High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover
Abstract
1. Introduction
2. Materials and Methods
2.1. Fenugreek Genotypes Collection
2.2. DNA Extraction and Library Preparation for Sequencing
2.3. Bioinformatics and Statistical Analyses
2.4. Population Structure Estimation
2.5. Phenotyping and Association Mapping
2.6. Homology Analysis to Predict Candidate Genes
3. Results
3.1. Sequencing Quality
3.2. Population Structure and Genetic Diversity
3.3. Association Mapping
3.4. Homology Analysis to Predict Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Trait | SNP | −LOG10 (P) | MAF | R2 | FDR | Sequences of ddRAD Primers |
---|---|---|---|---|---|---|
Seed Length | dDocent_Contig_466_145 | 6.71 | 0.36 | 0.39 | 0.007 | GAGACTGCTGAATTTTCCAAGTGTATTAAGTTTGAGAATGGTCTGCGTGC[T]GAGATTAAGTGGGCCATTGGGTACCAGAAGATCNNNNNNNNNNTAATTCT |
Seed Width | dDocent_Contig_466_145 | 8.36 | 0.36 | 0.46 | 0.000 | |
dDocent_Contig_39741_151 | 6.88 | 0.28 | 0.38 | 0.002 | TTGAAGGTTGCTAAGGAGGGCGCTGGCTCGGCAGGTCCGAAGGAGACTGC[T]GAGATTGCCAGCCTCAGTCGCGCAGAGTTGATCNNNNNNNNNNAATTCTG | |
Seed Color | dDocent_Contig_84790_24 | 6.32 | 0.05 | 0.28 | 0.016 | NAATTCTAACTCTTCCCGTAGTG[C]TGGCCCCCGTTCTCCAACTGAGTACGTTCATCTCGATTGGGATGACGGCC |
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Abd El-Wahab, M.M.H.; Aljabri, M.; Sarhan, M.S.; Osman, G.; Wang, S.; Mabrouk, M.; El-Shabrawi, H.M.; Gabr, A.M.M.; Abd El-Haliem, A.M.; O'Sullivan, D.M.; et al. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes 2020, 11, 893. https://doi.org/10.3390/genes11080893
Abd El-Wahab MMH, Aljabri M, Sarhan MS, Osman G, Wang S, Mabrouk M, El-Shabrawi HM, Gabr AMM, Abd El-Haliem AM, O'Sullivan DM, et al. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes. 2020; 11(8):893. https://doi.org/10.3390/genes11080893
Chicago/Turabian StyleAbd El-Wahab, Mustafa M. H., Maha Aljabri, Mohamed S. Sarhan, Gamal Osman, Shichen Wang, Mahmoud Mabrouk, Hattem M. El-Shabrawi, Ahmed M. M. Gabr, Ahmed M. Abd El-Haliem, Donal M. O'Sullivan, and et al. 2020. "High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover" Genes 11, no. 8: 893. https://doi.org/10.3390/genes11080893
APA StyleAbd El-Wahab, M. M. H., Aljabri, M., Sarhan, M. S., Osman, G., Wang, S., Mabrouk, M., El-Shabrawi, H. M., Gabr, A. M. M., Abd El-Haliem, A. M., O'Sullivan, D. M., & El-Soda, M. (2020). High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes, 11(8), 893. https://doi.org/10.3390/genes11080893