Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula

Gu, Chao; Han, Rui; Liu, Chaoyi; Fang, Gao‐Li; Yuan, Qi; Zheng, Zhimin; Yu, Qibin; Jiang, Jing; Liu, Sanzhen; Xie, Linan; Wei, Hairong; Zhang, Qingzhu

doi:10.1093/treephys/tpad085

Cited by 3 publications

(3 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous studies have revealed that a decrease in methylation modification in the promoter region of the BpPIN1 gene, a growth hormone transport protein, serves as a heritable epigenetic variation and a primary inducer of the fissured leaf trait in Betula pendula in both sexual and asexual reproduction processes [39]. However, in the circular leaf mutant Y72, we did not observe a significant restoration of methylation levels in BpPIN1 to the high levels found in the fissured leaf, as depicted in Figure 3C,D.…”

Section: Discussionmentioning

confidence: 99%

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in Betula pendula ‘Dalecarlica’

Zhang,

Gu,

Jiang

et al. 2024

Forests

Self Cite

View full text Add to dashboard Cite

The European white birch, scientifically known as Betula pendula, and its variant, B. pendula ‘Dalecarlica’, are characterized by a lobed leaf margin that enhances their aesthetic appeal. However, the lobed leaf trait can undergo random and spontaneous reversion to the typical ovoid or cordate shape during asexual reproduction. Investigating and elucidating the molecular mechanisms underlying this unpredictable reversion mutation is essential for comprehending the birch leaf development process. In this research, we employed an ovate−leaf mutant derived from a lobed–leaf birch clone during plant tissue culture. We adopted a multi-omics approach, including whole-genome resequencing, transcriptome sequencing, and methylation profiling, to analyze and compare genomic variations and gene expression modifications. The study revealed that the 24 variant genes affected by 1464 SNP/InDel sites in the genome of the ovate−leaf mutant are not associated with leaf development. While the overall methylation level in the mutant’s genome closely resembles that of the lobed–leaf birch, ten genes exhibit differential methylation accompanied by differential expression. Transcriptome sequencing demonstrated that the differentially downregulated genes in the mutant are significantly enriched in the GO:0009733 (response to auxin) and GO:0009734 (auxin-activated signaling) pathways. Validation through McrBC−PCR and qRT−PCR confirmed differential methylation and expression of BpIAA9 in the reversion mutant. The elevated methylation level in the BpIAA9 promoter leads to reduced expression, resulting in changes in the expression of auxin-responsive genes. This, in turn, leads to a transcriptional downregulation enrichment effect in auxin-related pathways in the reversion mutant, ultimately inhibiting the regulation of leaf veins by auxin during their development.

show abstract

Section: Discussionmentioning

confidence: 99%

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in Betula pendula ‘Dalecarlica’

Zhang,

Gu,

Jiang

et al. 2024

Forests

Self Cite

View full text Add to dashboard Cite

show abstract

“…Previous studies have revealed that a decrease in methylation modification in the promoter region of the BpPIN1 gene, a growth hormone transport protein, serves as a heritable epigenetic variation and a primary inducer of the fissured leaf trait in Betula pendula in both sexual and asexual reproduction processes [28]. However, in the circular leaf mutant Y72, we did not observe a significant restoration of methylation levels in BpPIN1 to the high levels found in the fissured leaf, as depicted in Figure 3, C to D. In comparison to fissured leaves, the global methylation levels across the genome of the circular leaf mutant showed no substantial changes in both genes and transposon elements, as shown in Figure 3, A to B.…”

Section: Discussionmentioning

confidence: 99%

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in Betula pendula ‘Dalecarlica’

Zhang,

Gu,

Jiang

et al. 2023

Preprint

View full text Add to dashboard Cite

The European white birch, scientifically known as Betula pendula, and its variant, B. pendula 'Dalecarlica' are characterized by a serrated leaf margin that enhances their aesthetic appeal. However, the lobed leaf trait can undergo random and spontaneous reversion to the typical ovoid or cordate shape during asexual reproduction. Investigating and elucidating the molecular mechanisms underlying this unpredictable reversion mutation is essential for comprehending the birch leaf development process. In this research, we employed a non-lobed-leaf mutant derived from a lobed-leaf birch clone during plant tissue culture. We adopted a multi-omics approach, including whole-genome resequencing, transcriptome sequencing, and methylation profiling, to analyze and compare genomic variations and gene expression modifications. The study revealed that the 24 variant genes affected by 1464 SNP/InDel sites in the genome of the non-lobed-leaf mutant are not associated with leaf development. While the overall methylation level in the mutant's genome closely resembles that of the serrated-leaf birch, ten genes exhibit differential methylation accompanied by differential expression. Transcriptome sequencing demonstrated that the differentially downregulated genes in the mutant are significantly enriched in the GO:0009733 (response to auxin) and GO:0009734 (auxin-activated signaling) pathways. Validation through McrBC-PCR and qRT-PCR confirmed differential methylation and expression of BpIAA9 in the reversion mutant. The elevated methylation level in the BpIAA9 promoter leads to reduced expression, resulting in changes in the expression of auxin-responsive genes. This, in turn, leads to a transcriptional downregulation enrichment effect in auxin-related pathways in the reversion mutant, ultimately inhibiting the regulation of leaf veins by auxin during their development.

show abstract

“…As the earliest discovered plant hormone, auxin plays an important role in diverse aspects of plant growth and development, such as embryogenesis, apical dominance, leaf expansion and aging, shoot elongation, root architecture, flower and fruit development, and abiotic stress responses, by regulating cell growth, division, and differentiation [2]. Recently, several genes involved in auxin transport and signal transduction were reported in B. pendula, such as PIN-formed (PIN) [3] and Gretchen Hagen 3 (GH3) [4], and a complex auxin signaling regulatory network was constructed at the molecular level in plants [5]. In the absence of auxin, auxin/indole-3-acetic acid (Aux/IAA) proteins formed heterodimers with auxin response factor (ARF) proteins to restrain ARF activity, which inhibited the transcription of auxin responsive genes, including AUX/IAA, GH3, and small auxin-up RNA (SAUR) [6].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Betula pendula

Mu,

Jin,

et al. 2023

Horticulturae

View full text Add to dashboard Cite

As the key transcription factors regulating auxin responsive genes expression, auxin response factors (ARFs) play critical roles in diverse aspects of plant growth and development. Betula pendula is a valuable ornamental tree, and the information on ARF gene family of B. pendula is needed for better understanding. The publication of the genome sequence of B. pendula enable to analyze the bioinformatics information and expression pattern of BpeARF gene family on the genome-wide basis. In this study, physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, conserved domain, motif composition, and cis-acting element of BpeARF gene family were analyzed, and expression patterns of BpeARF genes were investigated using completely random design in different tissues and under exogenous NAA and drought treatments. A total of 17 BpeARF genes was identified from B. pendula genome, which were unevenly distributed on 13 chromosomes and encoded adequate proteins ranging from 613 to 1135 amino acids in length. Three BpeARF gene pairs were formed by segmental duplication, and the Ka/Ks values of these BpeARF gene pairs were less than 1. According to the phylogenetic relationship among B. pendula, Betula platyphylla, Populus trichocarpa, and Arabidopsis thaliana, the BpeARF genes were divided into four classes, and the intron/exon structure, conserved domain, and motif composition showed high similarity among the BpeARF genes within the same class. The cis-acting elements in the promoter regions of BpeARF genes were related to tissue development, hormone response, and stress resistance. Quantitative real-time PCR exhibited diverse expression patterns of BpeARF genes in different tissues and in response to exogenous auxin treatment and drought stress. The expressions of one, ten, seven, and three BpeARF genes were the high levels in buds, young leaves, stems, and roots, respectively. Under exogenous NAA treatment, six BpeARF genes in stems and roots were upregulated expression at all timepoints. Under drought stress, BpeARF7 and BpeARF15 were upregulated in stems and roots, and BpeARF5 and BpeARF6 were downregulated in leaves, stems, and roots. Our results provided valuable information for the classification and putative functions of BpeARF gene family, which may be helpful for selecting candidate genes and verifying gene function in the genetic engineering of birch trees in further research.

show abstract

Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula

Cited by 3 publications

References 73 publications

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in Betula pendula ‘Dalecarlica’

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in Betula pendula ‘Dalecarlica’

Heritable Epigenetic Modification of BpIAA9 Causes the Reversion Mutation of Leaf Shapes in<em> Betula pendula</em> ‘Dalecarlica’

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Betula pendula

Contact Info

Product

Resources

About