scholarly journals Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yuanyuan Zhang ◽  
Jianli Liang ◽  
Xu Cai ◽  
Haixu Chen ◽  
Jian Wu ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Leaf Morphology ◽  
Expression Patterns ◽  
Leaf Traits ◽  
Leaf Angle ◽  
Leaf Petiole ◽  
Head Formation ◽  
Arabidopsis Mutant ◽  
Leafy Head ◽  
Mutant Complementation

AbstractThe leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and breeding. BREVIS RADIX (BRX) has been suggested to control root elongation, shoot growth, and tiller angle in Arabidopsis and rice. In Brassica rapa, three BrBRX homoeologs have been identified, but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions, indicating their functional diversification in leafy head formation. Here, we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications, motif compositions and expression patterns. Moreover, although the expression of these three BrBRX genes differed, compared with BrBRX.3, BrBRX.1, and BrBRX.2 displayed similar expression patterns. Arabidopsis mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype, whereas BrBRX.2 and BrBRX.3 could not. However, overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes, including epinastic leaf morphology, with an increase in leaf number and leaf petiole length and a reduction in leaf angle. These leaf traits are associated with leafy head formation. Further testing of a SNP (T/C) in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of B. rapa. Our results revealed that all three BrBRX genes may be involved in the leaf-heading trait, but they may have functionally diverged on the basis of their differential expression.

scholarly journals Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xu Cai ◽  
Lichun Chang ◽  
Tingting Zhang ◽  
Haixu Chen ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Structural Variation ◽  
De Novo ◽  
Individual Genome ◽  
Synonymous Mutations ◽  
Pan Genome ◽  
Intact Gene ◽  
Head Formation ◽  
Leafy Head

Abstract Background Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes. Results Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being “flexible.” We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation. Conclusions This pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Extended expression of MaKN1 contributes to the leaf morphology in aquatic forms of Myriophyllum aquaticum

Botany ◽  
2015 ◽  
Vol 93 (9) ◽  
pp. 611-621
Author(s):  
M.D. Shafiullah ◽  
Christian R. Lacroix
Keyword(s):  
Apical Meristem ◽  
Leaf Morphology ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Leaf Primordia ◽  
Leaf Primordium ◽  
Myriophyllum Aquaticum ◽  
Knox Gene ◽  
Leaf Morphogenesis

Myriophyllum aquaticum (Vell.) Verdc. is heterophyllous in nature with highly dissected simple leaves consisting of several lobes. KNOX (KNOTTED1-LIKE HOMEOBOX) genes are believed to have played an important role in the evolution of leaf diversity. Up-regulation of KNOX during leaf primordium initiation can lead to leaf dissection in plants with simple leaves and, if overexpressed, can produce ectopic meristems on leaves. A previous study on KNOX gene expression in the aerial form of this species showed that this gene is expressed in the shoot apical meristem (SAM), as well as in leaf primordia P0 to P8. Based on these results, it was hypothesized that the prolonged expression of the MaKN1 (Myriophyllum aquaticum Knotted1-like homeobox) gene beyond P8, might play an important role in the generation of more lobes, longer lobes, and hydathode formation in the aquatic leaves of M. aquaticum. The technique of in situ hybridization was carried out using a previously sequenced 300 bp fragment of MaKN1 to determine the expression patterns of this gene in the shoot of aquatic forms of the plant. Expression patterns of MaKN1 revealed that the SAM and leaf primordia of aquatic forms of M. aquaticum at levels P0 (youngest) to P4 were distributed throughout these structures. The level of expression of this MaKN1 gene progressively became more localized to lobes in older leaf primordia (levels P5 to P12). Previous studies of aerial forms of this plant showed MaKN1 expression until P8. Our results with aquatic forms show that the highly dissected leaf morphology in aquatic forms was the result of the prolonged expression of MaKN1 beyond P8. This resulted in the formation of elongated and slightly more numerous lobes, and hydathodes in aquatic forms. These findings support the view that KNOX genes are important developmental regulators of leaf morphogenesis and have played an important role in the evolution of leaf forms in the plant kingdom.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

2020 ◽  
Author(s):  
Alexander Calderwood ◽  
Jo Hepworth ◽  
Shannon Woodhouse ◽  
Lorelei Bilham ◽  
D. Marc Jones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Detailed Comparison ◽  
Developmental Time ◽  
Floral Transition ◽  
Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

scholarly journals Characterization of Brassica rapa RAP2.4-Related Proteins in Stress Response and as CUL3-Dependent E3 Ligase Substrates

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 336 ◽  
Author(s):  
Sutton Mooney ◽  
Raed Al-Saharin ◽  
Christina M. Choi ◽  
Kyle Tucker ◽  
Chase Beathard ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Stress Responses ◽  
Expression Patterns ◽  
Economic Value ◽  
E3 Ligase ◽  
26S Proteasome ◽  
Dependent Manner ◽  
E3 Ligases ◽  
Subsequent Degradation ◽  
Stress Dependent

The turnip Brassica rapa has important economic value and represents a good model system to study gene function in crop plants. ERF/AP2 transcription factors are a major group of proteins that are often involved in regulating stress-responses and developmental programs. Some ERF/AP2 proteins are targets of CULLIN3-based E3 ligases that use BTB/POZ-MATH proteins as substrate receptors. These receptors bind the transcription factor and facilitate their ubiquitylation and subsequent degradation via the 26S proteasome. Here, we show tissue and stress-dependent expression patterns for three Brassica rapa ERF/AP2 proteins that are closely related to Arabidopsis thaliana AtRAP2.4. Cloning of the Brassica genes showed that the corresponding proteins can assemble with a BPM protein and CULLIN3, and that they are instable in a 26S proteasome dependent manner. This work demonstrates the conserved nature of the ERF/AP2-CULLIN3-based E3 ligase interplay, and represents a first step to analyze their function in a commercially relevant crop plant.

scholarly journals The two Xenopus Gbx2 genes exhibit similar, but not identical expression patterns and can affect head formation

FEBS Letters ◽  
2001 ◽  
Vol 507 (2) ◽  
pp. 205-209 ◽  
Author(s):  
Ella Tour ◽  
Graciela Pillemer ◽  
Yosef Gruenbaum ◽  
Abraham Fainsod
Keyword(s):  
Expression Patterns ◽  
Head Formation

Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa ‘Tsuda’

2018 ◽  
Vol 45 (12) ◽  
pp. 1223 ◽  
Author(s):  
Haifang Yan ◽  
Bo Zhou ◽  
Wei He ◽  
Yuzhe Nie ◽  
Yuhua Li
Keyword(s):  
Blue Light ◽  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Transcript Level ◽  
Light Treatment ◽  
Anthocyanin Synthesis ◽  
Root Epidermis ◽  
High Or Low Temperature ◽  
Level Analysis

ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa ‘Tsuda’. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old ‘Tsuda’ turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of ‘Tsuda’ turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.

Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 963-973 ◽  
Author(s):  
Jianjun Zhao ◽  
Maria-João Paulo ◽  
Diaan Jamar ◽  
Ping Lou ◽  
Fred van Eeuwijk ◽  
...  
Keyword(s):  
Population Structure ◽  
Qtl Mapping ◽  
Association Mapping ◽  
Brassica Rapa ◽  
Morphological Traits ◽  
Genetic Basis ◽  
Leaf Traits ◽  
Structure Association ◽  
Phytate Content ◽  
Trait Associations

Association mapping was used to investigate the genetic basis of variation within Brassica rapa , which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker–trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

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