Comparative Analysis of the MADS-Box Genes Revealed Their Potential Functions for Flower and Fruit Development in Longan (Dimocarpus longan)

Abstract

Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mβ, Mγ) and type II (MIKC*, MIKCC) groups, and MIKCC genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKCC genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKCC genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.

Genome-Wide Identification of the MADS-Box Gene Family during Male and Female Flower Development in Chayote (Sechium edule)

“…Seventy SeMADS genes were divided into 14 subfamilies, type I Mα (7), Mβ (3), Mγ (4); Type II MICK* (3) and MICK c PI (3), Bs (1), SVP (9), AGL12 (1), AG (6), AGL15 (3), AGL17 (5), SOC1 (8), AGL6 (2), SEP (4), and AP1 (11). Some 80% of them belong to type II MADS, which is similar to that reported in the MADS gene family, indicating that type II MADS genes were more conservative than type I MADS genes [ 13 , 14 , 30 ]. The FLC gene was reported to regulate flowering with the spring flower pathway [ 14 , 27 ].…”

“…The deletion of the FLC subfamily genes was also found in the watermelon and cucumber of Cucurbitaceae [ 27 , 28 ]. BS subfamily genes were involved in seed pigmentation and endothelial development [ 30 ]. We found a Bs gene SeMADS49 , but no Bs gene was found in cucumbers, watermelon and melon in Cucurbitaceae [ 27 , 28 , 29 ].…”

“…We found that the gene length of the type II gene was longer and contained more exons than that of the type I gene, which was also an important feature in distinguishing type I from type II. Different subfamilies contain different numbers and types of conserved motifs [ 30 ]. We found that motif 1 was the most conserved motif, which was related to the SRF domain.…”

“…BLASTp and MCScanX software (California, USA, , accessed on 12 January 2022) were used to analyze the replication types of MADS-box genes in chayote [ 30 ], Arabidopsis and some representative species of Cucurbitaceae (cucumber, ChineseLong_v3; melon, DHL92; pumpkin, Cmoschata_v1; and watermelon, 97103_v2.5), and to analyze the collinearity within and between genomes. The genome data and annotation files of Arabidopsis and Cucurbitaceae were downloaded from the Arabidopsis database and the Cucurbitaceae website described above.…”

Genome-wide identification and bioinformatics analysis of the WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea (Rhododendron simsii)

“…The most significant factors in the growth of gene families during evolution are WGD and tandem duplication events ( Wang et al, 2012 ). Many transcription factor gene families, such as MADS-box, bHLH, and bZIP, most likely expanded through WGD duplication ( Liu et al, 2014 ; Wang B. et al, 2022 ; Wang X. J. et al, 2022 ). While other transcription factor gene families, such as NBS-LRR and ERF, were expanded as a result of tandem duplication ( Liu Z. et al, 2019 ; Li P. et al, 2020 ; Zhong et al, 2022 ).…”