Genome-wide identification and ABCE-class proposal of the MADS-box gene family in Salvia miltiorrhiza Bunge

Abstract

MADS-box transcription factors, as the heart of the classic ABCE model of floral development, play critical roles in several aspects of plant flowering. In recent years, to comprehensively utilise and improve the added value of Chinese herbal medicine, the non-medicinal part (flower) development of Salvia miltiorrhiza Bunge has been promoted, thereby focusing the attention of researchers on the flower organ of S. miltiorrhiza. However, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of S. miltiorrhiza genome sequencing. This work systematically characterised S. miltiorrhiza MADS-box genes (SmiMADSes) and predicted those likely involved in the floral development of this medicinal plant. Seventy-two MADS-box genes were identified in the S. miltiorrhiza genome and categorised into MIKC*, MIKCc, Mα, Mβ and Mγ groups based on phylogeny. Genomic localisation analysis revealed that these genes were evenly localised on 10 genome scaffolds. The expression profiles of all the SmiMADSes were analysed in four organs and four flower tissues, as well as in the three stages of floral development. Transcripts for 13 genes accumulated preferentially in flowers. SmiMADS44 was specifically expressed in stems. SmiMADS57 and SmiMADS31 showed specific expressions in roots and leaves, respectively. Based on transcriptome data and homology with functionally validated ABCE class genes in Arabidopsis, a prediction was made to gain insight into ABCE-class SmiMADSes that were strongly expressed in all flowering stages of S. miltiorrhiza, including the following: SmiMADS65 and SmiMADS67 of A-class; SmiMADS26, SmiMADS28 and SmiMADS29 of B-class; SmiMADS45, SmiMADS50 and SmiMADS51 of C-class; and SmiMADS70, SmiMADS71 and SmiMADS72 of E-class. The results of this study lay a foundation for the further exploration of molecular and regulatory mechanisms controlling floral organ development and provide a basis for the selection of candidate genes for functional validation studies.

Genome-Wide Analysis of the MADS-box Gene Family and Expression Analysis during Anther Development in Salvia miltiorrhiza

“…With the completion of whole genome sequencing, the MADS-box gene family has been extensively studied in various plants, such as A. thaliana (108) [ 10 ], rice (75) [ 11 ], maize (75) [ 12 ], grape (83) [ 13 ], alfalfa (120) [ 14 ], cucumber (43) [ 35 ], lettuce (82) [ 36 ], and pear (95) [ 37 ]. In this study, 63 SmMADS genes were identified in the male sterility ecotype S. miltiorrhiza _SC, which is different from the 72 genes found in the male fertility ecotype S. miltiorrhiza _SD [ 38 ]. They were both divided into two types and 17 subfamilies according to phylogenetic relationship.…”

“…Moreover, protein motif analysis showed that all SmMADS proteins had the highly conserved MADS domain, whereas type II genes contained unique I, K, and C domains, facilitating the formation of dimers and higher-order complexes between MADS-box proteins and transcriptional activation [ 6 , 7 , 8 , 9 ]. Therefore, type II SmMADS proteins have more complex protein structures, which also suggests that their regulatory mechanism may be more complex than type I. Additionally, we identified cis-acting elements in the promoter region of SmMADS genes that are associated with plant growth and development, plant hormones, and stress response, which was not analyzed in S. miltiorrhiza _SD [ 38 ]. These cis-acting elements play a crucial role in regulating the expression of related genes [ 40 ], enhancing the ability of S. miltiorrhiza to adapt to various adverse environments and ensure its normal growth and development.…”

“…These events mainly include WGD, segmental duplication, and tandem duplication [ 34 ]. In this study, 17 duplication gene pairs were found in SmMADS genes, and the majority of these pairs (82.35%) were found to be segmental duplications, which was lower than S. miltiorrhiza _SD (19 and 84.21%) [ 38 ]. This indicates that segmental duplication is the main force for the expansion of the SmMADS gene family, which is consistent with findings in other species, such as Fagopyrum tataricum [ 44 ], Rhododendron hainanense Merr.…”

“…Additionally, some collinear gene pairs were identified between S. miltiorrhiza _SC and all seven other species, indicating that these homologous pairs may have existed before the divergence of their common ancestor. These phenomena were also observed in S. miltiorrhiza _SD, although the analysis was limited to the collinearity between S. miltiorrhiza_SD , A. thaliana , and rice [ 38 ]. In summary, these results indicate that the MADS-box gene family in S. miltiorrhiza exhibits evolutionary conservation.…”

“…Gene expression profiling is important for determining gene function and biological processes. Most of the B-class and C-class MADS-box genes exhibited high expression levels in the stamen of S. miltiorrhiza _SD, indicating their significant roles in stamen development [ 38 ]. Our study demonstrated that all B-class ( SmMADS31/32/33/63 ) and C-class ( SmMADS21/26/38/39 ) genes were highly expressed during anther development in two ecotypes of S. miltiorrhiza , suggesting their crucial roles in anther development.…”