Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller & Bridge) in Coffea arabica L. variety Rume Sudan
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Date
2020
Authors
Gimase, James Mwita
Thagana, Wilson Muriithi
Omondi, Chrispine Ogutu
Cheserek, Jane Jerono
Gichimu, Bernard Mukiri
Gichuru, Elijah Kathurima
Journal Title
Journal ISSN
Volume Title
Publisher
Academic Journals
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.
Description
A research article published in African Journal of Agricultural
Research
Keywords
Coffee berry disease, linkage map, quantitative trait loci, genotyping by sequencing, single nucleotide, polymorphism, SL 28, R-gene
Citation
Gimase, J. M., Thagana, W. M., Omondi, C. O., Cheserek, J. J., Gichimu, B. M., & Gichuru, E. K. (2020). Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller Bridge) in Coffea arabica L. variety Rume Sudan. African Journal of Agricultural Research, 16(8), 1184-1194.