In terms of global demand, rapeseed is the third-largest oilseed crop after soybeans and palm, which produces vegetable oil for human consumption and biofuel for industrial production. Roots are vital organs for plant to absorb water and attain mineral nutrients, thus they are of great importance to plant productivity. However, the genetic mechanisms regulating root development in rapeseed remain unclear. In the present study, seven root-related traits and shoot biomass traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout the investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. A total of 367 differentially expressed genes (DEGs) with persistent differential expressions throughout root development were identified, and these DEGs were significantly enriched in GO terms, such as energy metabolism and response to biotic or abiotic stress. Totally, 485 stage-specific DEGs with different expressions at specific stage were identified, and these DEGs were enriched in GO terms, such as nitrogen metabolism. Four candidate genes were identified as key persistent genetic factors and eight as stage-specific ones by integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. These candidate genes were speculated to regulate root system development, and they were less than 100 kb away from peak SNPs of QTL clusters. The homologs of three genes (BnaA03g52990D, BnaA06g37280D, and BnaA09g07580D) out of 12 candidate genes have been reported to regulate root development in previous studies. Sixteen QTL clusters and four candidate genes controlling persistently root development, and 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed were detected in this study. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.

中文翻译：

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全基因组关联研究和转录组分析揭示影响油菜根生长动态的关键基因

就全球需求而言，油菜籽是仅次于大豆和棕榈的第三大油籽作物，生产供人类消费的植物油和用于工业生产的生物燃料。根系是植物吸收水分和获取矿质养分的重要器官，对植物的生产力具有重要意义。然而，调控油菜根发育的遗传机制仍不清楚。在本研究中，测量了 5 个连续营养阶段的 280 份甘蓝型油菜种质的 7 个根相关性状和枝条生物量性状，以建立油菜根生长的遗传基础。通过根动态分析揭示了持久性和阶段特异性遗传机制。通过全基因组关联研究 (GWAS) 鉴定了 16 个持久性和 32 个阶段特异性数量性状基因座 (QTL) 簇。在整个研究阶段具有对比（缓慢和快速）生长速率的根样本和那些具有明显的阶段特异性生长速率变化的根样本进行转录组分析。共鉴定出 367 个差异表达基因 (DEGs)，在整个根发育过程中持续差异表达，这些 DEGs 在能量代谢和对生物或非生物胁迫的响应等 GO 术语中显着丰富。总共鉴定出 485 个在特定阶段具有不同表达的阶段特异性 DEG，并且这些 DEG 富含 GO 术语，例如氮代谢。通过整合 GWAS、加权基因共表达网络分析 (WGCNA) 和差异表达分析，4 个候选基因被确定为关键的持久遗传因素，8 个候选基因为阶段特异性基因。推测这些候选基因调节根系发育，它们距离QTL簇的峰值SNP小于100 kb。在先前的研究中，已经报道了 12 个候选基因中的三个基因（BnaA03g52990D、BnaA06g37280D 和 BnaA09g07580D）的同源物调节根的发育。本研究检测到16个QTL簇和4个持续控制根系发育的候选基因，以及32个QTL簇和8个阶段特异性调控油菜根生长的候选基因。我们的结果通过鉴定油菜籽中的关键候选 QTL/基因，为根系生长的时间遗传机制提供了新的见解。和 BnaA09g07580D) 中的 12 个候选基因已被报道在先前的研究中调节根发育。本研究检测到16个QTL簇和4个持续控制根系发育的候选基因，以及32个QTL簇和8个阶段特异性调控油菜根生长的候选基因。我们的结果通过鉴定油菜籽中的关键候选 QTL/基因，为根系生长的时间遗传机制提供了新的见解。和 BnaA09g07580D) 中的 12 个候选基因已被报道在先前的研究中调节根发育。本研究检测到16个QTL簇和4个持续控制根系发育的候选基因，以及32个QTL簇和8个阶段特异性调控油菜根生长的候选基因。我们的结果通过鉴定油菜籽中的关键候选 QTL/基因，为根系生长的时间遗传机制提供了新的见解。