Abstract
Coffee Berry Disease (CBD) is a major constraint that limits Coffea arabica production, whose resistance is governed by three genes, T, R that are dominant and recessive k in varieties Hibrido de Timor (HDT), Rume Sudan (RS) and K7 respectively. This study identified the genomic region occupied by R-gene using F2 genotypes from varieties RS and SL28; and Single Nucleotide Polymorphic (SNP) markers obtained through Genotyping by Sequencing. Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. The Linkage map spread over 5525.39 cM across eleven coffee chromosomes (Chr). The QTL was analyzed by both Interval Mapping (IM) and Inclusive Composite Interval Mapping (ICIM) using SNP markers and CBD resistance mean scores of the F2 genotypes and their parents. Three QTLs, qCBD 1-1 in Chr 1, qCBD 2-1 and qCBD 2-2 in Chr 2 were significantly associated with CBD resistance, detected by both IM and ICIM at LOD ≥ 2.5 (P≤0.05). Two flanking markers that were closer to the three QTLs; 100025973|F|0-59:T>C-59:T>C at a distance of 3 centi Morgans (cM) from qCBD 1-1 and 100034991|F|0-44:C>T-44:C>T, that was flanking in both qCBD 2-1 and qCBD 2-2 at 12.5 cM, whose SNPs were significant (P≤0.05), are recommended for validation and use in marker-assisted breeding. Key words: Coffee berry disease, linkage map, quantitative trait loci, genotyping by sequencing, single nucleotide polymorphism, SL 28, R-gene.
Highlights
Coffee Berry Disease (CBD) is caused by the fungal pathogen Colletotrichum kahawae Waller & Bridge (Waller et al, 1993) and is a major constraint to Coffea arabica L. production in African countries with a possibility of occurrence in other coffee-growing countries in the world (Van Der Vossen et al, 2015)
This study aims to identify the genetic region for R-gene that confers resistance to CBD in Coffea arabica variety Rume Sudan through bi-parental quantitative trait loci (QTL) mapping using GBS-based Single Nucleotide Polymorphic (SNP) markers
1170 SNP markers were anchored to the 11 coffee chromosomes that were utilized for further analysis in the study
Summary
Coffee Berry Disease (CBD) is caused by the fungal pathogen Colletotrichum kahawae Waller & Bridge (Waller et al, 1993) and is a major constraint to Coffea arabica L. production in African countries with a possibility of occurrence in other coffee-growing countries in the world (Van Der Vossen et al, 2015). C. arabica L. is a simple tetraploid (2n = 4x = 44) and the only tetraploid species of coffee, formed out of two diploids species, Coffea canephora and Coffea eugenioides (Lashermes et al, 2011) This species is genetically less diverse in comparison to its parental diploid species (Baruah et al, 2003), a situation that has been associated with its susceptibility to diseases (Prakash et al, 2002) and hinders molecular breeding tools development for the breeding process (Sant’Ana et al, 2018). Studies on the source and selection for resistance to CBD date back to 1974 (Robinson, 1976) but significant breakthrough on selection was on the discovery of the hypocotyl inoculation test on six-weekold seedlings This revealed that the mechanism of CBD resistance in the field conditions was similar to the reaction of CBD inoculum in the hypocotyl of a six-weekold seedling (Van Der Vossen et al, 1976)
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