Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)
Abstract
:1. Introduction
2. Results
2.1. SNP Identification
2.2. Genetic Map
2.3. Genomic Heritability
2.4. Mapping of Additive QTL
2.5. Mapping of Epistatic QTL
2.6. Contribution of All Detected QTL to Marsh Spot Resistance
2.7. Favorable Alleles of QTL in RILs
2.8. Candidate Genes of Major QTL
3. Discussion
3.1. Genomic Heritability and Contribution of QTL to Marsh Spot Resistance
3.2. Statistical Models for QTL Identification and QTL Validation
3.3. Additive/Epistatic QTL and Genomics-Assisted Selection
3.4. Candidate Gene Prediction
4. Methods and Materials
4.1. Recombinant Inbred Lines (RILs)
4.2. Phenotyping of Marsh Spot Resistance
4.3. Genotyping by Sequencing and SNP Identification
4.4. Genomic Heritability
4.5. Construction of Linkage Map
4.6. QTL Identification
4.7. Favorable Alleles
4.8. Candidate Gene Prediction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Linage Group (Chromosome) | No. of Markers | Total Distance (cm) | No. of Recombination Intervals | |
---|---|---|---|---|
1 | 101 | 131 | 27 | 4.86 ± 13.40 |
2 | 263 | 305 | 96 | 3.18 ± 7.17 |
3 | 115 | 105 | 41 | 2.56 ± 3.75 |
4 | 160 | 257 | 69 | 3.73 ± 7.10 |
5 | 360 | 186 | 76 | 2.44 ± 4.39 |
6 | 71 | 114 | 28 | 4.08 ± 9.60 |
7 | 72 | 135 | 21 | 6.41 ± 11.52 |
8 | 9 | 144 | 4 | 36.11 ± 14.80 |
9 | 59 | 93 | 26 | 3.59 ± 7.73 |
10 | 44 | 91 | 26 | 3.50 ± 5.40 |
11 | 19 | 38 | 9 | 4.20 ± 6.32 |
Total | 1273 | 1599 | 434 | 3.78 ± 8.13 |
Phenotypic Dataset | Genomic Heritability (h2 ± s) (%) | Phenotypic Dataset | Genomic Heritability (h2 ± s) (%) |
---|---|---|---|
H2015 | 24.22 ± 0.09 | S2019 | 12.07 ± 0.07 |
H2016 | 18.43 ± 0.08 | T2015 | 32.48 ± 0.10 |
H2017 | 32.96 ± 0.10 | T2016 | 28.02 ± 0.01 |
H2018 | 33.13 ± 0.10 | T2017 | 45.53 ± 0.11 |
H2019 | 32.82 ± 0.10 | T2018 | 45.48 ± 0.10 |
S2015 | 27.03 ± 0.10 | T2019 | 41.12 ± 0.11 |
S2016 | 24.76 ± 0.10 | H-5 yrs | 46.46 ± 0.11 |
S2017 | 30.37 ± 0.10 | S-5 yrs | 47.14 ± 0.11 |
S2018 | 16.67 ± 0.08 | Overall | 55.91 ± 0.10 |
QTL | Flanking Markers and Position | LG Pos (cm) | Additive Effect | No. of Datasets (a) | Significant Datasets (b) | Average R2 (%) (c) | Model |
---|---|---|---|---|---|---|---|
QTL.1.1 | Chr1_48339634–Chr1_50146614 | 119.26–126.33 | 0.10 | 1 | 3 | 5.92 | GCIM |
QTL.2.1 | Chr2_872663–Chr2_1135128 | 0.06–5.22 | 0.05–0.11 | 6 | 11 | 8.30 | GCIM, RTM-GWAS |
QTL.2.2 | Chr2_32113326 | 97.46 | 0.07 | 1 | 17 | 9.12 | GCIM |
QTL.2.3 | Chr2_34070996–Chr2_35065692 | 147.11–151.45 | 0.15 | 1 | 16 | 11.43 | GCIM |
QTL.2.4 | Chr2_35130486–Chr2_35289581 | 143.04–142.69 | 0.07–0.10 | 5 | 18 | 10.42 | GCIM, ICIM-ADD |
QTL.2.5 | Chr2_35344261–Chr2_36750706 | 128.94–134.16 | 0.14 | 1 | 17 | 10.02 | ICIM-ADD |
QTL.2.6 | Chr2_37937595–Chr2_38452857 | 187.14–188.25 | 0.05–0.51 | 5 | 18 | 12.30 | ICIM-ADD, GCIM |
QTL.3.1 | Chr3_11944447–Chr3_19043093 | 47.42–51.49 | −0.08 | 5 | 17 | 24.52 | GCIM, RTM-GWAS, ICIM-ADD |
QTL.3.2 | Chr3_19701297–Chr3_30221015 | 48.9–50.4 | −0.57–0.17 | 13 | 17 | 21.78 | ICIM-ADD, GCIM, RTM-GWAS |
QTL.5.1 | Chr5_11498360–Chr5_19238819 | 56.2–57.31 | −0.46 | 1 | 4 | 7.39 | GCIM |
QTL.5.2 | Chr5_1647320–Chr5_31681432 | 12.94–38.3 | 0.06–0.10 | 6 | 18 | 9.23 | GCIM |
QTL.5.3 | Chr5_38536162–Chr5_38536272 | 171.77–171.75 | 0.06–0.13 | 10 | 17 | 10.72 | GCIM, ICIM-ADD |
QTL.5.4 | Chr5_623370–Chr5_673021 | 0–1.13 | −0.10–−0.07 | 12 | 17 | 11.61 | ICIM-ADD, RTM-GWAS |
QTL.6.1 | Chr6_1374720–Chr6_1504675 | 23.18–23.92 | 0.04–0.08 | 4 | 13 | 6.81 | GCIM, RTM-GWAS |
QTL.6.2 | Chr6_13598278–Chr6_14124318 | 39.58–38.48 | 0.05–0.07 | 2 | 5 | 7.52 | GCIM |
QTL.9.1 | Chr9_17827630–Chr9_20865151 | 42.84–46.75 | 0.20 | 2 | 3 | 7.82 | GCIM, RTM-GWAS |
QTL 1 | QTL 2 | No. Datasets with QTL (a) | No. Datasets with Significant Effect (b) | Average of R2 (%) (c) | Additive Effect of QTL 1 | Additive Effect of QTL 2 | Epistatic Effect | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
QTL 1 | Left Marker | Right Marker | LG Pos (cm) | QTL 2 | Left Marker | Right Marker | LG Pos (cm) | ||||||
QTL.5.4 | Chr5_673021 | Chr5_1647342 | 1.13–12.92 | QTL.2.7 | Chr2_36996368 | Chr2_37937763 | 160.01–178.45 | 1 | 18 | 30.64 | −0.05 | 0.04 | −0.11 |
QTL.5.4 | Chr5_673021 | Chr5_1647342 | 1.13–12.92 | QTL.2.8 | Chr2_37937763 | Chr2_37531627 | 178.45–184.57 | 2 | 18 | 30.69 | −0.05 | 0.04 | −0.11 |
QTL.2.3 | Chr2_34070996 | Chr2_35065692 | 147.11–151.45 | QTL.2.8 | Chr2_37937763 | Chr2_37531627 | 178.45–184.57 | 1 | 9 | 16.31 | −0.06 | 0.04 | −0.10 |
QTL | Gene | Chr | Gene Coordinates (a) | Annotation |
---|---|---|---|---|
QTL.1.1 | Phvul.001G250300 | 1 | 50100939–50102262 | Heavy metal transport/detoxification superfamily protein |
Phvul.001G247400 | 1 | 49894723–49895275 | Heavy metal transport/detoxification superfamily protein | |
QTL.2.3 | Phvul.002G184200 | 2 | 34468080–34481795 | ZIP metal ion transporter family |
QTL.3.1 | Phvul.003G086300 | 3 | 16877488–16879137 | Heavy metal transport/detoxification superfamily protein |
QTL.3.2 | Phvul.003G092500 | 3 | 21113140–21115717 | Heavy metal transport/detoxification superfamily protein |
Phvul.003G104900 | 3 | 23350962–23352673 | Heavy metal transport/detoxification superfamily protein | |
Phvul.003G099700 | 3 | 25708027–25708491 | Heavy metal transport/detoxification superfamily protein | |
Phvul.003G108900 | 3 | 27536901–27538128 | Heavy metal transport/detoxification superfamily protein | |
QTL.5.2 | Phvul.005G095400 | 5 | 29797811–29799135 | Heavy metal transport/detoxification superfamily protein |
Phvul.005G049300 | 5 | 5742223–5745905 | Cation efflux family protein | |
Phvul.005G048900 | 5 | 5682746–5684903 | Zinc transporter 1 precursor | |
QTL.9.1 | Phvul.009G137100 | 9 | 20653368–20662253 | Manganese tracking factor for mitochondrial SOD2 |
Phvul.009G127900 | 9 | 19429094–19433403 | NRAMP metal ion transporter 6 |
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Jia, B.; Conner, R.L.; Penner, W.C.; Zheng, C.; Cloutier, S.; Hou, A.; Xia, X.; You, F.M. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). Int. J. Mol. Sci. 2022, 23, 7639. https://doi.org/10.3390/ijms23147639
Jia B, Conner RL, Penner WC, Zheng C, Cloutier S, Hou A, Xia X, You FM. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). International Journal of Molecular Sciences. 2022; 23(14):7639. https://doi.org/10.3390/ijms23147639
Chicago/Turabian StyleJia, Bosen, Robert L. Conner, Waldo C. Penner, Chunfang Zheng, Sylvie Cloutier, Anfu Hou, Xuhua Xia, and Frank M. You. 2022. "Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)" International Journal of Molecular Sciences 23, no. 14: 7639. https://doi.org/10.3390/ijms23147639
APA StyleJia, B., Conner, R. L., Penner, W. C., Zheng, C., Cloutier, S., Hou, A., Xia, X., & You, F. M. (2022). Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). International Journal of Molecular Sciences, 23(14), 7639. https://doi.org/10.3390/ijms23147639