Detection of new candidate genes controlling seed weight by integrating gene coexpression analysis and QTL mapping in Brassica napus L.
Hongli Dong,
Lei Yang,
Yilin Liu,
Guifu Tian,
Huan Tang,
Shuangshuang Xin,
Yixin Cui,
Qing Xiong,
Huafang Wan,
Zhi Liu,
Christian Jung,
Wei Qian
Affiliations
Hongli Dong
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Lei Yang
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Yilin Liu
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Guifu Tian
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Huan Tang
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Shuangshuang Xin
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Yixin Cui
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Qing Xiong
Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210029, Jiangsu, China
Huafang Wan
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Zhi Liu
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
Christian Jung
Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
Wei Qian
College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; Corresponding author.
Seed weight is a component of seed yield in rapeseed (Brassica napus L.). Although quantitative trait loci (QTL) for seed weight have been reported in rapeseed, only a few causal quantitative trait genes (QTGs) have been identified, resulting in a limitation in understanding of seed weight regulation. We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species. Among the 10 modules in this gene coexpression network, modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein, and photosynthesis. A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19 (SCPL19) was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines. Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.
