title: Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus.
abstract: Seed coat color is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds such as seed dormancy, longevity, oil content, protein content and fiber content. In Brassica napus, inheritance of seed coat color is related to maternal effects and pollen effects (xenia effects). In this research we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus, which is named Embryonal Control of Yellow seed coat 1 (Ecy1). Microscopy of transverse sections of the mature seed show that pigment is deposited only in the outer layer of the seed coat. Using Illumina Hisequation 2000 sequencing technology, a total of 12 GB clean data, 116× coverage of coding sequences of B. napus, was achieved from seeds 26 d after pollination (DAP). It was assembled into 172,238 independent transcripts, and 55,637 unigenes. A total of 139 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus Only 49 of the TT orthologous genes are transcribed in seeds. However transcription of all orthologs was independent of embryonal control of seed coat color. Only 55 genes were found to be differentially expressed between brown seeds and the yellow mutant. Of these 55, 50 were upregulated and five were downregulated in yellow seeds as compared to their brown counterparts. By KEGG classification, 14 metabolic pathways were significantly enriched. Of these, five pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways, and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were present at higher levels in the embryos of yellow seeds as compared to those of brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the embryo. The pigment substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe, and disappearance of pigment in the yellow seeded mutant, suggests that embryonal control of seed coat color is related with Phe and Ala metabolism in the embryo of B. napus.
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Provincial Key Laboratory of Genetic Engineering on Plant Metabolism, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Fulin
authors.initials: F
authors.lastname: Wang
authors.affiliation: Research and Development Center, Hubei Tobacco China Industrial Company, Wuhan 430040, China.
authors.forename: Jiewang
authors.initials: J
authors.lastname: He
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Provincial Key Laboratory of Genetic Engineering on Plant Metabolism, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Jianghua
authors.initials: J
authors.lastname: Shi
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Provincial Key Laboratory of Genetic Engineering on Plant Metabolism, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Xu
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Provincial Key Laboratory of Genetic Engineering on Plant Metabolism, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Guanting
authors.initials: G
authors.lastname: Wu
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Provincial Key Laboratory of Genetic Engineering on Plant Metabolism, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China, Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China liurh@mail.zaas.ac.cn.
authors.forename: Renhu
authors.initials: R
authors.lastname: Liu
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Shengyi
authors.initials: S
authors.lastname: Liu
mesh_terms: D000409:Alanine / Q000378:metabolism*; D017360:Arabidopsis / Q000235:genetics; D029688:Brassica napus / Q000235:genetics* / Q000378:metabolism*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D010649:Phenylalanine / Q000378:metabolism*; D010858:Pigmentation / Q000235:genetics; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics* / Q000378:metabolism* / Q000648:ultrastructure; D059467:Transcriptome
chemical_list: D010649:Phenylalanine; D000409:Alanine
keywords: Brassica napus; free amino acids; transcriptome sequencing; xenia effect; yellow seed coat