Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 356-366 ◽  
Author(s):  
I AP Parkin ◽  
D J Lydiate ◽  
M Trick
Keyword(s):  
Brassica Napus ◽  
Genetic Linkage Map ◽  
Genome Duplication ◽  
Genomic Sequence ◽  
Brassica Species ◽  
Gene Identification ◽  
Marker Development ◽  
Chromosome 5 ◽  
Brassica Crop ◽  
Comprehensive Comparison

This study describes a comprehensive comparison of chromosome 5 of the model crucifer Arabidopsis with the genome of its amphidiploid crop relative Brassica napus and introduces the use of in silico sequence homology to identify conserved loci between the two species. A region of chromosome 5, spanning 8 Mb, was found in six highly conserved copies in the B. napus genome. A single inversion appeared to be the predominant rearrangement that had separated the two lineages leading to the formation of Arabidopsis chromosome 5 and its homologues in B. napus. The observed results could be explained by the fusion of three ancestral genomes with strong similarities to modern-day Arabidopsis to generate the constituent diploid genomes of B. napus. This supports the hypothesis that the diploid Brassica genomes evolved from a common hexaploid ancestor. Alignment of the genetic linkage map of B. napus with the genomic sequence of Arabidopsis indicated that for specific regions a genetic distance of 1 cM in B. napus was equivalent to 285 Kb of Arabidopsis DNA sequence. This analysis strongly supports the application of Arabidopsis as a tool in marker development, map-based gene cloning, and candidate gene identification for the larger genomes of Brassica crop species.Key Words: comparative mapping, Brassica species, model crucifer, genome evolution, genome duplication.

Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome

Genome ◽  
1998 ◽  
Vol 41 (1) ◽  
pp. 62-69 ◽  
Author(s):  
A C Cavell ◽  
D J Lydiate ◽  
IAP Parkin ◽  
C Dean ◽  
M Trick
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Physical Map ◽  
Brassica Species ◽  
Single Copy ◽  
Genetic Maps ◽  
Haploid Genome ◽  
Chromosome 4 ◽  
Crop Species ◽  
Brassica Crop

Arabidopsis thaliana (the model dicotyledonous plant) is closely related to Brassica crop species. Genome collinearity, or conservation of marker order, between Brassica napus (oilseed rape) and A. thaliana was assessed over a 7.5-Mbp region of the long arm of A. thaliana chromosome 4, equivalent to 30 cM. Estimates of copy number indicated that sequences present in a single copy in the haploid genome of A. thaliana (n = 5) were present in 2-8 copies in the haploid genome of B. napus (n = 19), while sequences present in multiple copies in A. thaliana were present in over 10 copies in B. napus. Genetic mapping in B. napus of DNA markers derived from a segment of A. thaliana chromosome 4 revealed duplicated homologous segments in the B. napus genome. Physical mapping in A. thaliana of homologues of Brassica clones derived from these regions confirmed the identity of six duplicated segments with substantial homology to the 7.5-Mbp region of chromosome 4 in A. thaliana. These six duplicated Brassica regions (on average 22cM in length) are collinear, except that two of the six copies contain the same large internal inversion. These results have encouraging implications for the feasibility of shuttling between the physical map of A. thaliana and genetic maps of Brassica species, for identifying candidate genes and for map based gene cloning in Brassica crops.

Patterns of genome duplication within the Brassica napus genome

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 291-303 ◽  
Author(s):  
I A.P Parkin ◽  
A G Sharpe ◽  
D J Lydiate
Keyword(s):  
Brassica Napus ◽  
Genome Duplication ◽  
Chromosomal Rearrangements ◽  
Centric Fusion ◽  
Linkage Groups ◽  
Gross Chromosomal Rearrangements ◽  
A Genome ◽  
C Genome ◽  
Homologous Locus ◽  
Duplicate Loci

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.

scholarly journals Suppression of Metacaspase- and Autophagy-Dependent Cell Death Improves Stress-Induced Microspore Embryogenesis in Brassica napus

2020 ◽  
Author(s):  
Eduardo Berenguer ◽  
Elena A Minina ◽  
Elena Carneros ◽  
Ivett Bárány ◽  
Peter V Bozhkov ◽  
...  
Keyword(s):  
Cell Death ◽  
Brassica Napus ◽  
Embryonic Development ◽  
Doubled Haploid ◽  
Microspore Embryogenesis ◽  
Brassica Species ◽  
Cysteine Proteases ◽  
Plant Production ◽  
Haploid Plant

Abstract Microspore embryogenesis is a biotechnological process that allows us to rapidly obtain doubled-haploid plants for breeding programs. The process is initiated by the application of stress treatment, which reprograms microspores to embark on embryonic development. Typically, a part of the microspores undergoes cell death that reduces the efficiency of the process. Metacaspases (MCAs), a phylogenetically broad group of cysteine proteases, and autophagy, the major catabolic process in eukaryotes, are critical regulators of the balance between cell death and survival in various organisms. In this study, we analyzed the role of MCAs and autophagy in cell death during stress-induced microspore embryogenesis in Brassica napus. We demonstrate that this cell death is accompanied by the transcriptional upregulation of three BnMCA genes (BnMCA-Ia, BnMCA-IIa and BnMCA-IIi), an increase in MCA proteolytic activity and the activation of autophagy. Accordingly, inhibition of autophagy and MCA activity, either individually or in combination, suppressed cell death and increased the number of proembryos, indicating that both components play a pro-cell death role and account for decreased efficiency of early embryonic development. Therefore, MCAs and/or autophagy can be used as new biotechnological targets to improve in vitro embryogenesis in Brassica species and doubled-haploid plant production in crop breeding and propagation programs.

scholarly journals Selenium Enhances Cadmium Accumulation Capability in Two Mustard Family Species—Brassica napus and B. juncea

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 904 ◽  
Author(s):  
Zhong-Wei Zhang ◽  
Yi-Ying Dong ◽  
Ling-Yang Feng ◽  
Zong-Lin Deng ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Brassica Juncea ◽  
Brassica Species ◽  
Dry Weight ◽  
Cadmium Accumulation ◽  
Cd Accumulation ◽  
Cd Toxicity ◽  
Valence States ◽  
Early Seedling ◽  
High Level

Oilseed rape (Brassica napus) is a Cadmium (Cd) hyperaccumulator. However, high-level Cd at the early seedling stage seriously arrests the growth of rape, which limits its applications. Brassica juncea had higher Cd accumulation capacity, but its biomass was lower, also limiting its applications. Previous studies have confirmed that Selenium (Se) can alleviate Cd toxicity. However, the regulatory mechanism of Se in different valence states of Cd accumulation was unclear. In this study, we investigated the ameliorating effects of three Se valence states, Na2SeO4 [Se(VI)], Na2SeO3 [Se(IV)] and Se-Met [Se(II)], to Cd toxicity by physiological and biochemical approaches in hydroponically-cultured Brassica juncea and Brassica napus seedlings. Although Se treatments slightly inhibited seedling Cd concentration, it tripled or quadrupled the Cd accumulation level per plant, because dry weight increased about four times more with Se and Cd application than with Cd treatment alone. Among the different valence states of Se, Se(II) had the most marked effect on reducing Cd toxicity as evidenced by decreased growth inhibition and Cd content. The application of Se(II) was effective in reducing Cd-induced reactive oxygen species accumulation, and promoted the antioxidant enzyme activity and photosynthesis of both Brassica species. In addition, Se(II) treatment increased the concentrations of Cd in the cell wall and soluble fractions, but the Cd concentration in the organelle part was reduced.

The Role of Phytoalexins in the Seedling Resistance to Leptosphaeria maculans in Some Crucifers

1995 ◽  
Vol 50 (1-2) ◽  
pp. 15-20 ◽  
Author(s):  
Michael Storck ◽  
Maria D. Sacristán
Keyword(s):  
Brassica Napus ◽  
Leptosphaeria Maculans ◽  
Brassica Species ◽  
Fungal Isolate ◽  
Time Intervals ◽  
Seedling Resistance ◽  
Sinapis Arvensis ◽  
Resistant Lines ◽  
Resistance Reaction

Abstract Brassica juncea, Brassica carinata and Sinapis arvensis resistant lines to Leptosphaeria maculans and four Brassica napus cuitivars susceptible to this pathogen in seedling stage were analyzed in relation to the accumulation of phytoalexins after inoculation with L. maculans. Cotyledon inoculations with spore suspensions of an aggressive and a non-aggressive isolate of L. maculans were performed on seedlings of these lines. The quantity of accumulated phytoalexins in the cotyledons was determined at different time intervals after inoculation. The content and composition of phytoalexins differed considerably among the tested species and according to the fungal isolate used. In the tested Brassica species seedling resistance against L. maculans could not be related to phytoalexin accumulation. However, in Sinapis arvensis phytoalexins might contribute to the resistance reaction to this pathogen.

scholarly journals Effect of Water Deficiency and Potassium Application on Plant Growth, Osmolytes and Grain Yield of Brassica Napus Cultivars

2014 ◽  
Vol 73 (2) ◽  
pp. 299-314 ◽  
Author(s):  
Murad Ali ◽  
Jehan Bakht ◽  
Gul Daraz Khan
Keyword(s):  
Brassica Napus ◽  
Grain Yield ◽  
Water Content ◽  
Relative Water Content ◽  
Field Experiments ◽  
Dependent Manner ◽  
Water Deficiency ◽  
Brassica Crop ◽  
Relative Water ◽  
Potassium Application

Abstract One of the major issues with brassica oil seed production is the water requirement of the brassica crop. To address the problem, field experiments were conducted to evaluate the effect of potassium (K) and water deficiency levels on canola (Brassica napus L.). Analysis of the data revealed that application of K, irrigation and interactions between irrigation and cultivar (I x C), irrigation and potassium (I x K), potassium and cultivar (K x C), and irrigation and cultivar and potassium (I x C x K) had a significant (p < 0.05) effect on shoot proline content, relative water content, plant fresh weight and grain yield. Potassium application, irrigation and interaction between I x C, K x C, and I x C x K had a significant (p < 0.05) effect on shoot sugar content. Water deficiency increased shoot proline and sugar contents and decreased relative water content. Potassium application increased shoot proline level in a dose dependent manner. Minimum proline and sugar contents and maximum relative water content, plant fresh and dry weight and yield were obtained when 100% irrigation was applied. Maximum grain yield was obtained upon application of 100% irrigation in combination with 120 kg ha−1 K.

scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

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