An Overview on MADS Box Members in Plants: A Meta-Review

Abstract

Most of the studied MADS box members are linked to flowering and fruit traits. However, higher volumes of studies on type II of the two types so far suggest that the florigenic effect of the gene members could just be the tip of the iceberg. In the current study, we used a systematic approach to obtain a general overview of the MADS box members' cross-trait and multifactor associations, and their pleiotropic potentials, based on a manually curated local reference database. While doing so, we screened for the co-occurrence of terms of interest within the title or abstract of each reference, with a threshold of three hits. The analysis results showed that our approach can retrieve multi-faceted information on the subject of study (MADS box gene members in the current case), which could otherwise have been skewed depending on the authors' expertise and/or volume of the literature reference base. Overall, our study discusses the roles of MADS box members in association with plant organs and trait-linked factors among plant species. Our assessment showed that plants with most of the MADS box member studies included tomato, apple, and rice after Arabidopsis. Furthermore, based on the degree of their multi-trait associations, FLC, SVP, and SOC1 are suggested to have relatively higher pleiotropic potential among others in plant growth, development, and flowering processes. The approach devised in this study is expected to be applicable for a basic understanding of any study subject of interest, regardless of the depth of prior knowledge.

Keywords: MADS box; biotic and abiotic factors; flowering; meta-review; pleiotropic.

Figure 1

General overview of MADS box studies. (a) Study-to-organism associations ranging from 1 (several species) to 363 (Arabidopsis). (b) MADS box gene-ID-to-study association ranging from 1 (several genes) to 76 (SVP), (c) putative cross-species MADS box gene-ID-to-study association ranging from 1 (several genes) to 12 (STMADS11). Gene-word sizes are relative to their frequencies in each gene pool. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 2

Genes with multi-organ associations. (a) Arabidopsis gene IDs associated with at least two of seven plant organs (root, shoot, leaf, apical meristem/SAM, flower, fruit, and seed). The genes shown had at least three hits for each of their respective organs. IDs with two hits among organs are in gray, and those with only one hit are in light gray. (b) Cross-species gene IDs associated with at least two of seven plant organs. The genes shown had at least two hits for each of their respective organs. IDs with only one hit are shown in gray. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 3

MADS box members associated with shoots (a), leaves (b), and roots (c). IDs with 1–2 hits are in light gray, and those with 3 hits are in dark gray. IDs with >3 hits are in any other random color. The text sizes are relative to their respective hit frequencies. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 4

MADS box members associated with SAM (a), flower (b), ovule (c), and pollen (d). IDs with 1–2 hits are in light gray and those with 3 hits are in dark gray. IDs with >3 hits are in any other random color. Text sizes are relative to their respective hit frequencies. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 4

MADS box members associated with SAM (a), flower (b), ovule (c), and pollen (d). IDs with 1–2 hits are in light gray and those with 3 hits are in dark gray. IDs with >3 hits are in any other random color. Text sizes are relative to their respective hit frequencies. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 5

MADS box members associated with seeds (a), fruits (b), and seed germination (c). The IDs with 1–2 hits are in light gray and those with 3 hits are in dark gray. The IDs with >3 hits are in any other random color. The text sizes are relative to their respective hit frequencies. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 6

MADS box members associated with hormones. (a) Auxin, (b) cytokinin, (c) ethylene, (d) gibberellin, (e) abscisic acid. The IDs with 1–2 hits are in light gray and those with 3 hits are in dark gray. The IDs with >3 hits are in any other random color. The text sizes are relative to their respective hit frequencies. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 7

MADS box members associated with biotic and abiotic factors. (a) Nutrient response; (b) tolerance, resistance, or susceptibility response; (c) light response; (d) heat response; (e) salt response; (f) osmotic response. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 7

MADS box members associated with biotic and abiotic factors. (a) Nutrient response; (b) tolerance, resistance, or susceptibility response; (c) light response; (d) heat response; (e) salt response; (f) osmotic response. {Note: High-resolution images of each subfigure have been provided with subfigure IDs in Supplementary Dataset S3}.

Figure 8

Trait-to-factor bridging MADS box members with the ‘flowering’ trait. Gene pools at the circles represent respective factor-to-flowering-associated MADS box members. The central gene pool was generated from all other gene pools to assess the most frequent MADS box members among them. The IDs with 1–2 hits are in light gray and those with 3 hits are in dark gray. The IDs with >3 hits are in any other random color. Their text sizes are relative to their respective hit frequencies within each gene pool. {Note: A high-resolution version of the image has been provided in Supplementary Dataset S3}.