Genetic Diversity Analysis and Core Collection Construction of the Actinidia chinensis Complex (Kiwifruit) Based on SSR Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and DNA Extraction
2.2. SSR Primer Screening and Genotyping
2.3. Analysis of Genetic Diversity and Genetic Structure
2.4. Construction and Evaluation of the Core Collection
3. Results
3.1. Genetic Diversity and Variation of the A. chinensis Complex
3.2. Cluster Analysis of the A. chinensis Complex
3.3. Genetic Structure of the A. chinensis Complex
3.4. Core Collection of the A. chinensis Complex
3.4.1. Construction of the Core Collection
3.4.2. Verification of the Core Collection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Locus | Na | Ne | Ho | He | PIC | I | Fis |
---|---|---|---|---|---|---|---|
A-Geo101 | 25 | 12.317 | 0.712 | 0.919 | 0.913 | 2.677 | 0.225 |
A-Geo114 | 28 | 7.392 | 0.665 | 0.865 | 0.855 | 2.485 | 0.23 |
A-Geo131 | 22 | 4.554 | 0.499 | 0.78 | 0.764 | 2.078 | 0.36 |
A-Geo014 | 28 | 12.012 | 0.7 | 0.917 | 0.911 | 2.71 | 0.236 |
A-Geo142 | 21 | 10.792 | 0.732 | 0.907 | 0.9 | 2.6 | 0.194 |
A-Geo156 | 38 | 15.964 | 0.599 | 0.937 | 0.934 | 3.106 | 0.361 |
A-Geo158 | 22 | 13.153 | 0.789 | 0.924 | 0.919 | 2.717 | 0.146 |
A-Geo167 | 16 | 2.448 | 0.612 | 0.591 | 0.571 | 1.461 | −0.034 |
A-Geo018 | 18 | 8.358 | 0.606 | 0.88 | 0.87 | 2.365 | 0.312 |
A-Geo188 | 26 | 12.697 | 0.687 | 0.921 | 0.916 | 2.782 | 0.254 |
A-Geo198 | 23 | 7.788 | 0.645 | 0.872 | 0.86 | 2.38 | 0.259 |
A-Geo218 | 19 | 5.226 | 0.628 | 0.809 | 0.793 | 2.098 | 0.223 |
A-Geo229 | 32 | 14.543 | 0.673 | 0.931 | 0.927 | 2.969 | 0.277 |
A-Geo249 | 21 | 9.654 | 0.67 | 0.896 | 0.888 | 2.503 | 0.252 |
A-Geo257 | 19 | 10.17 | 0.683 | 0.902 | 0.893 | 2.496 | 0.243 |
A-Geo266 | 20 | 4.45 | 0.61 | 0.775 | 0.758 | 2.059 | 0.213 |
A-Geo275 | 20 | 3.678 | 0.495 | 0.728 | 0.707 | 1.834 | 0.32 |
A-Geo290 | 22 | 10.877 | 0.665 | 0.908 | 0.901 | 2.57 | 0.268 |
A-Geo293 | 21 | 10.728 | 0.617 | 0.907 | 0.9 | 2.587 | 0.319 |
A-Geo302 | 23 | 11.647 | 0.655 | 0.914 | 0.908 | 2.634 | 0.284 |
A-Geo307 | 20 | 11.45 | 0.731 | 0.913 | 0.906 | 2.572 | 0.199 |
A-Geo316 | 22 | 9.692 | 0.606 | 0.897 | 0.888 | 2.463 | 0.324 |
A-Geo323 | 15 | 1.721 | 0.497 | 0.419 | 0.41 | 1.091 | −0.186 |
A-Geo335 | 21 | 11.157 | 0.683 | 0.91 | 0.904 | 2.617 | 0.249 |
A-Geo341 | 20 | 7.343 | 0.626 | 0.864 | 0.852 | 2.336 | 0.275 |
A-Geo350 | 22 | 8.995 | 0.607 | 0.889 | 0.879 | 2.45 | 0.317 |
A-Geo365 | 19 | 7.945 | 0.647 | 0.874 | 0.863 | 2.35 | 0.26 |
A-Geo369 | 14 | 1.901 | 0.347 | 0.474 | 0.448 | 1.076 | 0.269 |
A-Geo377 | 18 | 7.377 | 0.63 | 0.864 | 0.853 | 2.322 | 0.272 |
A-Geo038 | 29 | 7.166 | 0.659 | 0.86 | 0.849 | 2.469 | 0.235 |
A-Geo393 | 20 | 10.711 | 0.549 | 0.907 | 0.899 | 2.555 | 0.395 |
A-Geo401 | 21 | 7.018 | 0.644 | 0.858 | 0.842 | 2.22 | 0.249 |
A-Geo407 | 26 | 13.683 | 0.657 | 0.927 | 0.922 | 2.82 | 0.291 |
A-Geo415 | 18 | 7.864 | 0.632 | 0.873 | 0.861 | 2.33 | 0.276 |
A-Geo042 | 16 | 7.81 | 0.606 | 0.872 | 0.859 | 2.264 | 0.305 |
A-Geo426 | 24 | 11.999 | 0.716 | 0.917 | 0.911 | 2.693 | 0.219 |
A-Geo427 | 21 | 3.301 | 0.479 | 0.697 | 0.684 | 1.873 | 0.312 |
A-Geo054 | 31 | 14.269 | 0.711 | 0.93 | 0.926 | 2.878 | 0.236 |
A-Geo068 | 23 | 3.974 | 0.597 | 0.748 | 0.729 | 1.97 | 0.202 |
A-Geo083 | 24 | 6.5 | 0.32 | 0.846 | 0.832 | 2.318 | 0.622 |
Mean | 22.2 | 8.758 | 0.622 | 0.846 | 0.835 | 2.369 | 0.257 |
Population | n | Na | Ne | Ho | He | PIC | I | Fis |
---|---|---|---|---|---|---|---|---|
A. chinensis | 240 | 21.725 | 8.689 | 0.625 | 0.849 | 0.838 | 2.367 | 0.257 |
A. deliciosa | 54 | 17.150 | 6.442 | 0.611 | 0.786 | 0.771 | 2.086 | 0.225 |
Mean | 19.438 | 7.566 | 0.618 | 0.818 | 0.805 | 2.227 | 0.241 |
Source of Variation | Degrees of Freedom | Sum of Square | Mean of Square | Variance Component | Percentage of Variation (%) | p |
---|---|---|---|---|---|---|
Among variants | 1 | 259.56 | 259.56 | 2.13 | 2.90 | <0.001 |
Within variants | 292 | 20,869 | 71.47 | 71.47 | 97.10 | <0.001 |
Total | 293 | 21,128.56 | - | 73.60 | 100 | - |
Number | Name | Code | Variant | Category | Selection Method |
---|---|---|---|---|---|
1 | CSXZSIII | 3-0-2-4 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
2 | CXHY4 | 3-2-24 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
3 | Taibao No. 2 | 4-1-1-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
4 | Jinyang | 4-3-1-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
5 | Jinyi | 4-3-2-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
6 | Kuimi | 4-3-3-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
7 | Huayou | 4-4-2-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
8 | DH-1 | 4-6-5-2N | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
9 | DD-111 | 4-7-5-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
10 | Hongyang | 4-8-4-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
11 | Fengyue | 4-9-2-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
12 | Wanjin | 5-10-1-3 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
13 | Chuhong | 5-11-3-4 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
14 | Jinxia | 5-2-2-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
15 | Hort16A | 5-4-2-4 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
16 | Cuiyu | 5-7-2-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
17 | Taishanghuang | 5-8-1-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
18 | ZH8792 ♂ | 8-9-7-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
19 | FC-1-1-4 | A-13-2-3 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
20 | XB-48-2-10 | A-1-6-3 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
21 | XB-49-5-9 | A-2-5-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
22 | XB-51-1-3 | A-3-6-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
23 | CD-19-1-28 | B-20-1-1 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
24 | Wanmi | 5-8-2-2 | A. chinensis var. chinensis | Cultivars (lines) | PowerCore |
25 | P610726070 | 5-8-4-1 | A. chinensis var. chinensis | Wild resources | PowerCore |
26 | 17-SCLS-41 | A-10-2-1 | A. chinensis var. chinensis | Wild resources | PowerCore |
27 | 17-SCLS-50 | A-11-5-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
28 | 18-ANXN-31 | A-5-2-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
29 | 18-ANXN-33 | A-5-3-4 | A. chinensis var. chinensis | Wild resources | PowerCore |
30 | 17-SCLS-2 | A-5-5-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
31 | 17-SCLS-33 | A-9-2-1 | A. chinensis var. chinensis | Wild resources | PowerCore |
32 | 18-HN-1 | B-22-1-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
33 | 18-HN-13 | B-23-1-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
34 | 18-ZHLS-1 | B-23-6-5 | A. chinensis var. chinensis | Wild resources | PowerCore |
35 | 17-ZET-2 | B-25-7-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
36 | JXRJ | B-27-5-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
37 | YSZY44 ♂ | B-29-2-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
38 | 18-AHJX-02 | B-30-3-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
39 | 18-AHJX-04 | B-30-4-5 | A. chinensis var. chinensis | Wild resources | PowerCore |
40 | 18-AHQM-12 | B-31-7-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
41 | 18-AHQM-21 | B-32-2-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
42 | 18-AHQM-25 | B-32-3-5 | A. chinensis var. chinensis | Wild resources | PowerCore |
43 | 18-AHQM-28 | B-32-5-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
44 | 18-AHQS-07 | B-32-7-5 | A. chinensis var. chinensis | Wild resources | PowerCore |
45 | 18-AHQS-08 | B-32-8-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
46 | 18-AHQS-06 | B-33-1-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
47 | 18-AHQS-10 | B-33-3-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
48 | 18-AHQS-22 | B-33-7-5 | A. chinensis var. chinensis | Wild resources | PowerCore |
49 | 18-AHQY-19 | B-34-5-2 | A. chinensis var. chinensis | Wild resources | PowerCore |
50 | 18-AHXN-11 | B-35-2-4 | A. chinensis var. chinensis | Wild resources | PowerCore |
51 | 18-AHXN-12 | B-35-3-3 | A. chinensis var. chinensis | Wild resources | PowerCore |
52 | 18-AHXN-13 | B-35-3-4 | A. chinensis var. chinensis | Wild resources | PowerCore |
53 | 18-AHXN-16 | B-35-4-1 | A. chinensis var. chinensis | Wild resources | PowerCore |
54 | 18-AHXN-20 | B-35-4-4 | A. chinensis var. chinensis | Wild resources | PowerCore |
55 | Donghong | 3-10-9 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
56 | Moshan No. 2 ♂ | 3-7-4-2 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
57 | Lushanxiang | 4-1-4-2 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
58 | Tongshan 5 | 4-2-1-1S | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
59 | Moshan No. 4 | 4-2-2-2N | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
60 | Jinnong | 4-2-4-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
61 | Moshan No. 1 ♂ | 4-3-3-2 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
62 | Zaoxian | 4-4-1-1N | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
63 | Huabao No. 1 | 4-6-1-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
64 | Golden peach | 4-6-11-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
65 | Xiaya No. 1 | 4-6-4-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
66 | Guihai No. 4 | 4-8-1-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
67 | Moshan No. 7 ♂ | 4-8-1-2 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
68 | Jinyuan | 2-2-3-3 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
69 | Jinyan | 4-8-10-2 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
70 | Jinmei | 7-2-3-1 | A. chinensis var. chinensis | Cultivars (lines) | Supplementary cultivar |
71 | Jinmei | 2-4-3-2 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
72 | Longshanhong | 4-12-5-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
73 | Xinguan No. 2 | 4-3-5-2E | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
74 | Shixuana No. 2 | 4-4-5-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
75 | Dongmei | 4-5-1-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
76 | Qinxiang | 4-5-2-1N | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
77 | Chang’an No. 1 | 4-6-3-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
78 | Xiangma No. 6 | 4-6-4-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
79 | Xuxiang | 4-7-3-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
80 | Chuanmi No. 1 | 4-7-4-2 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
81 | Xuxiang ♂ | 4-8-4-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
82 | Qinmei | 5-10-4-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
83 | Guichang | 5-11-6-3 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
84 | Hayward | 5-9-1-4 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
85 | Huamei No. 1 | 5-9-2-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
86 | 18-20161395 | B-26-5-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
87 | Shixuana No. 1 | B-28-2-2 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
88 | Miliang No. 1 B2831 | B-14-1-1 | A. chinensis var. deliciosa | Cultivars (lines) | PowerCore |
89 | 18-AHHS-01 | B-29-5-1 | A. chinensis var. deliciosa | Wild resources | PowerCore |
90 | Moshan No. 3 ♂ | 3-19-2 | A. chinensis var. deliciosa | Cultivars (lines) | Supplementary cultivar |
91 | Sanxia No. 1 | 4-2-5-2 | A. chinensis var. deliciosa | Cultivars (lines) | Supplementary cultivar |
92 | Xianglv | 4-5-4-2E | A. chinensis var. deliciosa | Cultivars (lines) | Supplementary cultivar |
93 | Bruno | 4-7-5-3 | A. chinensis var. deliciosa | Cultivars (lines) | Supplementary cultivar |
Population | n | Na | Ne | Ho | He | PIC | I |
---|---|---|---|---|---|---|---|
All collection | 294 (100%) | 22.2 | 8.758 | 0.622 | 0.846 | 0.835 | 2.369 |
Core collection 1 | 73 (24.83%) | 21.1 | 9.081 | 0.635 | 0.849 | 0.84 | 2.407 |
Core collection 2 | 93 (31.63%) | 21.975 | 9.058 | 0.627 | 0.848 | 0.838 | 2.401 |
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Hu, G.; Jiang, Q.; Wang, Z.; Li, Z.; Liao, W.; Shen, D.; Zhong, C. Genetic Diversity Analysis and Core Collection Construction of the Actinidia chinensis Complex (Kiwifruit) Based on SSR Markers. Agronomy 2022, 12, 3078. https://doi.org/10.3390/agronomy12123078
Hu G, Jiang Q, Wang Z, Li Z, Liao W, Shen D, Zhong C. Genetic Diversity Analysis and Core Collection Construction of the Actinidia chinensis Complex (Kiwifruit) Based on SSR Markers. Agronomy. 2022; 12(12):3078. https://doi.org/10.3390/agronomy12123078
Chicago/Turabian StyleHu, Guangming, Quan Jiang, Zhi Wang, Zuozhou Li, Wenyue Liao, Dandan Shen, and Caihong Zhong. 2022. "Genetic Diversity Analysis and Core Collection Construction of the Actinidia chinensis Complex (Kiwifruit) Based on SSR Markers" Agronomy 12, no. 12: 3078. https://doi.org/10.3390/agronomy12123078