SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Growth Conditions
2.2. SNP Loci Selection, SeqSNP Assay Design and Target Sequencing
2.3. De Novo SNP Discovery, Target and Novel SNP Allele Counting, and Data Filtering
2.4. Converting Allele Counts into Allele Frequencies
2.5. Cluster and Principal Coordinate Analyses, Analysis of Molecular Variance (AMOVA), and Variant Analysis
3. Results
3.1. Cluster Analysis
3.2. Principal Coordinate Analysis
3.3. Analysis of Molecular Variance (AMOVA)
3.4. Region and/or Country-Specific Alleles and the Effects on Their Corresponding Genes
4. Discussion
4.1. Genic SNP Markers with Predicted Moderate to High Effects on Their Associated Genes
4.2. SNP Loci with Region/Country Specific Alleles
4.3. Genetic Relationship between Accessions
4.4. Analysis of Molecular Variance and Genetic Differentiation between Various Groups
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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GenBank | Africa | Asia | Europe | North America | Oceania | South America | Unknown | Total |
---|---|---|---|---|---|---|---|---|
NordGen | 0 | 0 | 33 | 1 | 0 | 0 | 0 | 34 |
Jerrestad AB | 0 | 0 | 13 | 0 | 0 | 0 | 0 | 13 |
PGRC | 0 | 24 | 3 | 3 | 0 | 0 | 0 | 30 |
CGN | 0 | 7 | 1 | 2 | 0 | 0 | 1 | 11 |
IPK | 1 | 8 | 64 | 8 | 1 | 2 | 2 | 86 |
NPGS | 1 | 2 | 8 | 1 | 0 | 0 | 0 | 12 |
A&A Canada | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 2 |
Total | 2 | 41 | 122 | 17 | 1 | 2 | 3 | 188 |
Consequence_Effect | Chromosome | Total | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
A01 | A02 | A03 | A04 | A05 | A06 | A07 | A08 | A09 | A10 | ||
Missense variant_Moderate | 12 | 5 | 9 | 5 | 0 | 9 | 7 | 6 | 0 | 13 | 66 |
Synonymous variant_Low | 4 | 0 | 1 | 4 | 1 | 0 | 4 | 2 | 0 | 5 | 21 |
Splice polypyrimidine tract variant_Low | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 4 |
Splice donor variant_High | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 3 |
Splice polypyrimidine tract variant/Intron variant_Low | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 3 |
Splice acceptor variant_High | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 |
Splice donor fifth base variant/Intron variant_Low | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 2 |
Splice donor region variant/Intron variant_Low | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 |
Splice region variant/Synonymous variant_Low | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 2 |
Missense variant/stop retained variant_Moderate | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Splice region variant/Intron variant_Low | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
Stop lost_High | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Total | 16 | 6 | 16 | 12 | 1 | 14 | 13 | 8 | 2 | 20 | 108 |
Source of Variation | Degrees of Freedom | Sum of Squares | Variance Components | Percentage of Variation | Fixation Index | p-Value |
---|---|---|---|---|---|---|
Among accession groups a | 5 | 2.311 | 0.015 | 19.0 | PhiPT = 0.194 | 0.001 |
Within accession groups a | 180 | 11.230 | 0.062 | 81.0 | ||
Total | 185 | 13.542 | 0.077 | |||
Among accession groups b | 2 | 0.954 | 0.012 | 17.5 | PhiPT = 0.175 | 0.001 |
Within accession groups b | 139 | 8.108 | 0.058 | 82.5 | ||
Total | 141 | 9.063 | 0.071 | |||
Among accession groups c | 4 | 2.227 | 0.025 | 38.0 | PhiPT = 0.378 | 0.001 |
Within accession groups c | 112 | 4.590 | 0.041 | 62.0 | ||
Total | 116 | 6.817 | 0.066 | |||
Among accession groups d | 4 | 2.332 | 0.023 | 27.0 | PhiPT = 0.268 | 0.005 |
Within accession groups d | 179 | 11.025 | 0.062 | 73.0 | ||
Total | 183 | 13.357 | 0.084 |
Source of Variation | Degrees of Freedom | Sum of Squares | Variance Components | Percentage of Variation | Fixation Index | p-Value |
---|---|---|---|---|---|---|
Among accession groups a | 6 | 58.4 | 0.38 Va | 23.49 | FST = 0.24 | 0.003 |
Within accession groups a | 175 | 217.0 | 1.24 Vb | 76.51 | ||
Total | 181 | 275.4 | 1.62 | |||
Among accession groups b | 2 | 9.0 | 0.15 Va | 17.08 | FST = 0.17 | 0.03 |
Within accession groups b | 145 | 105.6 | 0.73 Vb | 82.92 | ||
Total | 147 | 114.7 | 0.88 | |||
Among accession groups c | 7 | 100.3 | 0.85 Va | 51.07 | FST = 0.51 | 0 |
Within accession groups c | 150 | 122.8 | 0.82 Vb | 48.93 | ||
Total | 157 | 223.1 | 1.67 | |||
Among accession groups d | 3 | 96.3 | 1.47 Va | 58.97 | FST = 0.59 | 0 |
Within accession groups d | 170 | 174.1 | 1.02 Vb | 41.03 | ||
Total | 173 | 270.4 | 2.49 |
Accession-group a | Cultivar | Landrace | Wild | |||
---|---|---|---|---|---|---|
Cultivar | - | |||||
Landrace | 0.188 * | - | ||||
Wild | 0.208 * | 0.040 | - | |||
Accession-group b | China | Germany | India | Italy | Sweden | |
China | - | |||||
Germany | 0.188 * | - | ||||
India | 0.243 * | 0.368 * | - | |||
Italy | 0.340 * | 0.234 * | 0.475 * | - | ||
Sweden | 0.466 * | 0.133 * | 0.558 * | 0.388 * | - | |
Accession-group c | Africa | Asia | Europe | North America | South America | |
Africa | - | |||||
Asia | 0.276 * | - | ||||
Europe | 0.487 * | 0.308 * | - | |||
North America | 0.459 * | 0.334 * | 0.072 * | - | ||
South America | 0.198 | 0.317 * | 0.174 | 0.146 | - | |
Accession-group d | Jerrestad AB | CGN | IPK | NordGen | NPGS | PGRC |
Jerrestad AB | - | |||||
CGN | 0.538 * | - | ||||
IPK | 0.169 * | 0.363 * | - | |||
NordGen | 0.088 | 0.416 * | 0.105 * | - | ||
NPGS | 0.281 * | 0.194 * | 0.072 * | 0.187 * | - | |
PGRC | 0.407 * | 0.172 * | 0.167 * | 0.243 * | 0.076 * | - |
Accession Group a | Cultivar | Landrace | Wild | |||||
---|---|---|---|---|---|---|---|---|
Cultivar | - | |||||||
Landrace | 0.215 * | - | ||||||
Wild | 0.109 | 0.121 | - | |||||
Accession group b | Africa | Asia | Europe | North America | ||||
Africa | - | |||||||
Asia | 0.599 | - | ||||||
Europe | 0.521 | 0.835 | - | |||||
North America | 0.674 | 0.873 | −0.007 | - | ||||
Accession group c | Jerrestad AB | A&A Canada | CGN | IPK | NordGen | NPGS | PGRC | |
Jerrestad AB | - | |||||||
A&A Canada | −0.151 | - | ||||||
CGN | 0.495 * | 0.271 | - | |||||
IPK | −0.021 | −0.097 | 0.635 * | - | ||||
NordGen | 0.010 | −0.077 | 0.461 * | 0.021 | - | |||
NPGS | 0.441 | 0.234 | 0.221 | 0.500 * | 0.268 * | - | ||
PGRC | 0.041 | −0.113 | 0.310 | 0.088 | 0.020 | 0.153 | - | |
Accession group d | Austria | Bangladesh | Canada | Finland | Germany | Italy | Sweden | USA |
Austria | - | |||||||
Bangladesh | 0.953 | - | ||||||
Canada | −0.125 | 0.950 * | - | |||||
Finland | −0.045 | 0.792 * | 0.038 | - | ||||
Germany | 0.261 | 0.987 * | 0.196 | 0.028 | - | |||
Italy | 0.096 | 0.931 * | 0.157 | 0.133 | 0.480 | - | ||
Sweden | −0.089 | 0.908 * | −0.027 | 0.036 | 0.054 | 0.143 | - | |
USA | 0.040 | 0.951 | 0.106 | 0.049 | 0.650 | −0.078 | 0.078 | - |
Region Specific Allele | |||||||||
---|---|---|---|---|---|---|---|---|---|
Europe/France | Europe/France | Europe/ ** | Europe/Italy | Europe/ ** | Europe/ ** | Europe/ ** | Europe/ ** | North America/Cuba | |
Locus | Bn-A01-p1001022 | Bn-A02-p20845905 | NC_024796-2_ 3347226 | NC_024800-2_ 3070370 | NC_024803-2_ 35208073 | NC_024804-2_15703515 | NC_024803-2_33076115 | NC_024803-2_30767803 | NC_024795-2_25991653 |
Chromosome | A01 | A02 | A02 | A06 | A09 | A10 | A09 | A09 | A01 |
SNP position | 1061243 | 24397768 | 3347226 | 3070370 | 35208073 | 15703515 | 33076115 | 30767803 | 25991653 |
Ref/Alt alleles | A/C | A/C | T/A | T/C | C/T | C/T | T/C | G/T | C/T |
PA | C | C | A | C | T | T | C | T | T |
PA freq | 0.004 | 0.004 | 0.021 | 0.017 | 0.030 | 0.017 | 0.025 | 0.012 | 0.176 |
PA description | Upstream gene variant | Intergenic variant | Missense variant | Missense variant | Upstream gene variant | Downstream gene variant | Intergenic variant | Intergenicvariant | Intergenic variant |
PA effect | Modifier | Modifier | Moderate | Moderate | Modifier | Modifier | Modifier | Modifier | Modifier |
PA-associated gene | A01p002320.1_ BraROA | A02g509130.1_ BraROA * | A02p008020.1_ BraROA | A06p008790.1_ BraROA | A09g511940.1_ BraROA | A10p024240.1_ BraROA | A09g510750.1_BraROA * | A09g510320.1_BraROA * | A01p046190.1_BraROA * |
PA-associated Protein | homeobox-leucine zipper protein ATHB-40 | - | uncharacterized | phosphatidylinositol 4-phosphate 5-kinase 7 | UDP-glycosyltransferase 76F1 | uncharacterized | uncharacterized | uncharacterized | Pollen receptor-like kinase 4 |
Coding strand | Forward | Forward | Forward | Reverse | Forward | Reverse | Forward | Reverse | Reverse |
Codon change | - | - | Ttc/Atc | gAg/gGg | - | - | - | - | - |
AA change | - | - | Phe/Ile | Glu/Gly | - | - | - | - | - |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Geleta, M.; Sundaramoorthy, J.; Carlsson, A.S. SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape). Genes 2024, 15, 1187. https://doi.org/10.3390/genes15091187
Geleta M, Sundaramoorthy J, Carlsson AS. SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape). Genes. 2024; 15(9):1187. https://doi.org/10.3390/genes15091187
Chicago/Turabian StyleGeleta, Mulatu, Jagadeesh Sundaramoorthy, and Anders S. Carlsson. 2024. "SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape)" Genes 15, no. 9: 1187. https://doi.org/10.3390/genes15091187