Abstract
Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) are two key enzymes catalyzing the biosynthesis of isoflavonoids and flavonoids, both of which play diverse roles in stress responses. However, little is known about the evolutionary pattern of these genes in cultivated soybean and its wild progenitors. Herein, we investigated the nucleotide polymorphisms in Isoflavone synthase (IFS1, IFS2) and Flavanone 3-hydroxylase (F3H2) genes from 33 soybean accessions, including 17 cultivars (Glycine max) and 16 their wild progenitors (Glycine soja). Our data showed that the target genes shared the levels of nucleotide polymorphism with three reference genes involved in plant-microbe interactions, but possessed a much higher nucleotide polymorphism than other reference genes. Moreover, no significant genetic differentiation was found between cultivated soybean and its wild relatives in three target genes, despite of considering bottleneck and founder effect during domestication. These results indicate that IFS and F3H genes could have experienced gene introgressions or diversifying selection events during domestication process. Especially, F3H2 gene appears to evolve under positive selection and enjoy a faster evolutionary rate than IFS1 and IFS2 genes.
Highlights
Cultivated soybean [Glycine max (L.) Merr.] was domesticated from its annual wild relative [Glycine soja Sieb. and Zucc.] in East Asia more than 3,000 years ago [1,2]
Our results consistently suggest a distinctive evolution pattern in IFS1, IFS2 and F3H2 genes during soybean domestication compared with the reference genes (Table 1)
Data in table 1 showed that the average nucleotide diversities (p) of the target genes (0.44% in cultivated soybean, 0.44% in wild soybean) were similar to those (0.32% in cultivated soybean, 0.37% in wild soybean) of R1 genes in both cultivated and wild soybeans, while more than 5 fold higher than those in R2 genes (0.07% in wild soybean, 0.08% in wild soybean)
Summary
Cultivated soybean [Glycine max (L.) Merr.] was domesticated from its annual wild relative [Glycine soja Sieb. and Zucc.] in East Asia more than 3,000 years ago [1,2]. Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) genes encode two key enzymes involved in the phenylpropanoid pathway (see Figure S1). There were two copies of IFS genes in soybean genome, IFS1 and IFS2, both of which function in isoflavones synthesis. The flavanones in this reaction, including naringenin and liquiritigenin, are substrates for various other flavonoid biosynthesis processes. Soybean isoflavones are associated with many health benefits of soy consumption Because of their biological importance, the genes of isoflavone synthase i.e., IFS1, IFS2 and flavanone 3-hydroxylase F3H2 gene, were chosen as target genes in this study
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