Quantitative Trait Loci Mapping of First Pod Height in Faba Bean Based on Genotyping-by-Sequencing (GBS)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Population and Phenotypic Data Measurement
2.2. DNA Extraction and SNP Genotyping
2.3. Statistical Analysis
2.4. Comparison with Reference Genome
2.5. Genetic Linkage Map Construction
2.6. QTL Mapping
2.7. Candidate Gene Prediction for the QTLs of FPH
3. Results
3.1. Phenotypic Analysis and Correlation Analysis
3.2. Genotyping-by-Sequencing
3.3. Construction of High-Density Genetic Map
3.4. QTL Mapping of FPN and FPH
3.5. Mining of Candidate Genes
4. Discussion
4.1. High-Density Genetic Linkage Map of Faba Bean
4.2. Analysis of QTL for FPN and FPH
4.3. Candidate Genes Associated with FPH of Faba Bean
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Trait | Evn. | Parents | F3 Population | h2/% | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Qinghai13 | Qingcan19 | Min | Max | Mean | SD | CV/% | Skewness | Kurtosis | |||
FPN | XN | 5.11 ** | 9.70 ** | 3.00 | 11.50 | 5.67 | 1.45 | 25.57 | 1.44 | 2.30 | 87.67 |
GH | 5.00 ** | 9.40 ** | 4.00 | 11.00 | 5.48 | 1.26 | 22.99 | 2.14 | 5.24 | ||
HZ | 5.20 ** | 10.40 ** | 3.67 | 11.25 | 5.46 | 1.37 | 25.09 | 2.07 | 5.08 | ||
FPH/cm | XN | 27.89 ** | 64.65 ** | 10.00 | 61.00 | 22.95 | 8.59 | 37.43 | 1.72 | 3.59 | 81.53 |
GH | 17.70 ** | 46.20 ** | 11.20 | 63.25 | 21.37 | 8.27 | 38.70 | 2.12 | 5.37 | ||
HZ | 14.90 ** | 39.10 ** | 8.33 | 47.50 | 18.11 | 5.55 | 30.65 | 1.56 | 4.59 |
Evn. | Kolmogorov–Smirnov | Shapiro–Wilk | ||||
---|---|---|---|---|---|---|
Statistic | df | Sig. | Statistic | df | Sig. | |
XN | 0.168 | 240 | <0.001 | 0.881 | 240 | <0.001 |
GH | 0.195 | 232 | <0.001 | 0.783 | 232 | <0.001 |
HZ | 0.177 | 241 | <0.001 | 0.798 | 241 | <0.001 |
Chr | SNP | Genetic Distance (cM) | Mean Gap (cM) | Max. Gap (cM) |
---|---|---|---|---|
1L | 509 | 783.26 | 1.54 | 110.40 |
1S | 335 | 382.64 | 1.14 | 18.85 |
2 | 565 | 736.17 | 1.30 | 77.81 |
3 | 363 | 570.82 | 1.57 | 90.60 |
4 | 355 | 589.40 | 1.66 | 88.06 |
5 | 546 | 534.95 | 0.98 | 66.19 |
6 | 339 | 491.89 | 1.45 | 104.08 |
Total | 3012 | 4089.13 | 1.36 |
Chr | <1 (cM) | 1–5 (cM) | <5 (cM) | 5–10 (cM) | 10–20 (cM) | >20 (cM) | Ratio <5 (cM) | Ratio <1 (cM) |
---|---|---|---|---|---|---|---|---|
1L | 359 | 133 | 492 | 8 | 3 | 5 | 96.85 | 70.67 |
1S | 220 | 106 | 326 | 7 | 1 | 0 | 97.60 | 65.87 |
2 | 389 | 158 | 547 | 9 | 5 | 3 | 96.99 | 68.97 |
3 | 250 | 99 | 349 | 8 | 3 | 2 | 96.41 | 69.06 |
4 | 211 | 131 | 342 | 8 | 1 | 3 | 96.61 | 59.60 |
5 | 391 | 146 | 537 | 6 | 1 | 1 | 98.53 | 71.74 |
6 | 218 | 113 | 331 | 4 | 2 | 1 | 97.93 | 64.50 |
Total | 2038 | 886 | 2928 | 50 | 16 | 15 | 97.30 | 67.82 |
Trait | Chr. | QTL | Env. | Pos./cM | Marker Interval | Genetic Distance/cM | LOD | PVE/% | Add |
---|---|---|---|---|---|---|---|---|---|
FPN | 1L | qFPN1L-1 | GH | 79.0 | chr1L_SNP937–chr1L_SNP1943 | 65.5–92.5 | 3.36 | 0.89 | 0.02 |
HZ | 83.0 | chr1L_SNP937–chr1L_SNP1943 | 67.5–94.5 | 7.39 | 5.83 | −0.01 | |||
XN | 87.0 | chr1L_SNP937–chr1L_SNP1943 | 68.5–98.5 | 3.25 | 12.37 | −0.04 | |||
qFPN1L-2 | XN | 399.0 | chr1L_SNP1308–chr1L_SNP1302 | 397.5–400.5 | 4.22 | 2.41 | −0.40 | ||
qFPN1L-3 | HZ | 650.0 | chr1L_SNP81–chr1L_SNP243 | 648.5–654.5 | 6.37 | 5.81 | −0.01 | ||
qFPN1L-4 | HZ | 699.0 | chr1L_SNP249–chr1L_SNP1011 | 687.5–705.5 | 7.91 | 5.84 | 0.01 | ||
1S | qFPN1S-1 | XN | 36.0 | chr1S_SNP138–chr1S_SNP154 | 32.5–37.5 | 2.50 | 1.34 | 0.23 | |
qFPN1S-2 | XN | 352.0 | chr1S_SNP1127–chr1S_SNP1133 | 351.5–353.5 | 5.31 | 3.16 | 0.49 | ||
2 | qFPN2-1 | HZ | 31.0 | chr2_SNP1828–chr2_SNP1816 | 27.5–32.5 | 2.57 | 0.57 | −0.30 | |
3 | qFPN3-1 | GH | 201.0 | chr3_SNP664–chr3_SNP645 | 197.5–206.5 | 2.58 | 0.67 | 0.19 | |
qFPN3-2 | XN | 239.0 | chr3_SNP540–chr3_SNP526 | 238.5–244.5 | 2.73 | 1.59 | 0.35 | ||
qFPN3-3 | GH | 424.0 | chr3_SNP4–chr3_SNP113 | 399.5–440.5 | 5.38 | 6.59 | −0.07 | ||
4 | qFPN4-1 | XN | 129.0 | chr4_SNP1080–chr4_SNP1062 | 128.5–130.5 | 4.15 | 2.30 | 0.34 | |
5 | qFPN5-1 | HZ | 29.0 | chr5_SNP1020–chr5_SNP996 | 26.5–33.5 | 2.63 | 0.55 | 0.07 | |
qFPN5-2 | GH | 58.0 | chr5_SNP956–chr5_SNP966 | 56.5–59.5 | 3.07 | 0.80 | 0.04 | ||
qFPN5-3 | GH | 270.0 | chr5_SNP436–chr5_SNP435 | 269.5–272.5 | 6.49 | 1.70 | 0.43 | ||
HZ | 270.0 | chr5_SNP436–chr5_SNP435 | 269.5–272.5 | 7.21 | 1.55 | 0.54 | |||
qFPN5-4 | XN | 311.0 | chr5_SNP305–chr5_SNP304 | 310.5–312.5 | 12.39 | 7.55 | 0.77 | ||
qFPN5-5 | GH | 490.0 | chr5_SNP148–chr5_SNP1096 | 487.5–493.5 | 2.93 | 5.18 | −0.05 | ||
6 | qFPN6-1 | HZ | 39.0 | chr6_SNP630–chr6_SNP8 | 35.5–41.5 | 2.92 | 4.07 | −0.01 | |
XN | 41.0 | chr6_SNP630–chr6_SNP8 | 30.5–73.5 | 3.57 | 12.47 | 0.04 | |||
GH | 41.0 | chr6_SNP630–chr6_SNP8 | 31.5–70.5 | 6.54 | 6.63 | 0.08 | |||
qFPN6-2 | XN | 398.0 | chr6_SNP1256–chr6_SNP1266 | 396.5–399.5 | 4.43 | 2.55 | −0.01 | ||
qFPN6-3 | XN | 458.0 | chr6_SNP1460–chr6_SNP1466 | 455.5–458.5 | 3.54 | 1.98 | −0.11 | ||
FPH | 1L | qFPH1L-1 | HZ | 79.0 | chr1L_SNP937–chr1L_SNP1943 | 63.5–78.5 | 2.97 | 5.02 | 0.12 |
qFPH1L-2 | XN | 399.0 | chr1L_SNP1308–chr1L_SNP1302 | 397.5–400.5 | 7.11 | 5.35 | −3.36 | ||
1S | qFPH1S-1 | HZ | 213.0 | chr1S_SNP636–chr1S_SNP635 | 210.5–214.5 | 3.28 | 0.69 | 1.06 | |
qFPH1S-2 | GH | 328.0 | chr1S_SNP1026–chr1S_SNP1038 | 325.5–328.5 | 2.95 | 0.34 | 2.08 | ||
qFPH1S-3 | XN | 352.0 | chr1S_SNP1127–chr1S_SNP1133 | 351.5–353.5 | 6.46 | 4.88 | 3.20 | ||
2 | qFPH2-1 | HZ | 229.0 | chr2_SNP940–chr2_SNP916 | 226.5–232.5 | 2.85 | 0.67 | 0.31 | |
XN | 230.0 | chr2_SNP940–chr2_SNP916 | 225.5–233.5 | 2.54 | 1.73 | 0.94 | |||
qFPH2-2 | XN | 702.0 | chr2_SNP1857–chr2_SNP1869 | 694.5–707.5 | 2.54 | 1.77 | 1.46 | ||
3 | qFPH3-1 | GH | 200.0 | chr3_SNP664–chr3_SNP645 | 197.5–203.5 | 2.70 | 0.30 | 1.10 | |
qFPH3-2 | XN | 301.0 | chr3_SNP407–chr3_SNP404 | 297.5–305.5 | 2.71 | 1.85 | 1.37 | ||
qFPH3-3 | GH | 423.0 | chr3_SNP4–chr3_SNP113 | 411.5–437.5 | 9.89 | 3.32 | −0.09 | ||
HZ | 431.0 | chr3_SNP4–chr3_SNP113 | 417.5–443.5 | 2.90 | 5.11 | −0.22 | |||
qFPH3-4 | HZ | 491.0 | chr3_SNP113–chr3_SNP1599 | 480.5–493.5 | 2.93 | 5.04 | −0.49 | ||
GH | 528.0 | chr3_SNP113–chr3_SNP1599 | 526.5–533.5 | 10.04 | 3.35 | −0.80 | |||
5 | qFPH5-1 | XN | 55.0 | chr5_SNP971–chr5_SNP958 | 52.5–56.5 | 5.21 | 3.87 | −0.45 | |
qFPH5-2 | XN | 159.0 | chr5_SNP704–chr5_SNP701 | 158.5–161.5 | 5.46 | 3.94 | −2.78 | ||
qFPH5-3 | HZ | 178.0 | chr5_SNP655–chr5_SNP651 | 176.5–178.5 | 2.69 | 0.60 | 0.34 | ||
qFPH5-4 | XN | 311.0 | chr5_SNP305–chr5_SNP304 | 310.5–312.5 | 12.46 | 9.76 | 4.57 | ||
qFPH5-5 | GH | 323.0 | chr5_SNP277–chr5_SNP278 | 321.5–323.5 | 3.08 | 0.35 | 2.08 | ||
HZ | 323.0 | chr5_SNP277–chr5_SNP278 | 321.5–323.5 | 6.03 | 1.37 | 1.92 | |||
qFPH5-6 | XN | 353.0 | chr5_SNP234–chr5_SNP222 | 350.5–354.5 | 2.51 | 1.77 | −0.76 | ||
qFPH5-7 | GH | 505.0 | chr5_SNP148–chr5_SNP1096 | 490.5–514.5 | 10.58 | 3.41 | −0.99 | ||
HZ | 507.0 | chr5_SNP148–chr5_SNP1096 | 494.5–517.5 | 2.97 | 4.95 | −0.09 | |||
6 | qFPH6-1 | XN | 43.0 | chr6_SNP630–chr6_SNP8 | 29.5–73.5 | 2.62 | 13.44 | 0.34 | |
GH | 46.0 | chr6_SNP630–chr6_SNP8 | 33.5–52.5 | 11.21 | 3.35 | 0.61 | |||
GH | 63.0 | chr6_SNP630–chr6_SNP8 | 61.5–71.5 | 10.88 | 3.34 | 0.52 |
Gene ID | Annotation |
---|---|
Vfaba.Hedin2.R1.6g005240.1 | Phosphatase 2c |
Vfaba.Hedin2.R1.6g010640.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g010760.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g010960.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g017960.1 | Belongs to the protein kinase superfamily. Ser Thr protein kinase family |
Vfaba.Hedin2.R1.6g018200.1 | Serine threonine-protein kinase Nek5-like |
Vfaba.Hedin2.R1.6g018240.1 | Serine threonine-protein kinase Nek5-like |
Vfaba.Hedin2.R1.6g026360.1 | Auxin-responsive protein |
Vfaba.Hedin2.R1.6g027040.1 | Receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g027480.1 | Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5′-TGTCTC-3′ found in the auxin-responsive promoter elements (AuxREs) |
Vfaba.Hedin2.R1.6g028040.1 | Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5′-TGTCTC-3′ found in the auxin-responsive promoter elements (AuxREs) |
Vfaba.Hedin2.R1.6g032960.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g037560.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g040280.1 | May act as a component of the auxin efflux carrier |
Vfaba.Hedin2.R1.6g040680.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g042000.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g042600.1 | Serine threonine-protein kinase-like protein |
Vfaba.Hedin2.R1.6g045520.1 | Inactive leucine-rich repeat receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g046360.1 | Auxin transporter-like protein |
Vfaba.Hedin2.R1.6g047520.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g048160.1 | Auxin-induced protein |
Vfaba.Hedin2.R1.6g048200.1 | Auxin-induced protein |
Vfaba.Hedin2.R1.6g048640.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g048920.1 | Auxin-responsive protein |
Vfaba.Hedin2.R1.6g053960.1 | Belongs to the protein kinase superfamily. Ser Thr protein kinase family |
Vfaba.Hedin2.R1.6g056240.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g058160.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g062480.1 | Auxin-responsive protein |
Vfaba.Hedin2.R1.6g064920.1 | Serine threonine-protein kinase sepA-like |
Vfaba.Hedin2.R1.6g065000.1 | Serine threonine-protein kinase sepA-like |
Vfaba.Hedin2.R1.6g067520.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g071920.1 | Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5′-TGTCTC-3′ found in the auxin-responsive promoter elements (AuxREs) |
Vfaba.Hedin2.R1.6g075760.1 | Checkpoint serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g079880.1 | Serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g086080.1 | G-type lectin S-receptor-like serine threonine-protein kinase |
Vfaba.Hedin2.R1.6g087120.1 | Belongs to the protein kinase superfamily. Ser Thr protein kinase family |
No. | Name of Parent | Number of Progenies | Number of Markers | Map Length (cM) | Average Distance (cM) | LG | References |
---|---|---|---|---|---|---|---|
1 | Nura 9 × Farah | F4 (145) | 1850 | 1439 | 0.8 | 6 | [13] |
2 | HIVERNA, NOVA GRADISKA, SILIAN, and QUASAR | F3 (345) | 1728 | 1547.71 | 0.89 | 6 | [14] |
3 | Yundou 8137, H0003712, H000572 | F2 (371) | 6895 | 3324.48 | 0.48 | 6 | [15] |
4 | WY7 × TCX7 | F2 (121) | 12,023 | 1182.65 | 0.098 | 6 | [16] |
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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/).
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Lou, S.; Teng, C.; Hou, W.; Zhou, X.; Zhang, H.; Liu, Y. Quantitative Trait Loci Mapping of First Pod Height in Faba Bean Based on Genotyping-by-Sequencing (GBS). Agronomy 2024, 14, 2013. https://doi.org/10.3390/agronomy14092013
Lou S, Teng C, Hou W, Zhou X, Zhang H, Liu Y. Quantitative Trait Loci Mapping of First Pod Height in Faba Bean Based on Genotyping-by-Sequencing (GBS). Agronomy. 2024; 14(9):2013. https://doi.org/10.3390/agronomy14092013
Chicago/Turabian StyleLou, Shubao, Changcai Teng, Wanwei Hou, Xianli Zhou, Hongyan Zhang, and Yujiao Liu. 2024. "Quantitative Trait Loci Mapping of First Pod Height in Faba Bean Based on Genotyping-by-Sequencing (GBS)" Agronomy 14, no. 9: 2013. https://doi.org/10.3390/agronomy14092013