Genome-Wide Association Study Based on Plant Height and Drought-Tolerance Indices Reveals Two Candidate Drought-Tolerance Genes in Sweet Sorghum
Abstract
1. Introduction
2. Materials and Methods
2.1. Test Materials and Experimental Design
2.2. Measurements and Data Analysis
3. Results
3.1. Distribution of PH and Drought-Tolerance Indices in Sweet Sorghum
3.2. SNP Marker Density Distribution
3.3. Principal Component Analysis of Genotype Data
3.4. GWAS of Drought-Tolerance Indices
3.5. Gene Function Annotation
4. Discussion
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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Chromosome | Length (bp) | No. of SNPs | Average Density (SNPs/Mb) |
---|---|---|---|
1 | 72,621,628 | 392 | 5.4 |
2 | 77,923,599 | 340 | 4.4 |
3 | 74,347,826 | 379 | 5.1 |
4 | 67,928,809 | 243 | 3.6 |
5 | 61,993,318 | 615 | 10.0 |
6 | 61,563,909 | 284 | 4.6 |
7 | 64,298,007 | 266 | 4.1 |
8 | 54,875,046 | 271 | 4.9 |
9 | 59,493,343 | 2401 | 40.4 |
10 | 60,355,397 | 995 | 16.5 |
Marker | Variant | Effect | p-Value | Methods |
---|---|---|---|---|
SNP-9-46359555 | T/C | 0.259 | 1.34 × 10−6 | MP.GLM |
SNP-9-32010157 | T/C | −0.800 | 5.43 × 10−6 | MP.FarmCPU |
SNP-8-54701961 | C/T | −0.280 | 5.27 × 10−6 | MP.FarmCPU |
SNP-8-50726311 | C/G | −0.180 | 3.37 × 10−7 | MP.GLM |
SNP-8-42803746 | G/A | −0.100 | 1.22 × 10−7 | MP.FarmCPU |
SNP-8-42803746 | G/A | −0.140 | 1.57 × 10−6 | MP.GLM |
SNP-7-49761327 | G/C | −0.503 | 5.68 × 10−6 | MP.GLM |
SNP-6-21397577 | T/C | −0.776 | 1.73 × 10−12 | MP.FarmCPU |
SNP-6-21397577 | T/C | −0.745 | 1.84 × 10−6 | MP.MLM |
SNP-4-1724051 | C/T | −0.099 | 3.23 × 10−6 | MP.FarmCPU |
SNP-4-12346536 | A/T | −0.293 | 2.50 × 10−9 | MP.FarmCPU |
SNP-3-71564436 | A/C | −0.336 | 2.98 × 10−7 | MP.GLM |
SNP-3-69226243 | A/G | −0.287 | 1.40 × 10−6 | MP.GLM |
SNP-3-38408072 | C/A | −0.140 | 1.63 × 10−6 | MP.GLM |
SNP-2-62168227 | A/C | 0.137 | 1.72 × 10−6 | MP.FarmCPU |
SNP-1-60603003 | T/C | 0.316 | 3.69 × 10−6 | MP.GLM |
SNP-10-45922678 | T/C | −0.208 | 1.57 × 10−7 | MP.FarmCPU |
SNP-10-3166515 | C/T | 0.349 | 1.21 × 10−9 | MP.FarmCPU |
SNP-10-24652464 | T/C | 0.561 | 5.82 × 10−12 | MP.FarmCPU |
Marker | Variant | Effect | p-Value | Methods |
---|---|---|---|---|
SNP-9-40211466 | A/T | −0.920 | 1.42 × 10−6 | RDI.GLM |
SNP-9-40211466 | A/T | −1.479 | 5.15 × 10−9 | RDI.MLM |
SNP-9-40211299 | T/A | −1.059 | 6.28 × 10−9 | RDI.GLM |
SNP-9-40211299 | T/A | −1.504 | 8.32 × 10−10 | RDI.MLM |
SNP-9-18625001 | G/A | −0.991 | 3.42 × 10−18 | RDI.FarmCPU |
SNP-9-18625001 | G/A | −1.059 | 6.28 × 10−9 | RDI.GLM |
SNP-9-18625001 | G/A | −1.504 | 8.32 × 10−10 | RDI.MLM |
SNP-8-48976460 | T/C | −0.237 | 6.46 × 10−6 | RDI.GLM |
SNP-7-59879988 | T/A | 0.098 | 8.80 × 10−8 | RDI.FarmCPU |
SNP-7-57772159 | T/A | −0.059 | 3.74 × 10−7 | RDI.FarmCPU |
SNP-7-51913862 | T/C | 0.069 | 5.20 × 10−8 | RDI.FarmCPU |
SNP-7-2876065 | A/G | −0.102 | 5.05 × 10−7 | RDI.FarmCPU |
SNP-6-23330464 | C/G | −0.064 | 5.51 × 10−7 | RDI.FarmCPU |
SNP-6-153673 | A/G | −0.091 | 2.07 × 10−6 | RDI.GLM |
SNP-3-48129228 | T/G | 0.183 | 3.09 × 10−8 | RDI.FarmCPU |
SNP-3-48129228 | T/G | 0.270 | 1.30 × 10−6 | RDI.GLM |
SNP-2-60765047 | T/C | −0.064 | 5.09 × 10−10 | RDI.FarmCPU |
SNP-2-54990996 | T/A | −0.076 | 3.20 × 10−9 | RDI.FarmCPU |
SNP-10-7591972 | C/T | −0.125 | 1.82 × 10−7 | RDI.FarmCPU |
Marker | Variant | Effect | p-Value | Methods |
---|---|---|---|---|
SNP-1-60603003 | T/C | 0.122 | 3.11 × 10−6 | STI.FarmCPU |
SNP-9-21304761 | G/C | 0.169 | 1.26 × 10−6 | STI.FarmCPU |
SNP-9-21304761 | G/C | 0.210 | 5.34 × 10−6 | STI.GLM |
SNP-8-50726311 | C/G | −0.112 | 9.58 × 10−8 | STI.GLM |
SNP-8-43496503 | A/G | −0.136 | 7.33 × 10−6 | STI.GLM |
SNP-8-42803746 | G/A | −0.068 | 9.16 × 10−7 | STI.FarmCPU |
SNP-8-41546525 | T/C | −0.161 | 2.65 × 10−6 | STI.GLM |
SNP-8-38378608 | G/T | −0.157 | 9.75 × 10−7 | STI.GLM |
SNP-7-14894170 | T/C | −0.198 | 2.70 × 10−7 | STI.GLM |
SNP-6-24638786 | T/C | −0.116 | 6.40 × 10−6 | STI.GLM |
SNP-6-24155091 | C/G | −0.119 | 4.23 × 10−6 | STI.GLM |
SNP-6-23766693 | G/C | −0.120 | 1.90 × 10−6 | STI.GLM |
SNP-6-23020118 | T/C | −0.114 | 6.21 × 10−6 | STI.GLM |
SNP-6-22967016 | C/T | −0.114 | 4.32 × 10−6 | STI.GLM |
SNP-6-22966971 | A/G | −0.120 | 1.86 × 10−6 | STI.GLM |
SNP-6-21397577 | T/C | −0.398 | 1.07 × 10−7 | STI.FarmCPU |
SNP-6-21397577 | T/C | −0.426 | 7.49 × 10−6 | STI.MLM |
SNP-6-18184340 | T/C | −0.138 | 2.78 × 10−7 | STI.GLM |
SNP-6-16486758 | T/C | −0.147 | 1.48 × 10−7 | STI.GLM |
SNP-6-153673 | A/G | −0.108 | 7.35 × 10−7 | STI.GLM |
SNP-4-47497728 | T/C | −0.178 | 3.13 × 10−6 | STI.GLM |
SNP-4-22602002 | A/G | −0.249 | 5.12 × 10−8 | STI.GLM |
SNP-4-11561108 | T/G | −0.164 | 1.44 × 10−6 | STI.GLM |
SNP-4-11561107 | G/C | −0.164 | 1.44 × 10−6 | STI.GLM |
SNP-4-10100565 | G/C | −0.206 | 1.98 × 10−6 | STI.GLM |
SNP-3-73977961 | C/A | −0.145 | 9.30 × 10−9 | STI.GLM |
SNP-3-73977959 | T/A | −0.145 | 9.30 × 10−9 | STI.GLM |
SNP-3-73977947 | T/A | −0.145 | 9.30 × 10−9 | STI.GLM |
SNP-3-71564436 | A/C | −0.246 | 2.12 × 10−10 | STI.GLM |
SNP-3-70162204 | A/G | −0.165 | 6.51 × 10−7 | STI.GLM |
SNP-3-69226243 | A/G | −0.201 | 1.24 × 10−8 | STI.GLM |
SNP-3-63949295 | G/C | −0.213 | 8.63 × 10−8 | STI.GLM |
SNP-3-48129228 | T/G | 0.240 | 4.95 × 10−8 | STI.FarmCPU |
SNP-3-48129228 | T/G | 0.293 | 4.99 × 10−6 | STI.GLM |
SNP-2-75743471 | G/T | −0.159 | 4.57 × 10−8 | STI.GLM |
SNP-2-54990998 | T/C | −0.120 | 5.33 × 10−6 | STI.GLM |
SNP-2-54990996 | T/A | −0.120 | 5.33 × 10−6 | STI.GLM |
SNP-2-53243721 | C/T | 0.486 | 3.35 × 10−7 | STI.GLM |
SNP-2-49409474 | C/G | −0.176 | 3.93 × 10−6 | STI.GLM |
SNP-2-39852357 | A/G | −0.205 | 1.67 × 10−6 | STI.GLM |
SNP-1-159169 | G/T | −0.182 | 4.54 × 10−6 | STI.GLM |
SNP | Genes | Gene Function Annotation |
---|---|---|
SNP-1-159169 | Sb01g000300.1 | transcriptional corepressor Leunig-homolog-like [Sorghum bicolor], |
Zea mays LOC100285229 (pco116270) | ||
SNP-1-60603003 | Sb01g037050.1 | TF TGA2.2 [Sorghum bicolor], |
Zea mays putative bZIP TF | ||
(LOC100274089) | ||
SNP-1-60603003 | Sb01g037050.2 | TF TGA2.2 [Sorghum bicolor], |
Zea mays putative bZIP TF | ||
(LOC100274089) | ||
SNP-1-60603003 | Sb01g037050.3 | TF TGA2.2 [Sorghum bicolor], |
Setaria italica TF HBP-1b(c1)-like (LOC101767047), | ||
transcript variant X1, mRNA | ||
SNP-1-60603003 | Sb01g037050.4 | TF TGA2.2 [Sorghum bicolor], |
Zea mays putative bZIP TF | ||
(LOC100274089) | ||
SNP-8-50726311 | Sb08g019720.1 | TF LUX-like [Oryza brachyantha], |
Sorghum bicolor hypothetical protein, mRNA, | ||
MYB family TF EFM, Arabidopsis thaliana |
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Xin, Y.; Gao, L.; Hu, W.; Gao, Q.; Yang, B.; Zhou, J.; Xu, C. Genome-Wide Association Study Based on Plant Height and Drought-Tolerance Indices Reveals Two Candidate Drought-Tolerance Genes in Sweet Sorghum. Sustainability 2022, 14, 14339. https://doi.org/10.3390/su142114339
Xin Y, Gao L, Hu W, Gao Q, Yang B, Zhou J, Xu C. Genome-Wide Association Study Based on Plant Height and Drought-Tolerance Indices Reveals Two Candidate Drought-Tolerance Genes in Sweet Sorghum. Sustainability. 2022; 14(21):14339. https://doi.org/10.3390/su142114339
Chicago/Turabian StyleXin, Yue, Lina Gao, Wenming Hu, Qi Gao, Bin Yang, Jianguo Zhou, and Cuilian Xu. 2022. "Genome-Wide Association Study Based on Plant Height and Drought-Tolerance Indices Reveals Two Candidate Drought-Tolerance Genes in Sweet Sorghum" Sustainability 14, no. 21: 14339. https://doi.org/10.3390/su142114339
APA StyleXin, Y., Gao, L., Hu, W., Gao, Q., Yang, B., Zhou, J., & Xu, C. (2022). Genome-Wide Association Study Based on Plant Height and Drought-Tolerance Indices Reveals Two Candidate Drought-Tolerance Genes in Sweet Sorghum. Sustainability, 14(21), 14339. https://doi.org/10.3390/su142114339