QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.)
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation
2.2. SLAF Library Construction and Genotyping of the RIL Population
2.3. Construction of the Soybean Genetic Map
2.4. QTL Mapping of the RIL Population
2.5. Verification of Candidate Region and Screening of Linkage Markers
2.6. Analysis of Genome and Transcriptome
3. Discussion
3.1. Construction of the High-Density Genetic Map
3.2. QTL Mapping of Palmitic Acid Content
3.3. Analysis of Candidate Genes
4. Materials and Methods
4.1. Plant Material and Phenotyping
4.2. Genotype Analysis, Construction, and Genotyping of the SLAF Library, and Construction of the High-Density Genetic Map
4.3. QTL Analysis for Palmitic Acid Content
4.4. Validation of Candidate Region and Development of Linkage Marker
4.5. Re-Sequencing and RNA-Seq Analysis of Parents
4.6. Statistical Analysis
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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Year | Parents | RILs | ||||||
---|---|---|---|---|---|---|---|---|
DN42 | Hobbit | Mean | SD | Range | Skewness | Kurtosis | CV (%) | |
2017 | 11.99 | 9.32 | 9.97 | 0.8 | 1.69–11.2 | −6.17 | 61.25 | 0.08 |
2018 | 11.99 | 8.12 | 9.52 | 0.76 | 1.57–11.03 | −6.17 | 63.94 | 0.08 |
2019 | 10.86 | 8.92 | 9.92 | 0.81 | 1.9–11.69 | −5.25 | 51.7 | 0.08 |
Chromosome | Number of Markers | Map Distance (cM) | Average Map Distance (cM) | Gap < 5 cM (%) | Max Gap (cM) |
---|---|---|---|---|---|
1 | 539 | 184.4 | 0.34 | 100 | 4.53 |
2 | 170 | 102.71 | 0.6 | 99.41 | 6.15 |
3 | 754 | 106.6 | 0.14 | 100 | 2.93 |
4 | 136 | 156.16 | 1.15 | 100 | 3.24 |
5 | 319 | 117.18 | 0.37 | 99.06 | 12.36 |
6 | 356 | 137.53 | 0.39 | 99.72 | 5.46 |
7 | 401 | 131.11 | 0.33 | 99.75 | 5.23 |
8 | 190 | 128.56 | 0.68 | 100 | 3.26 |
9 | 420 | 96.8 | 0.23 | 100 | 3.24 |
10 | 269 | 117.89 | 0.44 | 98.88 | 12.47 |
11 | 145 | 116.45 | 0.8 | 99.31 | 5.2 |
12 | 134 | 98.46 | 0.73 | 96.99 | 7.57 |
13 | 684 | 146.24 | 0.21 | 99.85 | 6.49 |
14 | 699 | 112.55 | 0.16 | 99.71 | 8.86 |
15 | 414 | 149.5 | 0.36 | 100 | 4.95 |
16 | 845 | 123.57 | 0.15 | 100 | 2.93 |
17 | 969 | 136.54 | 0.14 | 100 | 4.53 |
18 | 1119 | 169.34 | 0.15 | 100 | 2.43 |
19 | 1093 | 158.84 | 0.15 | 99.73 | 11.84 |
20 | 324 | 112.15 | 0.35 | 100 | 4.53 |
Total | 9980 | 2602.58 | 0.39 | 19.62 | 5.91 |
QTL | Year | Chr. | Left Marker | Right Marker | Genetic Position (cM) | Physical Position (bp) | LOD | ADD | PVE (%) | ||
---|---|---|---|---|---|---|---|---|---|---|---|
Start | End | Start | End | ||||||||
qPA10-1 | 2017 | 10 | Marker7632755 | Marker7723217 | 76.341 | 76.341 | 39,427,048 | 39,517,256 | 2.298 | 0.174 | 4.151 |
qPA15-1 | 2018 | 15 | Marker5381863 | Marker5394023 | 43.494 | 43.78 | 9,218,139 | 9,387,049 | 6.528 | 0.259 | 10.066 |
qPA15-2 | 2019 | 15 | Marker5381863 | Marker5394023 | 43.494 | 43.78 | 9,218,139 | 9,387,049 | 3.999 | 0.261 | 9.526 |
Gene | SNP | Indel | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Intergenic | Upstream | Downstream | Nonsynonymous SNV | Synonymous SNV | Intronic | 3′UTR | Intergenic | Upstream | Downstream | Non-Frameshift Deletion | Non-Frameshift Insertion | 5′ UTR | |
Glyma.15g119200 | 5 | 10 | 2 | 3 | |||||||||
Glyma.15g119300 | 3 | 8 | 1 | 2 | 1 | ||||||||
Glyma.15g119400 | 3 | 1 | 1 | 4 | 3 | 1 | |||||||
Glyma.15g119500 | 7 | 6 | 1 | 3 | 4 | 7 | 1 | 3 | |||||
Glyma.15g119600 | 14 | 23 | 2 | 5 | |||||||||
Glyma.15g119700 | 15 | 13 | 2 | 1 | 4 | 3 | 1 | ||||||
Glyma.15g119800 | 21 | 20 | 5 | 8 | 3 | ||||||||
Total | 319 | 68 | 80 | 12 | 1 | 1 | 11 | 77 | 17 | 23 | 1 | 1 | 5 |
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Xue, Y.; Gao, H.; Liu, X.; Tang, X.; Cao, D.; Luan, X.; Zhao, L.; Qiu, L. QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.). Int. J. Mol. Sci. 2022, 23, 11273. https://doi.org/10.3390/ijms231911273
Xue Y, Gao H, Liu X, Tang X, Cao D, Luan X, Zhao L, Qiu L. QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.). International Journal of Molecular Sciences. 2022; 23(19):11273. https://doi.org/10.3390/ijms231911273
Chicago/Turabian StyleXue, Yongguo, Huawei Gao, Xinlei Liu, Xiaofei Tang, Dan Cao, Xiaoyan Luan, Lin Zhao, and Lijuan Qiu. 2022. "QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.)" International Journal of Molecular Sciences 23, no. 19: 11273. https://doi.org/10.3390/ijms231911273