Coffee Berry Disease (CBD) caused by the fungal pathogen Colletotrichum kahawae destroys about 80% of the crop on susceptible Coffea arabica cultivars if no control is applied. Resistance to CBD is governed by three genes: T, R that are dominant, and the recessive k in varieties Hibrido de Timor, Rume Sudan (RS), and K7 respectively. The marker for the T-gene had earlier been identified. The study aimed to identify the DNA marker for the R-gene from RS. The mapping population comprised of 106 F2 genotypes from varieties RS (resistant) and SL28 (susceptible). The genotypes were assessed for their reaction to CBD using hypocotyl inoculation test on a scale of 1–12. The Single Nucleotide Polymorphism (SNP) markers were obtained through Genotyping by Sequencing. The population structure was assessed by both principal component analysis and marker-based kinship while pairwise linkage disequilibrium was estimated using squared allele frequency correlations (r2). Genome-Wide Association Study was carried out using a compressed mixed linear model in Genomic Association and Prediction Integrated Tool. Two SNP markers were significantly associated with CBD resistance in coffee Chromosomes (Chr) 1 and 2 accounting for 12.5% and 11% respectively of the total phenotypic variation explained by the model. The sequence search for the markers was associated with proteins for disease resistance within the NCBI database. The two SNP markers 100025973|F|0-59:T > C-59:T > C and 100034991|F|0-44:C > T-44:C > T are identified as DNA markers for the genetic loci conferring resistance to CBD in RS, christened as Ck-2 and Ck-3 and are recommended for marker assisted selection.

中文翻译：

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全基因组关联研究确定了在阿拉比卡咖啡变种中赋予对咖啡浆果病 (Colletotrichum kahawae) 抗性的遗传位点。苏梅苏丹

如果不使用控制措施，由真菌病原体 Colletotrichum kahawae 引起的咖啡浆果病 (CBD) 会破坏易感小粒咖啡品种的约 80% 的作物。CBD 的抗性由三个基因控制：分别是 Hibrido de Timor、Rume Sudan (RS) 和 K7 品种中的显性 T、R 和隐性 k。T基因的标记早先已经被鉴定出来。该研究旨在从 RS 中鉴定 R 基因的 DNA 标记。作图群体由来自 RS（抗性）和 SL28（易感）品种的 106 个 F2 基因型组成。使用 1-12 级的下胚轴接种试验评估基因型对 CBD 的反应。单核苷酸多态性 (SNP) 标记是通过测序进行基因分型获得的。通过主成分分析和基于标记的亲属关系评估种群结构，而使用平方等位基因频率相关性 (r2) 估计成对连锁不平衡。使用基因组关联和预测集成工具中的压缩混合线性模型进行全基因组关联研究。两个 SNP 标记与咖啡染色体 (Chr) 1 和 2 中的 CBD 抗性显着相关，分别占模型解释的总表型变异的 12.5% 和 11%。标记的序列搜索与 NCBI 数据库中的抗病蛋白质相关。两个 SNP 标记 100025973|F|0-59:T > C-59:T > C 和 100034991|F|0-44:C > T-44:C > T 被鉴定为赋予抗性的基因座的 DNA 标记到 RS 的 CBD，