Abstract
The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKCC subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKCC subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKCC genes kept the important and conserved functions of the flower development, most MIKCC genes showed potentially essential roles in the seed development as well as the type I MADS.
Highlights
The MADS family, found in fungi [1], animals [2] and plants [3] [4], possesses a highly conserved N-terminal with a DNAbinding domain named MADS
The soybean MIKCC genes contained the MADS domains and K-box domains and were composed of 12 subfamilies: FLC (2 genes), SOC (TM3-like, 8 genes), AG (10 genes), AGL6 (6 genes), SEP (AGL2-like, 12 genes), SVP (STMADS11-like, 8 genes), AGL12 (2 genes), AGL15 (2 genes), AGL17 (8 genes), DEF/GLO (11 genes), SQUA (10 genes), and ABS (GGM13- (B(s))-like, 2 genes), and one ancient clade known in some flowering plant species, TM8 subfamily [5], was not found in the soybean
At least one ancestral MADS-box gene was present in the common ancestor of plants, animals, and fungi, and probably the duplication that gave rise to the animal MEF2- and SRF-like genes occurred after animals diverged from plants but before fungi diverged from animals about 1000 million year ago (MYA) [6,8]
Summary
The MADS family, found in fungi [1], animals [2] and plants [3] [4], possesses a highly conserved N-terminal with a DNAbinding domain named MADS. Based on the phylogenetic analysis, MADS gene family is divided into two large lineages, type I and type II, which was created through a gene duplication occurred before the divergence of plants (and fungi) and animals [5,6,7]. About 13 subfamilies compose of the MIKCC clade and most of them originate from ancestral seed plants and are often characterized by distinct sequence motifs in their C-terminal domains [5,12]. Heterogeneous type I MADS can be subgrouped into Ma, Mb, and Mc based on the sequence of the MADS domain and the presence of additional motifs [5,14,15,16]
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