DataSheet_1_Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM.pdf

IntroductionAlthough seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.
MethodsThe 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs.
ResultsSeven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress.
DiscussionThe above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits.

**引言**
尽管大豆种子含油量及其脂肪酸组成易受环境影响，但在全基因组关联研究（genome-wide association studies）中，关于数量性状核苷酸-环境互作（QTN-by-environment interactions, QEIs）与基因-环境互作（gene-by-environment interactions, GEIs）的研究报道仍较为罕见。

**方法**
本研究采用3VmrMLM方法，针对286份大豆种质资源在5至7种环境下获取的表型性状，与106013个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）开展关联分析，以鉴定数量性状核苷酸（QTNs）及其与环境的互作（QEIs）。

**结果**
本研究在598个数量性状核苷酸（QTNs）侧翼区域筛选得到7个油脂代谢基因（GmSACPD-A、GmSACPD-B、GmbZIP123、GmSWEET39、GmFATB1A、GmDGAT2D及GmDGAT1B），在54个QEIs侧翼区域筛选得到1个油脂代谢基因GmFATB2B，上述基因均已在既往研究中得到验证；本研究预测得到76个候选基因与66个候选基因-环境互作（GEIs），其中5个位于QEIs侧翼的基因在其他物种中已被证实参与油脂代谢过程，且在不同环境下呈现差异表达。单倍型分析（haplotype analysis）表明，这些基因与大豆种子含油量显著相关。此外，在共表达网络（co-expression network）中，大多数候选GEIs与抗旱响应基因（drought response genes）存在共表达现象；在干旱胁迫（drought stress）而非对照条件（control condition）下，有3条与干旱响应相关的KEGG通路（KEGG pathways）显著富集；在干旱胁迫下的共表达网络中，6个候选基因充当枢纽基因（hub genes）。

**讨论**
上述结果表明，基因-环境互作（GEIs）与共表达网络中的抗旱响应基因可能共同参与干旱响应，并与油脂代谢基因协同调控大豆种子油脂相关性状。本研究结果为解析种子油脂相关性状的遗传基础与分子机制，以及开展大豆种子油脂相关性状的遗传育种提供了重要理论参考与实践依据。