A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes i
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RESEARCH ARTICLE
Open Access
A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus Shurong Jin†, Shuangjuan Zhang†, Yuhua Liu, Youwei Jiang, Yanmei Wang, Jiana Li and Yu Ni*
Abstract Background: Brassica napus L. is one of the most important oil crops in the world. However, climate-changeinduced environmental stresses negatively impact on its yield and quality. Cuticular waxes are known to protect plants from various abiotic/biotic stresses. Dissecting the genetic and biochemical basis underlying cuticular waxes is important to breed cultivars with improved stress tolerance. Results: Here a genome-wide association study (GWAS) of 192 B. napus cultivars and inbred lines was used to identify single-nucleotide polymorphisms (SNPs) associated with leaf waxes. A total of 202 SNPs was found to be significantly associated with 31 wax traits including total wax coverage and the amounts of wax classes and wax compounds. Next, epidermal peels from leaves of both high-wax load (HW) and low-wax load (LW) lines were isolated and used to analyze transcript profiles of all GWAS-identified genes. Consequently, 147 SNPs were revealed to have differential expressions between HW and LW lines, among which 344 SNP corresponding genes exhibited up-regulated while 448 exhibited down-regulated expressions in LW when compared to those in HW. According to the gene annotation information, some differentially expressed genes were classified into plant acyl lipid metabolism, including fatty acid-related pathways, wax and cutin biosynthesis pathway and wax secretion. Some genes involved in cell wall formation and stress responses have also been identified. Conclusions: Combination of GWAS with transcriptomic analysis revealed a number of directly or indirectly waxrelated genes and their associated SNPs. These results could provide clues for further validation of SNPs for markerassisted breeding and provide new insights into the genetic control of wax biosynthesis and improving stress tolerance of B. napus. Keywords: Brassica napus L., Cuticular wax, Genome-wide association study, RNA-seq, Single nucleotide polymorphism
* Correspondence: [email protected] † Shurong Jin and Shuangjuan Zhang contributed equally to this work. College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the artic
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