Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map

Babula, D.; Kaczmarek, M.; Bara­kat, Abdelali; Delseny, Michel; Quirós, Carlos F.; Sadowski, Jan

doi:10.1007/s00438-002-0782-2

Cited by 90 publications

(29 citation statements)

References 46 publications

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“…It is worth noting that we could expect any remnants of the fusions only in the case of chromosomes 1, 2 and 5, where the ancient pericentromeric regions had been taken apart: in fusions that resulted in the formation of present chromosomes 3 and 4 only telomeric sequences could be expected. We also found that it is impossible to detect remnants of more ancient chromosomal rearrangements at the level of indel distribution, though they can be easily detected by bioinformatic (23,56,57) and hybridization approaches (58,59), where coding sequences are mainly involved.…”

Section: Discussionmentioning

confidence: 92%

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Ziolkowski

Koczyk

Gałgański

et al. 2009

Nucleic Acids Research

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Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are ∼8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.

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Section: Discussionmentioning

confidence: 92%

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Ziolkowski

Koczyk

Gałgański

et al. 2009

Nucleic Acids Research

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“…Moreover, Brassica and Arabidopsis diverged from a common ancestor approximately 14–20 million years ago (Yang et al, 1999), and the genome of Brassica species underwent polyploidization, accompanied by gene deletion and rearrangements (Cavell et al, 1998; Lagercrantz, 1998; Ryder et al, 2001; Babula et al, 2003; Lukens et al, 2003). Therefore, many comparative mapping studies have unraveled the extensive genome homology and microsynteny between the A, B, and C genomes of Brassica species and between Brassica species and A. thaliana (Parkin et al, 2005; Jiang et al, 2011; Wang et al, 2011; Yang et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Zhao

et al. 2016

Front. Plant Sci.

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Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.

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“…The homeologous IDBs in different chromosomes would enhance the chance of homeologous reciprocal or nonreciprocal translocations which were already found in several Canadian and Australian cultivars of B. napus where IDBs exchanged between A7 and C6 [53,54]. Lyask et al [25] found that the most frequent chromosome rearrangements involving the At4-b contig are inversions, whilst comparative mapping has indicated that 43% of Brassica genomicregions with homeology to Arabidopsis chromosomes involved inversions [35]. It has been suggested that rearrangements such as translocations or inversions might reduce or prevent undesirable pairing and recombination between homeologous chromosomes/chromosome regions and lead to reproductive isolation between populations, and eventually contribute to the speciation processes [55].…”

Section: Discussionmentioning

confidence: 99%

“…Recently, more detailed evidence for the ancestral segmental chromosomal duplications leading to effective triplication in Brassica diploids has been obtained from partial genome sequencing and comparative chromosome painting [22,25,32-34]. However, comparative sequence analysis indicates that various mechanisms of genome evolution have contributed to many situations where either more or less than three paralogous genes, corresponding to single orthologues in Arabidopsis , are present in the Brassica A or C genome [26,28,35-37]. …”

Section: Introductionmentioning

confidence: 99%

The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks

Wang

Long

et al. 2009

BMC Evol Biol

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BackgroundThe gene FLOWERING LOCUS T (FT) and its orthologues play a central role in the integration of flowering signals within Arabidopsis and other diverse species. Multiple copies of FT, with different cis-intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as Brassica napus (AACC), a member of the same plant family as Arabidopsis.ResultsWe have identified six BnFT paralogues from the genome of B. napus and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of Arabidopsis chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of BnFT paralogues showed 92-99% identities to each other and 85-87% identity with that of Arabidopsis. However, two of the paralogues on chromosomes A2 and C2, BnA2.FT and BnC2.FT, were found to lack the distinctive CArG box that is located within intron 1 that has been shown in Arabidopsis to be the binding site for theFLC protein. Three BnFT paralogues (BnA2.FT, BnC6.FT.a and BnC6.FT.b) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two BnFT paralogues (BnC6.FT.a and BnC6.FT.b) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three BnFT paralogues across 55 cultivars of B. napus showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral FT homologues in Brassica evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the divergence of B. rapa (AA) and B. oleracea (CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole B. napus genome.ConclusionSix orthologues of Arabidopsis FT were identified and mapped in the genome of B. napus which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of BnFT paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed Brassica. The prevalent inverted duplicated blocks, two of which were located by four of the six BnFT paralogues, contributed to gene duplications and might represent predominant pathway of evolution in Brassica.

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Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map

Cited by 90 publications

References 46 publications

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks

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