Table_1_Single-step genome-wide association study for susceptibility to Teratosphaeria nubilosa and precocity of vegetative phase change in Eucalyptus globulus.xlsx

IntroductionMycosphaerella leaf disease (MLD) is one of the most prevalent foliar diseases of Eucalyptus globulus plantations around the world. Since resistance management strategies have not been effective in commercial plantations, breeding to develop more resistant genotypes is the most promising strategy. Available genomic information can be used to detect genomic regions associated with resistance to MLD, which could significantly speed up the process of genetic improvement.
MethodsWe investigated the genetic basis of MLD resistance in a breeding population of E. globulus which was genotyped with the EUChip60K SNP array. Resistance to MLD was evaluated through resistance of the juvenile foliage, as defoliation and leaf spot severity, and through precocity of change to resistant adult foliage. Genome-wide association studies (GWAS) were carried out applying four Single-SNP models, a Genomic Best Linear Unbiased Prediction (GBLUP-GWAS) approach, and a Single-step genome-wide association study (ssGWAS).
ResultsThe Single-SNP (model K) and GBLUP-GWAS models detected 13 and 16 SNP-trait associations in chromosomes 2, 3 y 11; whereas the ssGWAS detected 66 SNP-trait associations in the same chromosomes, and additional significant SNP-trait associations in chromosomes 5 to 9 for the precocity of phase change (proportion of adult foliage). For this trait, the two main regions in chromosomes 3 and 11 were identified for the three approaches. The SNPs identified in these regions were positioned near the key miRNA genes, miR156.5 and miR157.4, which have a main role in the regulation of the timing of vegetative change, and also in the response to environmental stresses in plants.
DiscussionOur results demonstrated that ssGWAS was more powerful in detecting regions that affect resistance than conventional GWAS approaches. Additionally, the results suggest a polygenic genetic architecture for the heteroblastic transition in E. globulus and identified useful SNP markers for the development of marker-assisted selection strategies for resistance to MLD.

引言
球腔菌叶斑病（Mycosphaerella leaf disease, MLD）是全球范围内蓝桉（Eucalyptus globulus）人工林最常见的叶部病害之一。由于抗性管理策略在商业人工林中效果不佳，培育高抗性基因型成为最具前景的解决方案。现有基因组信息可用于检测与MLD抗性相关的基因组区域，这将显著加快遗传改良进程。
方法
本研究以经EUChip60K单核苷酸多态性（SNP）芯片分型的蓝桉育种群体为材料，解析其MLD抗性的遗传基础。MLD抗性通过幼叶抗性（落叶程度与叶斑严重度）以及转变为抗性成叶的早熟性进行评估。本研究采用4种单SNP模型、基因组最佳线性无偏预测结合全基因组关联分析（GBLUP-GWAS）方法以及单步全基因组关联分析（ssGWAS）开展全基因组关联分析。
结果
单SNP模型（K模型）与GBLUP-GWAS模型分别在2、3和11号染色体上检测到13个和16个SNP-性状关联；而ssGWAS在上述染色体上检测到66个SNP-性状关联，并在5至9号染色体上检测到与叶龄转变早熟性（成叶占比）相关的额外显著SNP-性状关联。针对该性状，三种分析方法均在3号和11号染色体上鉴定到两个核心基因组区域。上述区域内的SNP位点位于关键微RNA（miRNA）基因miR156.5和miR157.4附近，这两个基因在调控植物营养生长转变时机以及应对环境胁迫过程中发挥核心作用。
讨论
本研究结果表明，相较于传统全基因组关联分析方法，ssGWAS在检测抗性相关基因组区域时具有更高的效力。此外，研究结果揭示蓝桉的异形发育转变呈现多基因遗传架构，并为开发针对MLD抗性的标记辅助选择策略提供了具有应用价值的SNP标记。