jiang Z. Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae). International Journal of Molecular Sciences. 2012; 13(7):8805-8818. https://doi.org/10.3390/ijms13078805
Chicago/Turabian StyleChen, Jing, Chunlin Li, Ji Yang, Zhenhua Luo, Songhua Tang, Feng Li, Chunwang Li, Bingwan Liu, and Zhigang Jiang. 2012. "Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)" International Journal of Molecular Sciences 13, no. 7: 8805-8818. https://doi.org/10.3390/ijms13078805