African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6401

Full Length Research Paper

Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller & Bridge) in Coffea arabica L. variety Rume Sudan

James Mwita Gimase
  • James Mwita Gimase
  • Kenya Agricultural and Livestock Research Organization (KALRO) - Coffee Research Institute, P. O. Box 4-00232, Ruiru, Kenya.
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Wilson Muriithi Thagana
  • Wilson Muriithi Thagana
  • Department of Agricultural Science and Technology, School of Agriculture and Enterprise Development, Kenyatta University, P.O Box 43844 – 00100, Nairobi, Kenya.
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Chrispine Ogutu Omondi
  • Chrispine Ogutu Omondi
  • KALRO – Sugar Research Institute, P. O. Box 44- 40100, Kisumu, Kenya.
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Jane Jerono Cheserek
  • Jane Jerono Cheserek
  • Kenya Agricultural and Livestock Research Organization (KALRO) - Coffee Research Institute, P. O. Box 4-00232, Ruiru, Kenya.
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Bernard Mukiri Gichimu
  • Bernard Mukiri Gichimu
  • Department of Agricultural Resource Management, School of Agriculture, University of Embu, P. O. Box 6 - 60100, Embu, Kenya.
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Elijah Kathurima Gichuru
  • Elijah Kathurima Gichuru
  • Kenya Agricultural and Livestock Research Organization (KALRO) - Coffee Research Institute, P. O. Box 4-00232, Ruiru, Kenya.
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  •  Received: 10 March 2020
  •  Accepted: 23 June 2020
  •  Published: 31 August 2020

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.