Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Trait KASP Marker Development
2.2. Assay Verification and Routine Analysis
2.3. QC Marker Selection Pipeline
2.4. Routine Analysis with QC KASP Markers
2.4.1. Study Design
2.4.2. QC Data Analysis
3. Results
3.1. Trait Markers for Late Blight and PVY Resistance
3.2. Markers Tested on Two Different Breeding Populations
3.3. Tetraploid Calls Enhance QC Marker Efficiency
3.4. Discrepancy in Breeding Material Genetic Identity Revealed by QC Markers
3.5. Routine Use of KASP Markers
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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SNP ID | Intertek Id | Gene/QTL | Reference Sequence | Chromosome | Position |
---|---|---|---|---|---|
S9_61261167 | snpST00020 | R8-QTL | tgaaggtattcatttttctgatgaaatgcattcctggacttttcttcatc[a/c]tgtttgggcgctctttgtacaggacatgcattgctgttttctccccccca | 9 | 67380076 |
solcap_snp_c2_56418 | snpST00023 | R8-QTL | ggatactgtcgcaatggttgttgcaacggcaataactatgagtgctatag[t/g]tgctgttaattatggggagcaataaatatttgtaatggcaaagatgtaat | 9 | 66379267 |
M6F1R4_711 | snpST00052 | Ryadg | aaacatgagctactcggggtcaccacttaacaaagattttagttagataa[g/a]gacagaatacaaaatccactaactatcacatttatcacggatgggttcca | 11 | 2499608 |
M6F1R4_817 | snpST00073 | Ryadg | acgtgctaactagttagggattcaaattcaagattgtattaaacccggat[a/g]tacatatacagggaagctttaaccacacatgcaaggttcagatatcca | 11 | 2499502 |
La Molina | Huancayo | Oxapampa | Total | |
---|---|---|---|---|
Total samples (number of clones) | 114 (114) | 224 (114) | 38 (38) | 376 (114) |
r1 samples | 96 | |||
r2 samples | 77 | |||
r1 within plot samples | 17 |
SNP ID | Marker Name | Location † | Concordance ‡ |
---|---|---|---|
Late blight resistance | |||
snpST0010 | GBS_S9_58779951 | Chr9: 58779951 | 93% |
snpST0012 | GBS_S9_59226671 | Chr9: 59226671 | 0% |
snpST0013 | GBS_S9_59301204 | Chr9: 59301204 | 92% |
snpST0014 | GBS_S9_59997331 | Chr9: 59997331 | 95% |
snpST0015 | GBS_S9_60067335 | Chr9: 60067335 | 95% |
snpST0016 | GBS_S9_60225630 | Chr9: 60225630 | 71% |
snpST0017 | GBS_S9_60510506 | Chr9: 60510506 | 90% |
snpST0018 | GBS_S9_61095507 | Chr9: 61095507 | 93% |
snpST0019 | GBS_S9_61205320 | Chr9: 61205320 | 0% |
snpST0020* | GBS_S9_61261167 | Chr9: 61261167 | 99% |
snpST0023* | solcap_snp_c2_56418 | Chr9: 60182930 | 97% |
PVY resistance | |||
snpST0049 | M6F1R4_672 | Chr:11: 1708290 | 0% |
snpST0050 | M6F1R4_679 | Chr:11: 1708297 | 50% |
snpST0051 | M6F1R4_691 | Chr:11: 1708309 | 45% |
snpST0052* | M6F1R4_711 | Chr11: 1708329 | 100% |
snpST0053 | M6F1R4_732 | Chr11: 1708350 | 74% |
snpST0054 | M6F1R4_739 | Chr11: 1708357 | 55% |
snpST0071 | M6F1R4_797 | Chr11: 1708415 | 99% |
snpST0072 | M6F1R4_798 | Chr11: 1708416 | 0% |
snpST0073* | M6F1R4_817 | Chr11: 1708435 | 100% |
Marker ID | Trait | Number of Clones | α | β | s |
---|---|---|---|---|---|
snpST00052 | PVY | 78 | 0.0 | 0.16 | 0.83 |
snpST00073 | PVY | 78 | 0.0 | 0.16 | 0.83 |
snpST00020 | Late blight | 73 | 0.02 | 0.13 | 0.88 |
snpST00023 | Late blight | 77 | 0.22 | 0.35 | 0.65 |
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Kante, M.; Lindqvist-Kreuze, H.; Portal, L.; David, M.; Gastelo, M. Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains. Agronomy 2021, 11, 2315. https://doi.org/10.3390/agronomy11112315
Kante M, Lindqvist-Kreuze H, Portal L, David M, Gastelo M. Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains. Agronomy. 2021; 11(11):2315. https://doi.org/10.3390/agronomy11112315
Chicago/Turabian StyleKante, Moctar, Hannele Lindqvist-Kreuze, Leticia Portal, Maria David, and Manuel Gastelo. 2021. "Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains" Agronomy 11, no. 11: 2315. https://doi.org/10.3390/agronomy11112315