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Genome-wide association study and transcriptomic comparison reveal temporal genetic factors related to root growth in rapeseed

李可琪  Jie Wang  Lieqiong Kuang  Ze Tian  Xinfa Wang  Xiaoling Dun  王汉中  
【摘要】:【Research background】 Root growth is a complicated process that is mediated by both endogenous genetic factors and diverse environmental cues. These factors exhibit as temporal dynamics and spatial patterning in gene expression to coordinate root growth dynamics.【Materials and methods】 To identify the genetic basis of root growth in rapeseed, nine root-related traits in 280 Brassica napus accessions at five continuous stages during vegetation were measured. Further, comparative transcriptome analysis using four growth types with contrasting larger and smaller root growth rates at the continuously developmental stages or with changing growth rates at specific stages.【Results and analysis】 Two types of temporal genetic factors( "persistent and stage-specific") were revealed by dynamic root growth rate analysis and 16 persistent and 32 stage-specific quantitative trait loci(QTL) clusters, which were obtained by genome-wide association analysis(GWAS). Comparative transcriptome analysis suggested that 373 persistent differently expressed genes(DEGs) were enriched on energy metabolism and biotic or abiotic stress, and 485 stage-specific DEGs involved in nitrogen metabolism, whereas, both regulated cell wall organization. By integrating GWAS, weighted co-expression network analysis(WGCNA) and differential expression analysis, four and eight candidate genes with less than 100 kb physical distances to the peak SNPs of QTL clusters were identified as crucial persistent and stage-specific factors in B.napus, respectively. Furthermore, homologs of three candidate genes(BnaA03 g52990 D, BnaA06 g37280 D, BnaA09 g07580 D) had been reported to regulate root development in previous studies. 【Conclusion】 Our results provide new insights and useful candidate QTLs/genes into the temporal genetic mechanisms of root growth in rapeseed.

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