Inheritance and expression patterns of BN28, a low temperature induced gene in Brassica napus, throughout the Brassicaceae

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 704-710 ◽  
Author(s):  
G. P. Hawkins ◽  
C. L. Nykiforuk ◽  
A. M. Johnson-Flanagan ◽  
J. G. Boothe
Keyword(s):  
Brassica Napus ◽  
Low Temperature ◽  
Brassica Rapa ◽  
Southern Blot Analysis ◽  
Expression Patterns ◽  
Diploid Species ◽  
Homologous Genes ◽  
Brassicaceae Species ◽  
Agronomically Important Traits ◽  
Selection Of

Molecular genetics is becoming an important tool in the breeding and selection of agronomically important traits. BN28 is a low temperature induced gene in Brassicaceae species. PCR and Southern blot analysis indicate that BN28 is polymorphic in the three diploid genomes: Brassica rapa (AA), Brassica nigra (BB), and Brassica oleracea (CC). Of the allotetraploids, Brassica napus (AACC) is the only species to have inherited homologous genes from both parental genomes. Brassica juncea (AABB) and Brassica carinata (BBCC) have inherited homologues from the AA and CC genomes, respectively, while Sinapsis arvensis (SS) contains a single homologue from the BB genome and Sinapsis alba (dd) appears to be different from all the diploid parents. All species show message induction when exposed to low temperature. However, differences in expression were noticed at the protein level, with silencing occurring in the BB genome at the level of translation. Results suggest that silencing is occurring in diploid species where duplication may not have occurred. Molecular characterization and inheritance of BN28 homologues in the Brassicaceae may play an important role in determining their quantitative function during exposure to low temperature. Key words : Brassicaceae, BN28, inheritance, polymorphism.

scholarly journals Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus

2010 ◽  
Vol 155 (2) ◽  
pp. 851-865 ◽  
Author(s):  
Xue Chen ◽  
Martin Truksa ◽  
Crystal L. Snyder ◽  
Aliaa El-Mezawy ◽  
Saleh Shah ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Homologous Genes ◽  
Genes Encoding

scholarly journals A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

2016 ◽  
Vol 129 (10) ◽  
pp. 1887-1899 ◽  
Author(s):  
Wayne E. Clarke ◽  
Erin E. Higgins ◽  
Joerg Plieske ◽  
Ralf Wieseke ◽  
Christine Sidebottom ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Diploid Species ◽  
High Density ◽  
Snp Genotyping ◽  
Single Locus ◽  
Genotyping Array ◽  
Selection Of

scholarly journals Genome-Wide Identification and Characterization of NODULE-INCEPTION-Like Protein (NLP) Family Genes in Brassica napus

2018 ◽  
Vol 19 (8) ◽  
pp. 2270 ◽  
Author(s):  
Miao Liu ◽  
Wei Chang ◽  
Yonghai Fan ◽  
Wei Sun ◽  
Cunmin Qu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Nitrogen Deficiency ◽  
Three Dimensional ◽  
Group Iii ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Brassicaceae Species ◽  
History Of

NODULE-INCEPTION-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in responses to nitrogen deficiency. However, the evolutionary relationships and characteristics of NLP family genes in Brassica napus are unclear. In this study, we identified 31 NLP genes in B. napus, including 16 genes located in the A subgenome and 15 in the C subgenome. Subcellular localization predictions indicated that most BnaNLP proteins are localized to the nucleus. Phylogenetic analysis suggested that the NLP gene family could be divided into three groups and that at least three ancient copies of NLP genes existed in the ancestor of both monocots and dicots prior to their divergence. The ancestor of group III NLP genes may have experienced duplication more than once in the Brassicaceae species. Three-dimensional structural analysis suggested that 14 amino acids in BnaNLP7-1 protein are involved in DNA binding, whereas no binding sites were identified in the two RWP-RK and PB1 domains conserved in BnaNLP proteins. Expression profile analysis indicated that BnaNLP genes are expressed in most organs but tend to be highly expressed in a single organ. For example, BnaNLP6 subfamily members are primarily expressed in roots, while the four BnaNLP7 subfamily members are highly expressed in leaves. BnaNLP genes also showed different expression patterns in response to nitrogen-deficient conditions. Under nitrogen deficiency, all members of the BnaNLP1/4/5/9 subfamilies were upregulated, all BnaNLP2/6 subfamily members were downregulated, and BnaNLP7/8 subfamily members showed various expression patterns in different organs. These results provide a comprehensive evolutionary history of NLP genes in B. napus, and insight into the biological functions of BnaNLP genes in response to nitrogen deficiency.

scholarly journals Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

2021 ◽  
Vol 22 (19) ◽  
pp. 10354
Author(s):  
Xinrui Zheng ◽  
Hao Zhang ◽  
Limei Zhang ◽  
Fangsen Xu ◽  
Lei Shi ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Functional Study ◽  
Nuclear Factor ◽  
Nutrient Deficiencies ◽  
Abiotic Stress Response ◽  
Nuclear Factor Y ◽  
Homologous Genes ◽  
Y Family

Nuclear Factor-Y (NF-Y) transcription factors play vital roles in plant abiotic stress response. Here, the NF-Y family in Brassica napus, which is hyper-sensitive to nitrogen (N) deprivation, was comprehensively identified and systematically characterized. A total of 108 NF-Y family members were identified in B. napus and categorized into three subfamilies (38 NF-YA, 46 NF-YB and 24 NF-YC; part of the Arabidopsis NF-YC homologous genes had been lost during B. napus evolution). In addition, the expansion of the NF-Y family in B. napus was driven by whole-genome duplication and segmental duplication. Differed expression patterns of BnaNF-Ys were observed in response to multiple nutrient starvations. Thirty-four genes were regulated only in one nutrient deficient condition. Moreover, more BnaNF-YA genes were differentially expressed under nutrient limited environments compared to the BnaNF-YB and BnaNF-YC subfamilies. Sixteen hub genes responded diversely to N deprivation in five rapeseed tissues. In summary, our results laid a theoretical foundation for the follow-up functional study of the key NF-Y genes in B. napus in regulating nutrient homeostasis, especially N.

scholarly journals Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus

2019 ◽  
Author(s):  
Liming Miao ◽  
Yingying Gao ◽  
Kun Zhao ◽  
Lijun Kong ◽  
Shubo Yu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Expression Patterns ◽  
Bhlh Gene ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Brassica Crops ◽  
Ks Values

Abstract Background: The basic helix–loop–helix (bHLH) transcription factors exist widely in eukaryotes and play important roles in development and stress response regulation in plants. The bHLH gene family has been identified in many species, except for Brassica oleracea and Brassica napus thus far. This study aims to identify the bHLH family members in B. oleracea, Brassica rapa, and B. napus and elucidate the expression, duplication, phylogeny and evolution characters of these genes. Result: A total of 268 bHLH genes in B. oleracea, 440 genes in B. napus, and 251 genes in B. rapa, including 21 new bHLH members, have been identified. Subsequently, the analysis of the phylogenetic tree, conserved motifs and gene structures showed that the members in the same subfamily were highly conserved. Most Ka/Ks values of the homologous gene were <1, which indicated that the homologous genes suffered from strong purifying selection for retention. The Ks values of the three Brassica crops were concentrated in the range of 0.3–0.5. Hence, the divergence time of the bHLH gene family between Brassica crops and Arabidopsis thaliana is approximately 10–18 MYA. The retention rates of BrabHLH and BolbHLH genes were 51.6% and 55.1%, respectively. A total of 182 genes were lost in B. napus after tetraploid. GO annotations of BolbHLH genes showed that most genes focused on DNA-binding transcription factor, DNA-binding, and protein dimerization activities. The temporal and spatial expression patterns of 50 BolbHLH genes were diverse, some of which showing high expression in the reproduction tissue, while some had high expression in the root. The comparison of expression patterns between B. rapa and B. napus showed that they had similar expression patterns in the root and contrasting patterns in the stems, leaves, and reproduction tissues. However, the expression patterns of B. oleracea and B. napus were different. Conclusion: This study is the first to report about the gene family analysis of the bHLH gene in B. oleracea and B. napus. Our results not only offer useful information on the functional analysis of the bHLH gene but also provide new insights into the evolution of Brassica spp.

scholarly journals Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

2020 ◽  
Author(s):  
Mathieu Rousseau-Gueutin ◽  
Caroline Belser ◽  
Corinne Da Silva ◽  
Gautier Richard ◽  
Benjamin Istace ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Reference Genome ◽  
Crop Improvement ◽  
Genetic Maps ◽  
Sequencing Data ◽  
Long Reads ◽  
Gene Catalogue ◽  
Genome Assemblies ◽  
Agronomically Important Traits ◽  
Selection Of

AbstractBackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The Brassica genus is not exempt and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus.FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.ConclusionUsing these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Resynthesis of Brassica napus with Brassica oleracea or Brassica rapa Cytoplasm

2010 ◽  
Vol 36 (8) ◽  
pp. 1280-1285 ◽  
Author(s):  
Jun LI ◽  
Li-Xia LUO ◽  
Zhuan WANG ◽  
Jun LI ◽  
Kun-Rong CHEN ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Brassica Oleracea ◽  
Brassica Rapa

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

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