Genome-Wide Association Analysis of Grain Hardness in Common Wheat
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Grain Hardness (HI) Measurement and Grading
2.3. Statistical Analysis
2.4. Chip Typing and Population Structure Analysis
2.5. Correlation Analysis
2.6. Candidate Gene Screening
3. Results
3.1. Phenotype Analysis
3.2. Variance and Correlation Analysis
3.3. Grain Hardness Loci Identified by GWAS
3.4. Functional Prediction of Candidate Genes
4. Discussion
4.1. Phenotypic Variation of Wheat Grain Hardness
4.2. Genome-Wide Association Analysis of Wheat Grain Hardness
4.3. Candidate Gene Prediction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Type | Environment | Min | Max | Mean | SD | CV% |
---|---|---|---|---|---|---|
Hard wheat | E1 | 38.00 | 75.00 | 62.86 | 5.42 | 8.62 |
E2 | 54.00 | 74.00 | 64.57 | 4.53 | 7.01 | |
E3 | 48.00 | 83.00 | 66.08 | 6.97 | 10.55 | |
E4 | 56.00 | 73.00 | 63.88 | 4.75 | 7.44 | |
BLUP | 60.19 | 72.64 | 63.95 | 3.26 | 5.10 | |
Mix wheat | E1 | 47.00 | 61.00 | 55.14 | 3.38 | 6.12 |
E2 | 41.00 | 63.00 | 55.49 | 5.11 | 9.21 | |
E3 | 42.00 | 70.00 | 55.78 | 5.74 | 10.28 | |
E4 | 39.00 | 65.00 | 55.05 | 4.74 | 8.60 | |
BLUP | 47.99 | 59.95 | 55.18 | 2.95 | 5.34 | |
Soft wheat | E1 | 15.00 | 42.00 | 27.19 | 5.66 | 20.81 |
E2 | 15.00 | 44.00 | 28.90 | 5.71 | 19.77 | |
E3 | 15.00 | 42.00 | 28.44 | 6.12 | 21.53 | |
E4 | 21.00 | 64.00 | 32.69 | 7.99 | 24.44 | |
BLUP | 19.44 | 40.91 | 29.74 | 4.64 | 15.59 |
Type | Genotype | Environment | Genotype × Environment | H2 |
---|---|---|---|---|
Hardness wheat | 1.68 * | 3.62 | 0.98 | 0.63 |
Mix wheat | 1.77 * | 0.02 | 0.70 | 0.71 |
Soft wheat | 3.02 *** | 13.11 *** | 0.853 | 0.81 |
Classification Standard | SNP | Chr. | Position (Mb) | p Value | R2 (%) | Environment |
---|---|---|---|---|---|---|
Hardness Index | AX-111028882 | 1A | 27.39–31.94 | 1.10 × 10−4–9.74 × 10−4 | 7.63–10.66 | E1, E2, E3, E4, BLUP |
AX-110005500 | 7D | 568.20 | 1.17 × 10−4–8.84 × 10−4 | 7.52–10.57 | E1, E2, E3, E4, BLUP | |
Assignment | AX-108789085 | 1A | 24.86–32.43 | 9.75 × 10−5–9.44 × 10−4 | 7.77–10.86 | E1, E2, E3, BLUP |
AX-108899745 | 1A | 42.55–49.23 | 9.35 × 10−5–9.31 × 10−4 | 7.72–11.01 | E1, E2, E3, BLUP | |
AX-109815102 | 3B | 606.68 | 1.24 × 10−4–3.77 × 10−4 | 9.00–10.61 | E1, E2, BLUP | |
AX-111673206 | 4B | 656.90–661.26 | 3.60 × 10−4–9.83 × 10−4 | 7.63–9.00 | E1, E2, E4 | |
AX-110005500 | 7D | 568.20 | 8.12 × 10−5–8.55 × 10−4 | 7.91–11.12 | E1, E2, E3, BLUP |
SNP | Chr. | Position (Mb) | Gene | Gene Annotation or Coding Protein | Previously Reported |
---|---|---|---|---|---|
AX-108789085 | 1A | 24.86–32.43 | TraesCS1A01G045700 | Glutathione S-transferase | 2013_Mergoum_3 [13] |
AX-108899745 | 1A | 42.55–49.23 | TraesCS1A01G062500 | Protease inhibitor/seed storage/lipid transfer protein family protein | qHA1A.1 [34] |
AX-109815102 | 3B | 606.68 | TraesCS3B01G386000 | O-Glycosyl hydrolases family 17 protein | - |
AX-111673206 | 4B | 656.90–661.26 | TraesCS4B01G372800 | F-box family protein | qHA4B.3 [27] |
AX-110005500 | 7D | 568.20 | TraesCS7D01G448100 | Protease inhibitor/seed storage/lipid transfer family protein | - |
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He, X.; Lu, M.; Cao, J.; Pan, X.; Lu, J.; Zhao, L.; Zhang, H.; Chang, C.; Wang, J.; Ma, C. Genome-Wide Association Analysis of Grain Hardness in Common Wheat. Genes 2023, 14, 672. https://doi.org/10.3390/genes14030672
He X, Lu M, Cao J, Pan X, Lu J, Zhao L, Zhang H, Chang C, Wang J, Ma C. Genome-Wide Association Analysis of Grain Hardness in Common Wheat. Genes. 2023; 14(3):672. https://doi.org/10.3390/genes14030672
Chicago/Turabian StyleHe, Xianfang, Maoang Lu, Jiajia Cao, Xu Pan, Jie Lu, Li Zhao, Haiping Zhang, Cheng Chang, Jianlai Wang, and Chuanxi Ma. 2023. "Genome-Wide Association Analysis of Grain Hardness in Common Wheat" Genes 14, no. 3: 672. https://doi.org/10.3390/genes14030672
APA StyleHe, X., Lu, M., Cao, J., Pan, X., Lu, J., Zhao, L., Zhang, H., Chang, C., Wang, J., & Ma, C. (2023). Genome-Wide Association Analysis of Grain Hardness in Common Wheat. Genes, 14(3), 672. https://doi.org/10.3390/genes14030672