Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. DNA Isolation and SSR Genotyping
2.3. Data Analysis
2.3.1. Allelic Diversity of SSR Loci
2.3.2. SOM Analysis
2.3.3. DAPC Analysis
2.3.4. AMOVA Analysis
3. Results
3.1. Allelic Diversity of SSR Loci
3.2. SOM Analysis
3.3. DAPC Analysis
3.3.1. Germplasm of Various Continental Origins
3.3.2. Germplasm Originating in Various Countries
3.3.3. Germplasm of Three Temporal Groups
3.3.4. Germplasm of 50-Year Breeding Groups
3.4. AMOVA Analysis
4. Discussion
4.1. How Many Historical Introductions Are at the Origin of Modern Potato Lineages?
4.2. Are There Signs of Genetic Erosion over Time and Space in the Cultivated Potato?
4.3. Is the Impact of the Introduction of Exotic Potato Germplasm into the Modern Cultivated Potato Noticeable?
- (1)
- S. Tuberosum ssp. Andigena CPC 1673 in many breeding programs, which confers resistance to G. rostochiensis pathotypes Ro1 and Ro4 [36,79] as well as to G. pallida pathotype Pa2 [80]. Many resistant tetraploid potato cultivars have S. tuberosum ssp. Andigena CPC 1673 in their pedigree, including Agria, Alcmaria, Amaryl, Amex, Aminca, Carrera, Cherie, Elkana, Mara, Prominent, and Saturna;
- (2)
- Maris Piper and Ulster Glade, cultivars that have been bred with a dominant gene for resistance to cyst nematode, derived from S. tuberosum ssp. Andigena;
- (3)
- Lenape, which has in its second-generation ancestors a wild potato native to the Chaco region in South America, S. chacoense, selected to provide the qualities of resistance to certain diseases, including late blight;
- (4)
- BRA 9089, whose parents are from (Chilote x Svitez) and landrace cross, in the basis of important lineages in China with Mira (syn. Ora) as well as in Germany with Axilia, Leander, Hessenkrone, and Sitta;
- (5)
- Improved clones VTN 62-033-03 and AM 66-0042 using S. vernei and S. demissum for targeted resistance to certain diseases and high starch yield. These two ancestors are highly represented in the pedigree of modern varieties.
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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Country | No. of Accessions | 50-Year Temporal Group | |||||
---|---|---|---|---|---|---|---|
Heirloom | Old | Modern | |||||
<1800 | 1801–1850 | 1851–1900 | 1901–1950 | 1951–2000 | 2001–2021 | ||
Netherlands | 382 | / | / | 3 | 25 | 171 | 183 |
France | 262 | / | 5 | 9 | 9 | 123 | 116 |
Germany | 201 | / | / | 4 | 40 | 83 | 73 |
UK | 142 | 1 | 5 | 26 | 49 | 39 | 22 |
USA | 68 | 3 | / | 14 | 12 | 36 | 3 |
Austria | 35 | / | / | 1 | / | 14 | 20 |
China | 25 | / | / | / | / | 2 | 23 |
Denmark | 23 | / | / | / | / | 9 | 14 |
Belgium | 12 | / | / | / | / | 11 | 1 |
Czechia | 10 | / | / | / | 5 | 5 | / |
Andes | 9 | 9 | / | / | / | / | / |
Poland | 8 | / | / | / | 1 | 7 | / |
RD Congo | 8 | / | / | / | 1 | 7 | / |
Chiloe Island | 3 | 3 | / | / | / | / | / |
Hungary | 5 | / | / | / | 1 | 1 | 3 |
Ireland | 4 | / | 1 | 1 | / | 1 | 1 |
Russia | 4 | / | / | / | 2 | 2 | / |
Canada | 2 | / | / | / | / | 2 | / |
Japan | 2 | / | / | / | / | 2 | / |
Sweden | 2 | / | / | / | 1 | 1 | / |
Ukraine | 2 | / | / | / | / | 2 | / |
Others * | 10 | 3 | / | 1 | / | 3 | 3 |
Total | 1219 | 19 | 11 | 59 | 146 | 522 | 462 |
Marker Locus | LG | Multiplex Set | Dye Labeling | Alleles Size Range | No of Total Alleles | No of Rare Alleles | No of Unique Alleles | Mean Alleles per Accession | H1 | PIC |
---|---|---|---|---|---|---|---|---|---|---|
STG0016 g | I | 2 | Ned | 118–157 | 12 | 7 | 0 | 2.81 | 0.985 | 0.777 |
STM1049 d | I | 2 | Ned | 178–199 | 9 | 4 | 1 | 1.89 | 0.728 | 0.653 |
STM2020 d | I | 4 | Ned | 137–160 | 14 | 7 | 2 | 2.87 | 0.965 | 0.824 |
STM5127 g | I | 2 | Hex | 236–271 | 12 | 4 | 2 | 2.75 | 0.969 | 0.793 |
STG0006 g | II | 2 | Fam | 141–159 | 7 | 3 | 0 | 1.23 | 0.217 | 0.346 |
STI0036 f | II | 1 | Hex | 111–146 | 13 | 5 | 0 | 2.93 | 0.974 | 0.834 |
STM1064 d | II | 1 | Hex | 182–194 | 9 | 2 | 1 | 2.04 | 0.799 | 0.654 |
STI0013 f | III | 2 | Fam | 247–308 | 10 | 5 | 1 | 2.58 | 0.963 | 0.747 |
STI0050 f | III | 5 | Hex | 149–167 | 7 | 2 | 0 | 2.62 | 0.971 | 0.745 |
STI0001 f | IV | 5 | Hex | 177–198 | 8 | 2 | 1 | 2.46 | 0.909 | 0.752 |
STI0012 f | IV | 1 | Fam | 163–195 | 10 | 3 | 0 | 2.87 | 0.979 | 0.812 |
STM5140 e | IV | 4 | Ned | 162–201 | 8 | 3 | 0 | 2.73 | 0.982 | 0.766 |
LEMALX d | V | 4 | Fam | 117–133 | 8 | 4 | 2 | 1.91 | 0.720 | 0.656 |
STG0021 g | V | 3 | Hex | 108–140 | 9 | 3 | 1 | 2.55 | 0.960 | 0.745 |
STPOAC58 e | V | 3 | Ned | 227–247 | 12 | 6 | 1 | 2.53 | 0.925 | 0.763 |
STI0004 f | VI | 1 | Hex | 63–104 | 15 | 7 | 1 | 2.50 | 0.916 | 0.775 |
STI0011 f | VI | 5 | Hex | 56–77 | 10 | 3 | 1 | 2.28 | 0.888 | 0.717 |
STI0021 f | VI | 4 | Ned | 82–106 | 9 | 2 | 0 | 2.82 | 0.984 | 0.783 |
STI0033 f | VII | 3 | Ned | 111–135 | 8 | 2 | 0 | 2.75 | 0.976 | 0.769 |
STM1052 d | VII | 1 | Ned | 196–262 | 14 | 5 | 2 | 2.62 | 0.934 | 0.816 |
STM3009 d | VII | 5 | Fam | 138–170 | 18 | 13 | 2 | 2.58 | 0.932 | 0.779 |
SSR1 b | VIII | 4 | Fam | 198–225 | 15 | 5 | 1 | 2.73 | 0.970 | 0.793 |
STGBSS c | VIII | 1 | Ned | 121–142 | 13 | 5 | 0 | 2.20 | 0.824 | 0.715 |
STM1104 d | VIII | 2 | Hex | 160–181 | 15 | 7 | 1 | 2.11 | 0.792 | 0.707 |
STWAX-2 a | VIII | 1 | Fam | 209–244 | 15 | 7 | 1 | 2.48 | 0.938 | 0.759 |
STI0002 f | IX | 5 | Ned | 99–132 | 18 | 11 | 5 | 2.42 | 0.903 | 0.765 |
STI0014 f | IX | 2 | Hex | 113–132 | 8 | 4 | 0 | 2.33 | 0.942 | 0.668 |
STM3012 d | IX | 3 | Hex | 136–207 | 11 | 4 | 2 | 2.20 | 0.825 | 0.712 |
STG0025 g | X | 3 | Fam | 193–205 | 7 | 3 | 0 | 1.91 | 0.847 | 0.546 |
STI0023 f | X | 5 | Ned | 149–217 | 22 | 17 | 6 | 2.40 | 0.936 | 0.718 |
STG0001 g | XI | 3 | Fam | 126–145 | 15 | 6 | 1 | 2.85 | 0.971 | 0.831 |
STM0037 d | XI | 5 | Fam | 63–101 | 16 | 10 | 2 | 2.64 | 0.931 | 0.810 |
STM2005 d | XI | 4 | Hex | 147–191 | 6 | 2 | 1 | 2.57 | 0.961 | 0.726 |
STI0030 f | XII | 3 | Fam | 84–105 | 11 | 3 | 1 | 2.73 | 0.980 | 0.777 |
STM1097 d | XII | 4 | Hex | 225–280 | 13 | 8 | 2 | 2.01 | 0.746 | 0.667 |
Sum | 407 | 184 | 41 | |||||||
Mean | 11.6 | 5.3 | 1.2 | 2.45 | 0.893 | 0.734 |
Model | df | Sum of Square | Variance Component | Percentage of Variation | p-Value a |
---|---|---|---|---|---|
Germplasm of various continental origins | |||||
among continents | 6 | 797.63 | 2.71 | 7.6 | <0.0001 |
within continent | 1137 | 39,694.63 | 32.75 | 92.4 | <0.0001 |
Germplasm of various country origins | |||||
among countries | 6 | 1194.31 | 1.06 | 3.2 | <0.0001 |
within countries | 1134 | 39,297.95 | 32.39 | 96.8 | <0.0001 |
Germplasm of three temporal groups b | |||||
among temporal groups | 2 | 653.31 | 1.51 | 4.4 | <0.0001 |
within temporal groups | 1140 | 39,838.95 | 32.76 | 95.6 | <0.0001 |
Germplasm of 50-year groups | |||||
among breeding periods | 5 | 959.03 | 1.00 | 3.0 | <0.0001 |
within breeding periods | 1137 | 39,533.23 | 32.59 | 97.0 | <0.0001 |
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Spanoghe, M.; Marique, T.; Nirsha, A.; Esnault, F.; Lanterbecq, D. Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview. Biology 2022, 11, 604. https://doi.org/10.3390/biology11040604
Spanoghe M, Marique T, Nirsha A, Esnault F, Lanterbecq D. Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview. Biology. 2022; 11(4):604. https://doi.org/10.3390/biology11040604
Chicago/Turabian StyleSpanoghe, Martin, Thierry Marique, Alexandra Nirsha, Florence Esnault, and Deborah Lanterbecq. 2022. "Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview" Biology 11, no. 4: 604. https://doi.org/10.3390/biology11040604
APA StyleSpanoghe, M., Marique, T., Nirsha, A., Esnault, F., & Lanterbecq, D. (2022). Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview. Biology, 11(4), 604. https://doi.org/10.3390/biology11040604