Abstract
Genome wide association studies (GWAS) have been traditionally used for the identification and comprehension of loci associate with phenotypic variation and identification of markers useful in genetic breeding programs. The GWAS was used in this work to identify chromosomal regions with significant associations with the main agronomic trait of Coffea canephora. The studied population comprised 165 clones of the two varietal groups Conilon and Robusta and intervarietal hybrids from crosses between these groups. Coffee trees were genotyped using 17 885 single nucleotide polymorphisms (SNP) markers distributed throughout the genome and phenotyped with eight morpho agronomic traits. Significant SNPs were found associated with plant height, diameter of the canopy projection, vegetative vigor, rust incidence, and cercosporiosis incidence. SNP marker distribution was quite uniform, with few gaps in the centromeric regions, with 27.72% and 9.09% present in intergenic and coding regions, respectively; the latter led to 70% amino acid exchanges and 30% silent mutations. Candidate genes, in which SNP markers were inserted, were identified and their function was related to traits of plant architecture and coffee diseases resistance. SNPs with significant associations were found in all chromosomes of the species, especially in chromosomes 0, 2, 6, 9, and 11. This methodology was efficient in C. canephora populations and helped identify several SNPs in candidate genes involved in important biological processes of coffee. Therefore, these SNPs can be used as strategies to accelerate the coffee breeding program through molecular marker assisted selection.
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Acknowledgements
This work was supported by the Brazilian Coffee Research and Development Consortium (Consórcio Pesquisa Café – CBP&D/Café), by the Foundation for Research Support of the state of Minas Gerais (FAPEMIG), by the National Council of Scientific and Technological Development (CNPq), by the National Institutes of Science and Technology of Coffee (INCT/Café) and Coordination for the Improvement of Higher Education Personnel (CAPES).
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Conceptualization, ETC, LFS; methodology, LFS, ERA, RAS and TVS; data analysis, LFS, MN, PRRMB, BGL; validation and formal analysis, ETC and MN; investigation, LFS, ACAS, ETC; writing—original draft preparation, LFS, ACAS; writing—review and editing LFS, ACAS, MN, ETC; supervision, ETC, MN; funding acquisition, ETC.
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de Faria Silva, L., Alkimim, E.R., Barreiro, P.R.R.M. et al. Genome-wide association study of plant architecture and diseases resistance in Coffea canephora. Euphytica 218, 92 (2022). https://doi.org/10.1007/s10681-022-03042-8
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DOI: https://doi.org/10.1007/s10681-022-03042-8