The Leafminers, representing a diverse group of insects from various genera within the Agromyzidae family, pose a significant threat to spinach (Spinacia oleracea L.) production. This study aimed to identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance through a genome-wide association study (GWAS) and to evaluate the prediction accuracy (PA) for selecting resistant spinach using genomic prediction (GP). Using a dataset of 84 301 SNPs obtained from whole-genome resequencing, seven GWAS models, including BLINK, FarmCPU, MLM, and MLMM in GAPIT 3, as well as MLM, GLM, and SMR in TASSEL 5, were employed to perform GWAS on a panel of 286 USDA spinach germplasm accessions. Three SNP markers, namely 1_115279256_C_T, 3_157082529_C_T, and 4_168510908_T_G on chromosomes 1, 3, and 4, respectively, were identified as associated with leafminer resistance. In the 30 kb flanking regions of these markers, four candidate genes (SOV1g031330, SOV1g031340, SOV4g047270, and SOV4g047280), encoding LOB domain-containing protein, KH domain-containing protein, were discovered. Nodulin-like domain-containing protein, and SAM domain-containing protein, were discovered. The PA for leafminer resistance selection was estimated using ten different SNP sets, including two GWAS-derived marker sets (three and 51 SNPs) and eight random marker sets (ranging from 51 to 10 K SNPs) analyzed by seven GP models. The findings emphasized the superior performance of GWAS-derived SNP sets, reaching a PA of up to 0.79 using the cBLUP model. Notably, this research marks the pioneering application of GP in the context of insect resistance, providing a significant advancement in the understanding and management of leafminer resistance in spinach cultivation.

中文翻译：

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通过 GWAS 方法和基因组预测对菠菜潜叶蛾抗性的基因组见解


潜叶號代表了 Agromyzidae 家族中来自不同属的不同昆虫群，对菠菜 （Spinacia oleracea L.） 的生产构成重大威胁。本研究旨在通过全基因组关联研究 （GWAS） 鉴定与潜叶菠菜抗性相关的单核苷酸多态性 （SNP） 标记，并使用基因组预测 （GP） 评估选择抗性菠菜的预测准确性 （PA）。使用从全基因组重测序获得的 84 301 个 SNP 数据集，采用 7 个 GWAS 模型，包括 GAPIT 3 中的 BLINK、FarmCPU、MLM 和 MLMM，以及 TASSEL 5 中的 MLM、GLM 和 SMR，对 286 个 USDA 菠菜种质种质进行 GWAS。1 、 3 和 4 号染色体上的 1_115279256_C_T 、 3_157082529_C_T 和 4_168510908_T_G 三个 SNP 标记分别被鉴定为与潜叶鱼抗性有关。在这些标记的 30 kb 侧翼区域，发现了四个候选基因 （SOV1g031330 、 SOV1g031340 、 SOV4g047270 和 SOV4g047280），编码包含 LOB 结构域的蛋白质，包含 KH 结构域的蛋白质。发现了包含 Nodulin 样结构域的蛋白和包含 SAM 结构域的蛋白。使用 10 个不同的 SNP 集估计潜叶鱼抗性选择的 PA，包括 2 个 GWAS 衍生的标记集（3 个和 51 个 SNP）和 8 个随机标记集（范围从 51 到 10 K SNP），由 7 个 GP 模型分析。研究结果强调了 GWAS 衍生的 SNP 集的卓越性能，使用 cBLUP 模型达到高达 0.79 的 PA。值得注意的是，这项研究标志着 GP 在抗虫性方面的开创性应用，为理解和管理菠菜种植中潜叶蛾的抗性提供了重大进展。