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Detection of candidate gene networks involved in resistance to Sclerotinia sclerotiorum in soybean
Journal of Applied Genetics ( IF 2.4 ) Pub Date : 2021-09-11 , DOI: 10.1007/s13353-021-00654-z
Yu Zhang 1 , Yuexing Wang 2 , Wanying Zhou 1 , Shimao Zheng 1 , Runzhou Ye 3
Affiliation  

Quantitative trait locus (QTL) mapping often yields associations with dissimilar loci/genes as a consequence of diverse factors. One trait for which very limited agreement between mapping studies has been observed is resistance to white mold in soybean. To explore whether different approaches applied to a single data set could lead to more consistent results, haplotype-trait association and epistasis interaction effects were explored as a complement to a more conventional marker-trait analysis. At least 10 genomic regions were significantly associated with Sclerotinia sclerotiorum resistance in soybean, which have not been previously reported. At a significance level of α = 0.05, haplotype-trait association showed that the most prominent signal originated from a haplotype with 4-SNP (single nucleotide polymorphism) on chromosome 17, and single SNP-trait analysis located a nucleotide polymorphism at position rs34387780 on chromosome 3. All of the peak-SNPs (p-value < 0.05) of each chromosome also appeared in their respective haplotypes. Samples with extreme phenotypes were singled-out for association studies, 25–30% from each end of the phenotypic spectrum appeared in the present investigation to be the most appropriate sample size. Some key genes were identified by epistasis interaction analysis. By combining information on the nearest positional genes indicated that most loci have not been previously reported. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggest potential candidate genes underlying callose deposition in the cell wall and mitogen-activated protein kinase (MAPK) signaling pathway-plant, as well as plant-pathogen interaction pathway, were activated. Integration of multi-method genome-wide association study (GWAS) revealed novel genomic regions and promising candidate genes in novel regions, which include Glyma.01g048500, Glyma.03g129100, Glyma.17g072200, and the Dishevelled (Dvl) family of proteins on chromosomes 1, 3, 17, and 20, respectively.



中文翻译:

大豆核盘菌抗性候选基因网络的检测

由于多种因素,数量性状基因座 (QTL) 作图通常会产生与不同基因座/基因的关联。已观察到绘图研究之间一致性非常有限的一个性状是对大豆中的白霉病的抗性。为了探索应用于单个数据集的不同方法是否可以导致更一致的结果,探索了单倍型 - 性状关联和上位相互作用效应作为更传统的标记 - 性状分析的补充。至少有 10 个基因组区域与大豆中的核盘菌抗性显着相关,这在以前没有报道过。在显着性水平α = 0.05,单倍型-性状关联显示最显着的信号来自17号染色​​体上具有4-SNP(单核苷酸多态性)的单倍型,单SNP-性状分析定位于3号染色体上rs34387780位的核苷酸多态性。峰值 SNP ( p-value < 0.05) 每条染色体也出现在它们各自的单倍型中。具有极端表型的样本被挑选出来进行关联研究,在本研究中,表型谱两端的 25-30% 似乎是最合适的样本量。通过上位相互作用分析鉴定了一些关键基因。通过结合最近位置基因的信息表明大多数基因座以前没有被报道过。基因本体论 (GO) 和京都基因和基因组百科全书 (KEGG) 富集分析表明潜在的候选基因是细胞壁中胼胝质沉积和丝裂原活化蛋白激酶 (MAPK) 信号通路-植物以及植物-病原体相互作用通路的潜在候选基因, 被激活。

更新日期:2021-09-13
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