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The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication
Author(s) -
Lu Xiang,
Li QingTian,
Xiong Qing,
Li Wei,
Bi YingDong,
Lai YongCai,
Liu XinLei,
Man WeiQun,
Zhang WanKe,
Ma Biao,
Chen ShouYi,
Zhang JinSong
Publication year - 2016
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13181
Subject(s) - domestication , biology , quantitative trait locus , gene , trait , transcriptome , locus (genetics) , gene expression , genetics , gibberellin , expression quantitative trait loci , cultivar , botany , genotype , single nucleotide polymorphism , computer science , programming language
Summary 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, GA 20 OX and NFYA . GA 20 OX encodes an enzyme in a rate‐limiting step of gibberellin biosynthesis, and NFYA encodes a transcription factor. Overexpression of GA 20 OX 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 GA 20 OX 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.