title: The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication.
abstract: Cultivated soybean has undergone many transformations during domestication. In this paper we report a comprehensive assessment of the evolution of gene co-expression networks based on the analysis of 40 transcriptomes from developing soybean seeds in cultivated and wild soybean accessions. We identified 2680 genes that are differentially expressed during seed maturation and established two cultivar-specific gene co-expression networks. Through analysis of the two networks and integration with quantitative trait locus data we identified two potential key drivers for seed trait formation, GA20OX and NFYA. GA20OX encodes an enzyme in a rate-limiting step of gibberellin biosynthesis, and NFYA encodes a transcription factor. Overexpression of GA20OX and NFYA enhanced seed size/weight and oil content, respectively, in seeds of transgenic plants. The two genes showed significantly higher expression in cultivated than in wild soybean, and the increases in expression were associated with genetic variations in the promoter region of each gene. Moreover, the expression of GA20OX and NFYA in seeds of soybean accessions correlated with seed weight and oil content, respectively. Our study reveals transcriptional adaptation during soybean domestication and may identify a mechanism of selection by expression for seed trait formation, providing strategies for future breeding practice.
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Lu
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Qing-Tian
authors.initials: QT
authors.lastname: Li
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xiong
authors.affiliation: Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China.
authors.forename: Ying-Dong
authors.initials: YD
authors.lastname: Bi
authors.affiliation: Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China.
authors.forename: Yong-Cai
authors.initials: YC
authors.lastname: Lai
authors.affiliation: Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China.
authors.forename: Xin-Lei
authors.initials: XL
authors.lastname: Liu
authors.affiliation: Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China.
authors.forename: Wei-Qun
authors.initials: WQ
authors.lastname: Man
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Wan-Ke
authors.initials: WK
authors.lastname: Zhang
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Biao
authors.initials: B
authors.lastname: Ma
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Shou-Yi
authors.initials: SY
authors.lastname: Chen
authors.affiliation: State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Jin-Song
authors.initials: JS
authors.lastname: Zhang
mesh_terms: D000071278:Domestication; D005838:Genotype; D030821:Plants, Genetically Modified / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D012639:Seeds / Q000235:genetics*; D013025:Glycine max / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
keywords: Glycine max; Glycine soja; promoter variation; seed trait formation; soybean domestication; transcriptomic signature