Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species

Chen, Daozong; Chen, Haidong; Dai, Guoqiang; Zhang, Haimei; Liu, Yi; Shen, Wenjie; Zhu, Bo; Cui, Cheng; Tan, Chen

doi:10.1186/s12864-022-08666-7

Cited by 17 publications

(12 citation statements)

References 56 publications

(78 reference statements)

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“…4, Supplementary Table S2). This was different from the results we discovered that only PAP1/2 homologous copies were differentially expressed in green and purple leaves of five Brassica crops [5], indicating the different transcriptional regulations of anthocyabetween vegetative and reproductive organs in Brassica crops. At the same time, DFR(AT5G42800), MYB5(AT3G13540) and AHA10(AT1G17260) were differentially expressed in eight developmental stages of five Brassica crops, especially DFR(AT5G42800), which iwa generally considered to be the target gene of the MBW transcriptional regulatory complex, was not differentially expressed only in B. juncea (Fig.…”

Section: Co-expression Analysis Of Anthocyanin-related Genescontrasting

confidence: 99%

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Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Chen

Dai

et al. 2023

BMC Genomics

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Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.

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Section: Co-expression Analysis Of Anthocyanin-related Genescontrasting

confidence: 99%

“…The read counts of each gene were calculated using the htseq-count function in htseq software [1]. The R package DEseq2 (v1.16.1) was used to identify the differentially expressed genes (DEGs) between leaves of different colors based on the following criteria: padj < 0.05 & log2FoldChange > 2 [5].…”

Section: Expression Profiles Analysis Based On Rna-seq Datamentioning

confidence: 99%

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Chen

Dai

et al. 2023

BMC Genomics

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“…The evolution of the R2R3-MYB gene family in Brassica has been tracked in previous research [ 21 ]. In order to specifically understand the evolutionary relationship of target genes, we analyzed the homologous relationship among Arabidopsis , B. napus (A and C subgenomes), B. rapa (A genome), and B. oleracea (C genome) ( Figure 5 ).…”

Section: Resultsmentioning

confidence: 99%

“…In a recent study [ 21 ], 2120 R2R3-MYB genes were identified in six brassica plants, including 130 in Arabidopsis , 236 in B. rapa , 247 in B. oleracea , 248 in B. nigra , 425 in B. napus , 422 in B. juncea and 412 in B. carinata . However, the number of R2R3-MYBs in Arabidopsis , B. rapa and B. napus were different from those found in previous studies, namely, 126 in Arabidopsis [ 18 ], 256 in B. rapa [ 22 ], and 249 in B. napus [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and Phylogenetic Analysis of the R2R3-MYB Subfamily in Brassica napus

Luo

Mei

Wei

et al. 2023

Plants

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The R2R3-MYB sub-family proteins are composed of most members of MYB (v-Myb avian myeloblastosis viral oncogene homolog) protein, a plant-specific transcription factor (TF) that is classified into four classes depending on the number of MYB repeats. R2R3-MYB TFs are involved in physiological and biochemical processes. However, the functions of the Brassica napus R2R3-MYB genes are still mainly unknown. In this study, 35 Brassica napus MYB (BnaMYB) genes were screened in the genome of Brassica napus, and details about their physical and chemical characteristics, evolutionary relationships, chromosome locations, gene structures, three-dimensional protein structures, cis-acting promoter elements, and gene duplications were uncovered. The BnaMYB genes have undergone segmental duplications and positive selection pressure, according to evolutionary studies. The same subfamilies have similar intron–exon patterns and motifs, according to the genes’ structure and conserved motifs. Additionally, through cis-element analysis, many drought-responsive and other stress-responsive cis-elements have been found in the promoter regions of the BnaMYB genes. The expression of the BnaMYB gene displays a variety of tissue-specific patterns. Ten lignin-related genes were chosen for drought treatment. Our research screened four genes that showed significant upregulation under drought stress, and thus may be important drought-responsive genes. The findings lay a new foundation for understanding the complex mechanisms of BnaMYB in multiple developmental stages and pathways related to drought stress in rapeseed.

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“…The read counts of each gene were calculated using the htseq-count function in htseq software (Anders et al, 2015). The R package DEseq2 (v1.16.1) was used to identify the differentially expressed genes (DEGs) between leaves of different colors based on the following criteria: padj < 0.05 & log2FoldChange > 2 (Chen et al, 2022).…”

Section: Expression Pro Les Analysis Based On Rna-seq Datamentioning

confidence: 99%

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Chen

Dai

et al. 2022

Preprint

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Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The variation of the seed coat color of Brassica crops was related to the specific expression of transcription factors which regulated the up-regulated expression of catalytic enzymes in the anthocyanin synthesis pathway. Although there have been previous reports on the regulation mechanism of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the seed coat color of Brassica crops is affected by events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B.napus (AACC) and the worst in B.carinata (BBCC). The comparison of gene expression related to anthocyanin metabolic pathways in seed coats during seed development revealed differences in anthocyanin metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analysis of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 may be gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.

show abstract

Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species

Cited by 17 publications

References 56 publications

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Identification and Phylogenetic Analysis of the R2R3-MYB Subfamily in Brassica napus

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

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