Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits in Coffea arabica
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Data Evaluation
2.2. Structure Analysis
2.3. SNP Marker Analysis
2.4. Genome-Wide Association Study
2.5. Candidate Genes
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Experimental Conditions
4.2. Phenotypic Evaluation
- y: Equals the data vector;
- u: Equals the vector referring to the overall average in each evaluation year;
- g: Equals the vector of progeny effects (random effect—;
- p: Equals the permanent variance between plants (random effect—);
- r: Equals the variance between types of populations (random effect—);
- b: Equals the between-plot variance (random effect—);
- i: Equals the variance of the interaction progenies years (random effect—);
- e: Equals the vector of residuals (random effect—).
4.3. DNA Extraction and Genotyping
4.4. Quality Control of Molecular Markers
4.5. Genome-Wide Association Study (GWAS)
- is the adjusted phenotype;
- is the population mean;
- i is the fixed effect of the ith SNP, adjusted as a covariate (allele substitution effect);
- is the fixed effect of the kth individual principal component K;
- is the error associated with .
- Rz is the ratio between the phenotypic mean of individuals possessing a specific pair of alleles and the whole population;
- µs is the phenotypic mean of individuals selected for 0, 1, or 2 alleles;
- µg is the general average of all individuals.
4.6. Putative Candidate Genes Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Trait | h2 | Minimum | Maximum | Mean | SD |
---|---|---|---|---|---|
Y | 0.55 | 0.10 | 14.00 | 5.00 | 3.84 |
LL | 0.42 | 2.00 | 17.90 | 12.16 | 1.79 |
LW | 0.44 | 2.40 | 7.90 | 5.13 | 0.89 |
BL | 0.78 | 30.80 | 120.00 | 66.42 | 15.02 |
NRN | 0.49 | 1.00 | 185.00 | 8.52 | 8.24 |
NVN | 0.44 | 1.00 | 22.00 | 9.31 | 2.68 |
NF | 0.49 | 1.00 | 286.00 | 61.38 | 50.26 |
FV | 0.57 | 0.40 | 225.00 | 119.13 | 72.21 |
PH | 0.90 | 1.83 | 283.10 | 164.11 | 31.92 |
CD | 0.90 | 1.33 | 229.10 | 148.57 | 29.26 |
SD | 0.01 | 2.24 | 8.70 | 5.32 | 2.68 |
RFS | 0.50 | 1.00 | 3.00 | 2.33 | 0.60 |
MU | 0.30 | 1.00 | 4.00 | 2.71 | 0.78 |
MC | 0.72 | 1.00 | 5.00 | 2.80 | 0.91 |
Rus | 0.61 | 1.00 | 5.00 | 2.34 | 0.99 |
Cer | 0.38 | 1.00 | 5.00 | 2.51 | 0.72 |
LM | 0.30 | 1.00 | 4.00 | 2.06 | 0.69 |
Vig | 0.70 | 4.00 | 10.00 | 7.23 | 1.19 |
Traits | Type of Evaluation | |
---|---|---|
Yield | (Y) | Liters of fresh cherries harvested per plant |
Leaf length (cm) | (LL) | Measured in the leaf of the third or fourth pair of a plagiotropic branch of the middle third of the plant (cm) |
Leaf width (cm) | (LW) | |
Branch length (cm) | (BL) | Measured in the plagiotropic branch of the middle third of the plant |
Number of reproductive nodes | (NRN) | |
Number of vegetative nodes | (NVN) | |
Total number of fruits | (NF) | |
Fruit volume | (FV) | |
Plant height (cm) | (PH) | Measured in the orthotropic branch (from the soil surface to the final branch growth point) |
Canopy diameter (cm) | (CD) | Measured transversely to the planting row, considering the greatest canopy longest |
Stem diameter (cm) | (SD) | Measured at the stem region of the plant (about 5 cm from the soil surface) |
Ripening fruit size | (RFS) | Evaluated by a score scale ranging from 1 to 3 |
Maturation uniformity | (MU) | Evaluated by a score scale ranging from 1 to 4 |
Maturation cycle | (MC) | Evaluated by a score scale ranging from 1 to 5 |
Rust incidence | (Rus) | |
Cercosporiosis incidence | (Cer) | |
Leaf miner infestation | (LM) | |
Vegetative vigor | (Vig) | Evaluated by a score scale ranging from 1 to 10 |
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da Silva, R.A.; Caixeta, E.T.; Silva, L.d.F.; Sousa, T.V.; Barreiros, P.R.R.M.; Oliveira, A.C.B.d.; Pereira, A.A.; Barreto, C.A.V.; Nascimento, M. Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits in Coffea arabica. Plants 2024, 13, 1876. https://doi.org/10.3390/plants13131876
da Silva RA, Caixeta ET, Silva LdF, Sousa TV, Barreiros PRRM, Oliveira ACBd, Pereira AA, Barreto CAV, Nascimento M. Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits in Coffea arabica. Plants. 2024; 13(13):1876. https://doi.org/10.3390/plants13131876
Chicago/Turabian Styleda Silva, Ruane Alice, Eveline Teixeira Caixeta, Letícia de Faria Silva, Tiago Vieira Sousa, Pedro Ricardo Rossi Marques Barreiros, Antonio Carlos Baião de Oliveira, Antonio Alves Pereira, Cynthia Aparecida Valiati Barreto, and Moysés Nascimento. 2024. "Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits in Coffea arabica" Plants 13, no. 13: 1876. https://doi.org/10.3390/plants13131876
APA Styleda Silva, R. A., Caixeta, E. T., Silva, L. d. F., Sousa, T. V., Barreiros, P. R. R. M., Oliveira, A. C. B. d., Pereira, A. A., Barreto, C. A. V., & Nascimento, M. (2024). Identification of SNP Markers and Candidate Genes Associated with Major Agronomic Traits in Coffea arabica. Plants, 13(13), 1876. https://doi.org/10.3390/plants13131876