Ariyoshi Caroline, Sant'ana Gustavo César, Felicio Mariane Silva, Sera Gustavo Hiroshi, Nogueira Livia Maria, Rodrigues Lucas Mateus Rivero, Ferreira Rafaelle Vecchia, da Silva Bruna Silvestre Rodrigues, de Resende Mário Lúcio Vilela, Destéfano Suzete Aparecida Lanza, Domingues Douglas Silva, Pereira Luiz Filipe Protasio
Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil.
Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil.
Front Plant Sci. 2022 Oct 18;13:989847. doi: 10.3389/fpls.2022.989847. eCollection 2022.
Bacteria halo blight (BHB), a coffee plant disease caused by pv. , has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of , we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C Ethiopian accessions from a historical FAO collection, 11 C cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to (Chr_0_434_435) and genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a susceptible cultivar and in a cultivar with quantitative resistance, when infected with pv. . However, peaks of upregulation were observed in a cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in . In addition, the findings contribute to increasing understanding of the domestication history.
细菌性晕疫病（BHB）是一种由[病原菌名称]pv.引起的咖啡植株病害，在山区、温和气候地区以及咖啡苗圃中日益受到关注。大多数咖啡品种对这种病害敏感。相比之下，埃塞俄比亚种质中存在丰富的遗传多样性和对BHB的抗性。为了鉴定与BHB抗性相关的数量性状核苷酸（QTNs）以及这些基因组区域在[咖啡品种名称]驯化过程中的影响，我们进行了群体结构分析和全基因组关联研究（GWAS）。为此，我们使用了简化基因组测序（GBS）以及对来自联合国粮农组织历史收集的120份埃塞俄比亚种质、11个[咖啡品种名称]品种和BA - 10基因型的BHB抗性进行表型分析。基于单核苷酸多态性（SNP）标记的群体结构分析表明，这132份种质分为3个簇：大多数野生埃塞俄比亚种质、驯化的埃塞俄比亚种质和品种。GWAS使用单基因座模型MLM以及多基因座模型mrMLM、FASTmrMLM、FASTmrEMMA和ISIS EM - BLASSO，鉴定出11个与BHB抗性相关的QTNs。在这些QTNs中，与BHB抗性关联值最高的4个与[基因名称1]（Chr_0_434_435）和[基因名称2]基因相关，预计它们分别编码一种丝氨酸/苏氨酸激酶蛋白和一个富含亮氨酸重复序列的核苷酸结合位点（NBS - LRR）。当用[病原菌名称]pv.感染时，这些基因在一个[咖啡品种名称]易感品种和一个具有数量抗性的[咖啡品种名称]品种中显示出相似的转录下调谱。然而，在一个具有质量抗性的[咖啡品种名称]品种中，这两个基因均观察到上调峰值。我们的结果提供了有潜力应用于标记辅助选择（MAS）的SNP，并扩展了我们对[咖啡品种名称]中BHB抗性复杂遗传控制的理解。此外，这些发现有助于增进对[咖啡品种名称]驯化历史的了解。
