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.

Correlating the Genetic and Physical Map of Barley Chromosome 3H Revealed Limitations of the FISH-Based Mapping of Nearby Single-Copy Probes Caused by the Dynamic Structure of Metaphase Chromosomes

2017 ◽  
Vol 152 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Fernanda O. Bustamante ◽  
Lala Aliyeva-Schnorr ◽  
Jörg Fuchs ◽  
Sebastian Beier ◽  
Andreas Houben
Keyword(s):  
Dna Sequences ◽  
Physical Map ◽  
Dynamic Structure ◽  
Single Copy ◽  
Physical Distance ◽  
Genetic Distances ◽  
Genetic Maps ◽  
Metaphase Chromosomes ◽  
Physical Maps

Genetic maps are based on the recombination frequency of molecular markers which often show different positions in comparison to the corresponding physical maps. To decipher the position and order of DNA sequences genetically mapped to terminal and interstitial regions of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes was performed with 16 genomic single-copy probes derived from fingerprinted BAC contigs. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H. Nonoverlapping FISH signals were frequently obtained for probes with a physical distance of at least 30-60 kb. Only 8% of the analyzed chromosomes showed a symmetric order of FISH signals on both sister chromatids. Due to the dynamic packing of metaphase chromatin, the order of 2 adjacent single-copy signals along the chromosome arms outside the (peri)centromeric region can only reliably be determined if the cytological distance is approximately 3%, corresponding to 21.6 Mb.

Contrasting genome organisation: two regions of the Brassica oleracea genome compared with collinear regions of the Arabidopsis thaliana genome

Genome ◽  
2001 ◽  
Vol 44 (5) ◽  
pp. 808-817 ◽  
Author(s):  
C D Ryder ◽  
L B Smith ◽  
G R Teakle ◽  
G J King
Keyword(s):  
Arabidopsis Thaliana ◽  
Linkage Group ◽  
Brassica Oleracea ◽  
Crop Species ◽  
Brassica Crop ◽  
Marker Loci ◽  
Model Plant Arabidopsis Thaliana ◽  
Chromosome I ◽  
Arabidopsis Thaliana Genome ◽  
Locus Order

Brassica crop species are of worldwide importance and are closely related to the model plant Arabidopsis thaliana for which the complete genome sequence has recently been established. We investigated collinearity of marker order by comparing two contrasting regions of the Brassica oleracea genome with homologous regions of A. thaliana. Although there is widespread replication of marker loci in both A. thaliana and B. oleracea, we found that a combination of genetic markers mapped in B. oleracea, including RFLPs, CAPS, and SSRs allowed comparison and interpretation of medium-scale chromosomal organisation and rearrangements. The interpretation of data was facilitated by hybridising probes onto the whole A. thaliana genome, as represented by BAC contigs. Twenty marker loci were sampled from the whole length of the shortest B. oleracea linkage group, O6, and 21 from a 30.4-cM section of the longest linkage group, O3. There is evidence of locus duplication on linkage group O6. Locus order is well conserved between a putative duplicated region of 10.5 cM and a discrete region comprising 25 cM of A. thaliana chromosome I. This was supported by evidence from seven paralogous loci, three of which were duplicated in a 30.6-cM region of linkage group O6. The pattern of locus order for the remainder of linkage group O6 and the sampled section of linkage group O3 was more complex when compared with the A. thaliana genome. Although there was some conservation of locus order between markers on linkage group O3 and approximately 9 cM of A. thaliana chromosome I, this was superimposed upon a complex pattern of additional loci that were replicated in both A. thaliana and B. oleracea. The results are discussed in the context of the ability to use collinear information to assist map-based cloning.Key words: comparative mapping, BAC, physical contig, MADS box.

Genetic analysis and genome mapping in Raphanus

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 423-430 ◽  
Author(s):  
Kirstin E Bett ◽  
Derek J Lydiate
Keyword(s):  
Genetic Map ◽  
Comparative Mapping ◽  
Genome Mapping ◽  
Brassica Species ◽  
Genetic Maps ◽  
Rflp Markers ◽  
Raphanus Raphanistrum ◽  
Crop Species ◽  
Marker Loci ◽  
Reference Map

The first genetic map of the Raphanus genome was developed based on meiosis in a hybrid between Raphanus sativus (cultivated radish) and Raphanus raphanistrum (wild radish). This hybrid was used to produce a BC1 population of 54 individuals and an F2 population of 85 individuals. A total of 236 marker loci were assayed in these populations using a set of 144 informative Brassica RFLP probes previously used for genetic mapping in other crucifer species. The genetic maps derived from the BC1 and F2 populations were perfectly collinear and were integrated to produce a robust Raphanus map. Cytological observations demonstrated strict bivalent pairing in the R. sativus × R. raphanistrum hybrids. Productive pairing along the length of each chromosome was confirmed by the identification of nine extensive linkage groups and the lack of clustering of marker loci. Indeed, the distributions of both marker loci and crossovers was more random than those reported for other crop species. The genetic markers and the reference map of Raphanus will be of considerable value for future trait mapping and marker-assisted breeding in this crop, as well as in the intergenomic transfer of Raphanus genes into Brassica crops. The future benefits of comparative mapping with Arabidopsis and Brassica species are also discussed.Key words: radish, genetic map, RFLP markers, comparative mapping, segregation distortion.

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 ◽  
I.A.P. Parkin ◽  
C. Dean ◽  
M. Trick
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Chromosome 4

scholarly journals Comparison of Flowering Time Genes in Brassica rapa, B. napus and Arabidopsis thaliana

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1123-1129 ◽  
Author(s):  
T C Osborn ◽  
C Kole ◽  
I A P Parkin ◽  
A G Sharpe ◽  
M Kuiper ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Quantitative Trait Loci ◽  
Flowering Time ◽  
Brassica Rapa ◽  
Quantitative Trait ◽  
Chromosome 4 ◽  
Chromosome 5 ◽  
Major Qtls ◽  
Segregating Population

The major difference between annual and biennial cultivars of oilseed Brassica napus and B. rapa is conferred by genes controlling vernalization-responsive flowering time. These genes were compared between the species by aligning the map positions of flowering time quantitative trait loci (QTLs) detected in a segregating population of each species. The results suggest that two major QTLs identified in B. rapa correspond to two major QTLs identified in B. napus. Since B. rapa is one of the hypothesized diploid parents of the amphidiploid B. napus, the vernalization requirement of B. napus probably originated from B. rapa. Brassica genes also were compared to flowering time genes in Arabidopsis thaliana by mapping RFLP loci with the same probes in both B. napus and Arabidopsis. The region containing one pair of Brassica QTLs was collinear with the top of chromosome 5 in A. thaliana where flowering time genes FLC, FY and CO are located. The region containing the second pair of QTLs showed fractured collinearity with several regions of the Arabidopsis genome, including the top of chromosome 4 where FRI is located. Thus, these Brassica genes may correspond to two genes (FLC and FRI) that regulate flowering time in the latest flowering ecotypes of Arabidopsis.

Development of amplified consensus genetic markers (ACGM) in Brassica napus from Arabidopsis thaliana sequences of known biological function

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 387-402 ◽  
Author(s):  
Dominique Brunel ◽  
Nicole Froger ◽  
Georges Pelletier
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Genetic Markers ◽  
Biological Function ◽  
Parental Species ◽  
Direct Sequencing ◽  
Brassica Species ◽  
Degenerate Primers ◽  
Coding Sequences ◽  
Pcr Products

A method for the development of consensus genetic markers between species of the same taxonomic family is described in this paper. It is based on the conservation of the peptide sequences and on the potential polymorphism within non-coding sequences. Six loci sequenced from Arabidopsis thaliana, AG, LFY3, AP3, FAD7, FAD3, and ADH, were analysed for one ecotype of A. thaliana, four lines of Brassica napus, and one line for each parental species, Brassica oleracea and Brassica rapa. Positive amplifications with the degenerate primers showed one band for A. thaliana, two to four bands in rapeseed, and one to two bands in the parental species. Direct sequencing of the PCR products confirms their peptide similarity with the "mother" sequence. By comparison of intron sequences, the correspondence between each rapeseed gene and its homologue in one of the parental species can be determined without ambiguity. Another important result is the presence of a polymorphism inside these fragments between the rapeseed lines. This variability could generally be detected by differences of electrophoretic migration on long non-denaturing polyacrylamide gels. This method enables a quick and easy shuttle between A. thaliana and Brassica species without cloning.Key words: consensus genetics markers, PCR specific, Brassica, Arabidopsis, targeted markers, DSCP.

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.

Physical Map and Organization of Arabidopsis thaliana Chromosome 4

Science ◽  
1995 ◽  
Vol 270 (5235) ◽  
pp. 480-483 ◽  
Author(s):  
R. Schmidt ◽  
J. West ◽  
K. Love ◽  
Z. Lenehan ◽  
C. Lister ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Physical Map ◽  
Chromosome 4

Comparative analysis of the Brassica oleracea genetic map and the Arabidopsis thaliana genome

Genome ◽  
2009 ◽  
Vol 52 (7) ◽  
pp. 620-633 ◽  
Author(s):  
Malgorzata Kaczmarek ◽  
Grzegorz Koczyk ◽  
Piotr A. Ziolkowski ◽  
Danuta Babula-Skowronska ◽  
Jan Sadowski
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Map ◽  
Physical Map ◽  
A Priori ◽  
Brassica Species ◽  
Cdna Clones ◽  
Map Construction ◽  
Gene Copies ◽  
In Silico Study ◽  
Comprehensive Comparison

We further investigated genome macrosynteny for Brassica species and Arabidopsis thaliana . This work aimed at comparative map construction for B. oleracea and A. thaliana chromosomes based on 160 known A. thaliana probes: 147 expressed sequence tags (ESTs) and 13 full-length cDNA clones. Based on an in silico study of the A. thaliana genome, most of the selected ESTs (83%) represented unique or low-copy genes. We identified conserved segments by the visual inspection of comparative data with a priori assumptions, and established their significance with the LineUp algorithm. Evaluation of the number of B. oleracea gene copies per A. thaliana EST revealed a fixed upward trend. We established a segregation distortion pattern for all genetic loci, with particular consideration of the type of selection (gametic or zygotic), and discuss its possible impact on genetic map construction. Consistent with previous reports, we found evidence for numerous chromosome rearrangements and the genome fragment replication of B. oleracea that have taken place since the divergence of the two species. Also, we found that over 54% of the B. oleracea genome is covered by 24 segments conserved with the A. thaliana genome. The average conserved segment is composed of 5 loci covering 19.3 cM in the B. oleracea genetic map and 2.42 Mb in the A. thaliana physical map. We have also attempted to use a unified system of conserved blocks (previously described) to verify our results and perform a comprehensive comparison with other Brassica species.

Identification of a single-copy gene encoding a Type I chlorophyll a/b-binding polypeptide of photosystem I in Arabidopsis thaliana

1992 ◽  
Vol 84 (4) ◽  
pp. 561-567 ◽  
Author(s):  
Poul E. Jensen ◽  
Michael Kristensen ◽  
Tine Hoff ◽  
Jan Lehmbeck ◽  
Bjarne M. Stummann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Chlorophyll A ◽  
Photosystem I ◽  
Single Copy ◽  
Type I ◽  
Single Copy Gene ◽  
Gene Encoding ◽  
Copy Gene
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