Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.)

Ma, Jian; Yang, Yujie; Luo, Wei; Yang, Congcong; Ding, Ping; Liu, Yaxi; Qiao, Liang; Chang, Zhijian; Geng, Hao; Wang, Penghao; Jiang, Qiantao; Wang, Jirui; Chen, Guoyue; Wei, Yuming; Zheng, Youliang; Lan, Xiujin

doi:10.1371/journal.pone.0181443

Cited by 80 publications

(64 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of all SBP sequences with three exons, motif numbers fluctuated between 5 and 20, and the SBP-box domain had no fixed position in the sequence (Figure 2). Similar results have been seen in other species, including moss [80], moso bamboo [11], and maize [17]. At the same time, we also noticed that there were similar motifs and orders of motifs in the proteins for each group.…”

Section: Discussionsupporting

confidence: 89%

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Song

Yin

et al. 2019

Agronomy

View full text Add to dashboard Cite

Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat.

show abstract

Section: Discussionsupporting

confidence: 89%

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Song

Yin

et al. 2019

Agronomy

View full text Add to dashboard Cite

show abstract

“…Y. Zhao et al, 2006;Yamada et al, 2009;Yang et al, 2017). Although overviews on MADS-box genes in wheat are available (T. Paolacci et al, 2007;Ma et al, 2017), a detailed genome-wide phylogenetic and functional characterization of wheat MIKC-type MADS-box genes is still missing.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

et al. 2019

View full text Add to dashboard Cite

Summary Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine‐tuning important traits is of great importance. MADS‐box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC‐type MADS‐box genes. Homoeolog retention is significantly above the average genome‐wide retention rate for wheat genes, indicating that many MIKC‐type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily‐specific expression pattern, indicating broad conservation of function of MIKC‐type genes during wheat evolution. We also found extensive expansion of some MIKC‐type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC‐type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC‐type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.

show abstract

“…(2014) demonstrated the relevant role of the chloroplast DEAD-box RH3 on the growth and stress response in Arabidopsis thaliana . Interestingly, it is reported that in bread wheat the MIKC-type MADS-box TFs have key roles in plant growth (Ma et al ., 2017; Li et al ., 2018); however, even if one of these transcription factors (Traes_5AL_13E2DEC48) was a central node in the durum wheat-specific network, it was down-regulated under N starvation in comparison to the optimal N condition.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

Beleggia

Omranian

Gioia

et al. 2020

Preprint

View full text Add to dashboard Cite

Glutamate 28 2 Summary 29Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not 30 only yield but also development and defense. Using a combined transcriptomics and metabolomics 31 approach, we studied the response of seedlings to N starvation of two different tetraploid wheat 32 genotypes from the two main domesticated subspecies, emmer (Triticum turgidum ssp. dicoccum) 33 and durum wheat (Triticum turgidum ssp. durum). We found that durum wheat exhibits broader and 34 stronger response in comparison to emmer as evidenced by the analysis of the differential expression 35 pattern of both genes and metabolites and gene enrichment analysis. Emmer and durum wheat showed 36 major differences in the responses to N starvation for transcription factor families. While emmer 37 showed differential reduction in the levels of primary metabolites to N starvation, durum wheat 38 exhibited increased levels of most metabolites, including GABA as an indicator of metabolic 39 imbalance. The correlation-based networks including the differentially expressed genes and 40 metabolites revealed tighter regulation of metabolism in durum wheat in comparison to emmer, as 41 evidenced by the larger number of significant correlations. We also found that glutamate and GABA 42 had highest values of centrality in the metabolic correlation network, suggesting their critical role in 43 the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, 44 this finding indicates that there might be contrasting strategies associated to GABA and Glutamate 45 signaling modulating shoot vs root growth in the two different wheat subspecies. 47Availability and uptake of nitrogen (N) is considered a major driver of growth (Lea and Azevedo, 48 2006). Indeed, N is an essential nutrient for all organisms, including plants, and is required for the 49 biosynthesis of macromolecules, such as proteins, nucleic acids, and chlorophyll, and for the synthesis 50 of many secondary metabolites with different roles in adaptation and signaling (Miller et al., 2007). 51As a result, N deficiency (limited availability) and starvation (complete absence) dramatically affects 52 plant growth and metabolism (Obata and Fernie, 2012). 53However, only 30-50% of supplied N is taken up by crops (Raun and Johnson, 1999), and the 54 remainder is lost by denitrification or leaching into terrestrial ecosystems, causing eutrophication and 55 contamination of drinking water (Cassman et al., 2003). Therefore, plant breeding efforts should be 56 combined with improvement of crop management towards a more efficient use of N also to limit the 57 use of fossil energy and environmental pollution (Ayadi et al., 2014; Ruisi et al., 2015). Towards this 58 key objective, it is necessary to understand how plants react and cope with low N availability and 59 identify the molecular basis of the natural genetic variation for adaptation to low N conditions. 60Understanding the molecular mechanisms underlying the variation ...

show abstract

Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.)

Cited by 80 publications

References 51 publications

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-Like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

Contact Info

Product

Resources

About