Developmental dynamic transcriptome and systematic analysis reveal the major genes underlying isoflavone accumulation in soybean

Abstract

Introduction: Soy isoflavone, a class of polyphenolic compounds exclusively occurred in legumes, is an important bioactive compound for both plants and human beings. The outline of isoflavones biosynthesis pathway has been drawn up basically in the previous research. However, research on the subject has been mostly restricted to investigate the static regulation of isoflavone content in soybean, rather than characterize its dynamic variation and modulation network in developing seeds.

Methods: In this study, by using eight recombinant inbred lines (RIL), the contents of six isoflavone components in the different stages of developing soybean seeds were determined to characterize the dynamic variation of isoflavones, and the isoflavones accumulation pattern at physiological level was investigated. Meanwhile, we integrated and analyzed the whole genome expression profile of four lines and 42 meta-transcriptome data, based on the multiple algorithms.

Results: This study: 1) obtained 4 molecular modules strongly correlated with isoflavone accumulation; 2) identified 28 novel major genes that could affect the accumulation of isoflavones in developing seeds free from the limitation of environments; 3) discussed the dynamic molecular patterns regulating isoflavones accumulation in developing seed; 4) expanded the isoflavone biosynthesis pathway.

Discussion: The results not only promote the understandings on the biosynthesis and regulation of isoflavones at physiological and molecular level, but also facilitate to breed elite soybean cultivars with high isoflavone contents.

Keywords: dynamic accumulation patterns; dynamic regulation networks; meta-analysis; soy isoflavone; transcriptome.

Figure 1

The isoflavone content of samples in this study (The distance between central point and vertex of each color block represents the content of isoflavone component in a sample).

Figure 2

Dynamic variation of six isoflavone compounds in developing soybean seed (Each broken line represents the variation trend of isoflavone content, while each full line represents the real situation of the change of isoflavone content).

Figure 3

Venn analysis and correlation analysis among the RNA-seq of different samples (A) Venn analysis and correlation analysis of horizontal comparison; (B) Venn analysis and correlation analysis of lengthways comparison.

Figure 4

Major genes underlying isoflavone accumulation free from the limitation of environments (A) Major genes underlying isoflavone accumulation and their effects (The underlined words are isoflavone components, and the italicized words are QTL name, and the bold words are gene module generated by WCGNA); (B) QTG underlying isoflavone accumulation and corresponded stable QTL (The underlined words are isoflavone components, and the italicized words are gene name, and the bold words are gene annotation description); (C) Expansion of isoflavone biosynthesis pathway (The gene in the blue frame was predicted major gene, and the gene in the purple frame was the major gene identified by previous study, and the gene behind orange point was transcription factor. The arrow means the possible way that major genes regulate isoflavone).

Figure 5

Comparing the variation of major genes expression and total isoflavone content during seed development.

Figure 6

Dynamic molecular mechanisms regulating isoflavone accumulation in developing seeds (A) Trend of isoflavone dynamic variation; (B) Dynamic molecular network regulating isoflavone.