High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and DNA Extraction
2.2. Source of Genic Sequences, SSR Identification and Primer Design
2.3. PCR Amplification and Polyacrylamide Gel Electrophoresis
2.4. Data Statistics and Analysis Results
3. Results
3.1. Distribution of the SSRs in the Capsicum Frutescens Genome
3.2. Analysis of the SSR Repeat Motif Types and Frequencies
3.3. Primer Design of the Pepper Plant Genomic SSR Markers
3.4. Polymorphism Analysis with SSR
3.5. Genetic Diversity Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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No. | Primers | Forward Primer Sequence (5′-3′) | Reverse Primer Sequence (5′-3′) | Repeat Unit | Repeat Number |
---|---|---|---|---|---|
1 | Chr1SSR8 | GACTATAGCAAACATGTCCCCAG | CCAGATTTTGTGGATCCTATTGA | TCA | 4 |
2 | Chr1SSR12 | ATTCAAAGAGGGCATGATGTAGA | TGTCAACTTAGTGGGTGGGTTAG | GGTAGG | 6 |
3 | Chr1SSR18 | TTAGTGTTGTCAAAATACCCGTG | CAATAAACATATCACACGTGCAAC | ATAG | 6 |
4 | Chr2SSR12 | GAAAGATCCGTCTAAGCAAACAA | AAATCTCATGATTTTCGGTGATG | AAT | 4 |
5 | Chr2SSR14 | TGAATTTCGGAGTGTTACGTAGAG | GCGAAGGTGAGTCTGTTCAATTA | TAA | 4 |
6 | Chr2SSR15 | AATTTGAAGAGCGTGCATAAAAA | ACCATACCATACCATGGAAACAA | ATGGT | 4 |
7 | Chr3SSR5 | ATAAAATAGACCCCACCCACTTC | GGGCTGCTGTACTAAAGAAGAAGA | TTC | 4 |
8 | Chr3SSR6 | CTCTCTAGAATGAAAAGTGCCGA | TTGTCGATTTGTTCTTCTTCCAT | CAC | 4 |
9 | Chr3SSR13 | ACCCTAAAAGCTATGGAGTTGCT | CCCACCATTCTTCTAAACTTTCC | AC | 6 |
10 | Chr4SSR11 | CCTACAAGTGAGGTCTGAGGAGA | CAGCAAGTTGGAGAAACTAATGC | ACCCT | 4 |
11 | Chr4SSR14 | AGTGGAAAGTGCTGTTACGATGT | GCGTGATAATTTTTCCACAAGAA | TTTA | 5 |
12 | Chr4SSR20 | AAAACAACACGACACACAGCTTA | TATATTTTTCTTGGGAACGAGCA | TATAT | 6 |
13 | Chr5SSR13 | TAAAACCTTGTCACATGTACCCC | AAATGAATAAATCCTCTGCATGG | TGCA | 4 |
14 | Chr5SSR14 | TAAGTTGTTCGAGAAATCAGACG | CTGTCTCGTATTGAAGGGTGTTT | CGGTGA | 4 |
15 | Chr5SSR16 | CACTGTGAGAGCAACTTTCTGTG | CACTATTTTCTCATGCACTTTACCA | ACGGGC | 4 |
16 | Chr6SSR12 | TTCGACCTCCGTATCACTATCAG | CGTACTCTATCGCTTGTTGCTTT | ACTC | 7 |
17 | Chr6SSR17 | TCTGAAAAATCCTCGGCTAAAGT | ACTGTCCCACCTTACATCCCTAT | AAAAG | 5 |
18 | Chr6SSR19 | CAGAGGCAGTTAGGTAGTAGCGA | TGCTAAACCCACCTTCAGTCTTA | GGATTC | 4 |
19 | Chr6SSR20 | TCTGCTTTCCCACAGTATCTCTC | TCAACAGATAAGCGTCAAGTGAA | TCACCA | 4 |
20 | Chr7SSR2 | CTGCTTAAAAAGTTGAAGATGAGAA | TTGATACGCTAATAAAATTGTTGAAA | AAT | 4 |
21 | Chr7SSR15 | GCCTGGCATGTTTTGTATTTCTA | TTTGGTGACCGACAATATAAAGG | ATT | 4 |
22 | Chr8SSR6 | TGAGTCAAGAAAACTTGCAGAAA | TTTGAAAATAATTGAAGTTCCGC | AAAGCA | 4 |
23 | Chr8SSR13 | TAGATGTTGAACCCCTATTGGAA | GGTAGAGGGTAGAGTGTACGCAG | TACCAC | 4 |
24 | Chr8SSR15 | GGTGTCATGCGTAAGCTCATAGT | GGTGTCATGCGTAAGCTCATAGT | GAGTTG | 4 |
25 | Chr9SSR16 | CCCCACCGATGAATTTAGTAGA | TGATGATGTGTCATGGTGTATGA | CCCCCA | 4 |
26 | Chr9SSR17 | ATTCCCCATATCGAAACTTCTTC | AAATCAAGGAGACGATTGTTGAA | CTGGTG | 5 |
27 | Chr10SSR12 | ACGAGAGTTTGCTTTCTTTTCCT | TCAGAGGTAGAGGTATGGACTGC | AAC | 4 |
28 | Chr10SSR14 | TTTTTCAGGCTTTTGTGTATGTAAA | CGGAAACAACCTCTCTACTTCAG | CAA | 5 |
29 | Chr11SSR4 | AATTTTCAACAACAAACTCCACG | CAGCAGTGAGGATGAAAAAGTTTA | GAG | 4 |
30 | Chr11SSR14 | TTTTAACTTTTTGTAATTTCGTGTCA | ATCCAATTTTGTTAGGCCTATTG | ATCAAA | 4 |
31 | Chr11SSR16 | ACGAGTGAACACGTACATGAAAA | GGTAGGAGCTAGGAGTAGTGACG | TTA | 6 |
32 | Chr12SSR10 | AAAAGGGACTTGTTTTCCTATCA | AAATGGGAATGCGATTATCTAAA | AAAAAT | 4 |
33 | Chr12SSR19 | TCTTTCCTTCGGATTAAGTTTCC | GAGGCAAGAAATAAGAGATGCCT | CAAATC | 4 |
Primer | Allele Size | Na | Ne | MAF | Ho | He | I | PIC | Gene Diversity |
---|---|---|---|---|---|---|---|---|---|
Chr1SSR8 | 134 | 2.0000 | 1.0615 | 0.9701 | 0.0000 | 0.0584 | 0.1342 | 0.0562 | 0.0579 |
Chr1SSR12 | 294 | 3.0000 | 1.2132 | 0.9048 | 0.1837 | 0.1763 | 0.3680 | 0.1665 | 0.1757 |
Chr1SSR18 | 278 | 4.0000 | 2.7999 | 0.4532 | 0.0360 | 0.6452 | 1.1545 | 0.5758 | 0.6428 |
Chr2SSR12 | 286 | 2.0000 | 1.1104 | 0.9476 | 0.0350 | 0.0997 | 0.2057 | 0.0945 | 0.0994 |
Chr2SSR14 | 294 | 2.0000 | 1.1764 | 0.9184 | 0.0272 | 0.1504 | 0.2827 | 0.1387 | 0.1499 |
Chr2SSR15 | 278 | 3.0000 | 1.3743 | 0.8417 | 0.2014 | 0.2733 | 0.4998 | 0.2452 | 0.2723 |
Chr3SSR5 | 286 | 2.0000 | 1.1259 | 0.9406 | 0.1189 | 0.1122 | 0.2254 | 0.1056 | 0.1118 |
Chr3SSR6 | 290 | 2.0000 | 1.3729 | 0.8379 | 0.0345 | 0.2725 | 0.4431 | 0.2347 | 0.2716 |
Chr3SSR13 | 272 | 3.0000 | 1.4543 | 0.8162 | 0.2059 | 0.3135 | 0.5784 | 0.2837 | 0.3124 |
Chr4SSR11 | 290 | 2.0000 | 1.1012 | 0.9517 | 0.0000 | 0.0922 | 0.1934 | 0.0877 | 0.0919 |
Chr4SSR14 | 204 | 3.0000 | 2.1276 | 0.5392 | 0.0588 | 0.5326 | 0.8242 | 0.4252 | 0.5300 |
Chr4SSR20 | 292 | 6.0000 | 2.3599 | 0.5822 | 0.0137 | 0.5782 | 1.0946 | 0.5175 | 0.5763 |
Chr5SSR13 | 282 | 2.0000 | 1.4302 | 0.8156 | 0.3404 | 0.3019 | 0.4780 | 0.2556 | 0.3008 |
Chr5SSR14 | 278 | 2.0000 | 1.0516 | 0.9748 | 0.0216 | 0.0493 | 0.1176 | 0.0479 | 0.0491 |
Chr5SSR16 | 292 | 3.0000 | 2.1992 | 0.5068 | 0.9863 | 0.5472 | 0.8578 | 0.4426 | 0.5453 |
Chr6SSR12 | 248 | 2.0000 | 1.9541 | 0.5766 | 0.0081 | 0.4902 | 0.6814 | 0.3691 | 0.4883 |
Chr6SSR17 | 288 | 3.0000 | 1.1656 | 0.9236 | 0.0000 | 0.1426 | 0.2931 | 0.1338 | 0.1421 |
Chr6SSR19 | 294 | 3.0000 | 1.3276 | 0.8571 | 0.0136 | 0.2476 | 0.4375 | 0.2195 | 0.2467 |
Chr6SSR20 | 280 | 2.0000 | 1.0894 | 0.9571 | 0.0857 | 0.0823 | 0.1769 | 0.0787 | 0.0820 |
Chr7SSR2 | 282 | 2.0000 | 1.0288 | 0.9858 | 0.0000 | 0.0281 | 0.0744 | 0.0276 | 0.0280 |
Chr7SSR15 | 294 | 4.0000 | 3.6226 | 0.3231 | 0.0476 | 0.7264 | 1.3273 | 0.6718 | 0.7240 |
Chr8SSR6 | 288 | 2.0000 | 1.5732 | 0.7604 | 0.0486 | 0.3656 | 0.5506 | 0.2980 | 0.3644 |
Chr8SSR13 | 294 | 3.0000 | 1.4308 | 0.8265 | 0.1361 | 0.3021 | 0.5775 | 0.2795 | 0.3011 |
Chr8SSR15 | 286 | 4.0000 | 3.4282 | 0.4021 | 0.0699 | 0.7108 | 1.3023 | 0.6566 | 0.7083 |
Chr9SSR16 | 250 | 2.0000 | 1.9678 | 0.5640 | 0.0560 | 0.4938 | 0.6849 | 0.3709 | 0.4918 |
Chr9SSR17 | 294 | 3.0000 | 1.6031 | 0.7721 | 0.0748 | 0.3775 | 0.6873 | 0.3430 | 0.3762 |
Chr10SSR12 | 270 | 4.0000 | 3.5014 | 0.3556 | 0.0000 | 0.7171 | 1.3058 | 0.6606 | 0.7144 |
Chr10SSR14 | 292 | 2.0000 | 1.5026 | 0.7877 | 0.0411 | 0.3356 | 0.5170 | 0.2785 | 0.3345 |
Chr11SSR4 | 292 | 3.0000 | 1.3060 | 0.8699 | 0.0000 | 0.2351 | 0.4723 | 0.2206 | 0.2343 |
Chr11SSR14 | 76 | 2.0000 | 1.2321 | 0.8947 | 0.0000 | 0.1909 | 0.3365 | 0.1706 | 0.1884 |
Chr11SSR16 | 294 | 2.0000 | 1.7306 | 0.6973 | 0.0884 | 0.4236 | 0.6132 | 0.3331 | 0.4222 |
Chr12SSR10 | 278 | 3.0000 | 2.5179 | 0.4928 | 0.1007 | 0.6050 | 0.9921 | 0.5226 | 0.6028 |
Chr12SSR19 | 294 | 4.0000 | 1.3399 | 0.8571 | 0.2313 | 0.2546 | 0.5140 | 0.2366 | 0.2537 |
Mean | 271 | 2.7576 | 1.7055 | 0.7547 | 0.0989 | 0.3313 | 0.5758 | 0.2893 | 0.3300 |
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Zhong, Y.; Cheng, Y.; Ruan, M.; Ye, Q.; Wang, R.; Yao, Z.; Zhou, G.; Liu, J.; Yu, J.; Wan, H. High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens. Horticulturae 2021, 7, 187. https://doi.org/10.3390/horticulturae7070187
Zhong Y, Cheng Y, Ruan M, Ye Q, Wang R, Yao Z, Zhou G, Liu J, Yu J, Wan H. High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens. Horticulturae. 2021; 7(7):187. https://doi.org/10.3390/horticulturae7070187
Chicago/Turabian StyleZhong, Yangmin, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao, Guozhi Zhou, Jia Liu, Jiahong Yu, and Hongjian Wan. 2021. "High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens" Horticulturae 7, no. 7: 187. https://doi.org/10.3390/horticulturae7070187