title: Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.).
abstract: Hypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Zhifei
authors.initials: Z
authors.lastname: Xue
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Ma
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Kaining
authors.initials: K
authors.lastname: Hu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Ziru
authors.initials: Z
authors.lastname: Zeng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Shengwei
authors.initials: S
authors.lastname: Dou
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Jinxing
authors.initials: J
authors.lastname: Tu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Jinxiong
authors.initials: J
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yi
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, P.R. China.
authors.forename: Tingdong
authors.initials: T
authors.lastname: Fu
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D014644:Genetic Variation; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D036226:Seedlings / Q000235:genetics*; D059467:Transcriptome