Genome-wide association study of plant architecture and diseases resistance in Coffea canephora

• Published in: Euphytica Vol. 218; no. 7
• Main Authors: de Faria Silva, Letícia, Alkimim, Emilly Ruas, Barreiro, Pedro Ricardo Rossi Marques, Leichtweis, Bruno Grespan, Silva, Ana Carolina Andrade, da Silva, Ruane Alice, Sousa, Tiago Vieira, Nascimento, Moysés, Caixeta, Eveline Teixeira
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-07-2022; Springer; Springer Nature B.V
• Subjects: Agronomy; Amino acids; Biological activity; Biomedical and Life Sciences; Biotechnology; Breeding; Chromosomes; Coffea canephora; Coffee; Coffee industry; Genes; Genetic aspects; Genome-wide association studies; Genomes; Genomics; Hybrids; Life Sciences; Marker-assisted selection; Markers; Medical research; Medicine, Experimental; Mutation; Nucleotides; Phenotypic variations; Plant diseases; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Population studies; Review; Rust fungi; Single nucleotide polymorphisms; Single-nucleotide polymorphism; SNP markers; Cofee; SAM; Candidate genes
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-022-03042-8

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.