Genome-wide identification and analysis of the MADS-box gene family in apple

Tian, Yi; Dong, Qinglong; Ji, Zhirui; Chi, Fu-mei; Peng, Cong; Zhou, Zhongshi

doi:10.1016/j.gene.2014.11.018

Cited by 106 publications

(110 citation statements)

References 50 publications

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“…The P. equestris genome carried more of type II MADS-box genes than type I MADS-box genes. A similar trend was reported with closely related genomes Apostasia shenzhenica (Zhang et al 2017) and Dendrobium catenatum (Zhang et al 2016) and in other plant genomes such as Glycine max (Fan et al 2013), Brachypodium distachyon (Wei et al 2014) and Malus domestica (Tian et al 2015) as well (Table 2). This indicates, presumably, that the type II group members are evolutionarily more advanced than the type I group members (Lin et al 2016).…”

Section: Discussionsupporting

confidence: 87%

“…This inconsistency within the type I groups in different plant species indicate the varying birth and death rate of type I genes (Nam et al 2004). Among type II MADS-box proteins, nine subgroups were formed in P. equestris (Cai et al 2015), while nine in E. pusilla (Lin et al 2016) and B. distachyon (Wei et al 2014), 10 in C. sativus (Hu and Liu 2012), eight in M. domestica (Tian et al 2015), 14 in O. sativa (Arora et al 2007) and 13 were reported in Vitis vinifera (Diaz-Riquelme et al 2009). The variability in number of subgroups in different plant species might be due to the requirement of specific functions of these groups (Shimeld 1999).…”

Section: Discussionmentioning

confidence: 99%

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Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

et al. 2019

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Orchids are indispensable to the floriculture industry due to their unique floral organization. The flowers have two outer whorls of tepals including a lip (labellum), and two inner whorls, pollinia and gynostemiun (column). The floral organization and development is controlled at the molecular level, mainly by the MADS-box gene family, comprising homeotic genes divided into type I and type II groups. The type I group has four subgroups , Mα, Mβ, Mγ, and Mδ, playing roles in seed, embryo, and female reproductive organ development; the type II group genes form classes A, B, C, D, and E, which are a part of the MIKC C subgroup with specific roles in florigenesis and organization. The coordinated functioning of these classes regulates the development of various floral whorls. The availability of genome and transcriptome sequence data for Phalaenopsis equestris offers an opportunity to validate the ABCDE model of flower development. Hence, this study sought to characterize the MADS-box gene family and elucidate of the ABCDE model. A total of 48 identified MADS-box proteins, including 20 type I [Mα (12), Mγ (8)] and 28 type II [MIKC C (27), MIKC* (1)] members, were characterized for physico-chemical features and domains and motifs organization. The exon-intron distribution and the upstream cis-regulatory elements in the promoter regions of MADS-box genes were also analysed. The discrete pace of duplication events in type I and type II genes suggested differential evolutionary constraints between groups. The correlation of spatio-temporal expression pattern with the presence of specific cis-regulatory elements and putative proteinprotein interaction within the different classes of MADS-box gene family endorse the ABCDE model of floral development.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

et al. 2019

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“…The Ma and Mg genes usually had no intron or a single intron, whereas MIKC genes and several Md genes contained multiple introns. The similar situation existed in arabidopsis, rice, cucumber, and apple (Malus •domestica) (Arora et al, 2007;Hu et al, 2012;Parȇnicov a et al, 2003;Tian et al, 2015). These results suggested that the structure of MADS-box genes was conservative relatively in these species.…”

Section: Discussionmentioning

confidence: 56%

Genome-wide Identification and Analysis of the MADS-box Gene Family in Melon

Hao

Zhao

et al. 2016

J. Amer. Soc. Hort. Sci.

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The MADS-box genes encode transcription factors with key roles in plant growth and development. A comprehensive analysis of the MADS-box gene family in bread wheat (Triticum aestivum) has not yet been conducted, and our understanding of their roles in stress is rather limited. Here, we report the identification and characterization of the MADS-box gene family in wheat. A total of 180 MADS-box genes classified as 32 Mα, 5 Mγ, 5 Mδ, and 138 MIKC types were identified. Evolutionary analysis of the orthologs among T. urartu, Aegilops tauschii and wheat as well as homeologous sequences analysis among the three sub-genomes in wheat revealed that gene loss and chromosomal rearrangements occurred during and/or after the origin of bread wheat. Forty wheat MADS-box genes that were expressed throughout the investigated tissues and development stages were identified. The genes that were regulated in response to both abiotic stresses (i.e., phosphorus deficiency, drought, heat, and combined drought and heat) and biotic stresses (i.e., Fusarium grami-nearum, Septoria tritici, stripe rust and powdery mildew) were detected as well. A few notable MADS-box genes were specifically expressed in a single tissue and those showed relatively higher expression differences between the stress and control treatment. The expression patterns of considerable MADS-box genes differed from those of their orthologs in Brachypodium, rice, and Arabidopsis. Collectively, the present study provides new insights into the possible roles of MADS-box genes in response to stresses and will be valuable for further functional studies of important candidate MADS-box genes.

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“…Indeed, MD09G1009100 was down-regulated from January to March, specifically during the transition from the ecodormancy stage to the budbreak stage. So far, there have been inconsistencies regarding the presence and identification of apple FLC-LIKE genes in previous studies by different researchers, for example, Tian et al (2015) did not detect any FLC-LIKE genes when they examined the apple MADS-box gene family. Thus, we identified apple FLC-LIKE genes using a recently updated version of the apple genome.…”

Section: Levels In Terminal Flower Budsmentioning

confidence: 97%

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

Takeuchi¹,

Matsushita²,

Nishiyama³

et al. 2018

J. Amer. Soc. Hort. Sci.

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Endodormancy release and the fulfillment of the chilling requirement (CR) are critical physiological processes that enable uniform blooming in fruit tree species, including apple (Malus ×domestica). However, the molecular mechanisms underlying these traits have not been fully characterized. The objective of this study was to identify potential master regulators of endodormancy release and the CR in apple. We conducted RNA-Sequencing (RNA-seq) analyses and narrowed down the number of candidates among the differentially expressed genes (DEGs) based on the following two strict screening criteria: 1) the gene must be differentially expressed between endodormant and ecodormant buds under different environmental conditions and 2) the gene must exhibit chill unit (CU)–correlated expression. The results of our cluster analysis suggested that global expression patterns varied between field-grown buds and continuously chilled buds, even though they were exposed to similar amounts of chilling and were expected to have a similar dormancy status. Consequently, our strict selection strategy resulted in narrowing down the number of possible candidates and identified the DEGs strongly associated with the transition between dormancy stages. The genes included four transcription factor genes, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS C (FLC)-LIKE, APETALLA2 (AP2)/ETHYLENE-RESPONSIVE 113 (ERF113), and MYC2. Their expressions were upregulated during endodormancy release, and were correlated with the CU, suggesting that these transcription factors are closely associated with chilling-mediated endodormancy release in apple.

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Genome-wide identification and analysis of the MADS-box gene family in apple

Cited by 106 publications

References 50 publications

Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

Tracing the footprints of the ABCDE model of flowering inPhalaenopsis equestris(Schauer) Rchb.f. (Orchidaceae)

Genome-wide Identification and Analysis of the MADS-box Gene Family in Melon

RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

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