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.

Frequent nonreciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1112-1121 ◽  
Author(s):  
A. G. Sharpe ◽  
I. A. P. Parkin ◽  
D. J. Keith ◽  
D. J. Lydiate
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Doubled Haploid ◽  
Microspore Culture ◽  
Homoeologous Recombination ◽  
Linkage Groups ◽  
Rflp Map ◽  
A Genome ◽  
C Genome ◽  
Marker Loci

A RFLP map of Brassica napus, consisting of 277 loci arranged in 19 linkage groups, was produced from genetic segregation in a combined population of 174 doubled-haploid microspore-derived lines. The integration of this map with a B. napus map derived from a resynthesized B. napus × oilseed rape cross allowed the 10 linkage groups of the B. napus A genome and the 9 linkage groups of the C genome to be identified. Collinear patterns of marker loci on different linkage groups suggested potential partial homoeologues. RFLP patterns consistent with aberrant chromosomes were observed in 9 of the 174 doubled-haploid lines. At least 4 of these lines carried nonreciprocal, homoeologous translocations. These translocations were probably the result of homoeologous recombination in the amphidiploid genome of oilseed rape, suggesting that domesticated B. napus is unable to control chromosome pairing completely. Evidence for genome homogenization in oilseed rape is presented and its implications on genetic mapping in amphidiploid species is discussed. The level of polymorphism in the A genome was higher than that in the C genome and this might be a general property of oilseed rape crosses.Key words: restriction fragment length polymorphism, genetic linkage map, homoeologous recombination, microspore culture, doubled haploid.

scholarly journals Mutator genes for suppression of gross chromosomal rearrangements identified by a genome-wide screening inSaccharomyces cerevisiae

2004 ◽  
Vol 101 (24) ◽  
pp. 9039-9044 ◽  
Author(s):  
Stephanie Smith ◽  
Ji-Young Hwang ◽  
Soma Banerjee ◽  
Anju Majeed ◽  
Amitabha Gupta ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Gross Chromosomal Rearrangements ◽  
Genome Wide ◽  
A Genome ◽  
Mutator Genes

Production and genetic analysis of partial hybrids from intertribal sexual crosses between Brassica napus and Isatis indigotica and progenies

Genome ◽  
2010 ◽  
Vol 53 (2) ◽  
pp. 146-156 ◽  
Author(s):  
Y. Q. Tu ◽  
J. Sun ◽  
X. H. Ge ◽  
Z. Y. Li
Keyword(s):  
Brassica Napus ◽  
Genetic Analysis ◽  
Medicinal Plant ◽  
Chromosome Numbers ◽  
Chromosome Elimination ◽  
Low Fertility ◽  
Isatis Indigotica ◽  
A Genome ◽  
C Genome ◽  
Sexual Crosses

With the dye and medicinal plant Isatis indigotica (2n = 14) as pollen parent, intertribal sexual hybrids with Brassica napus (2n = 38, AACC) were obtained and characterized. Among a lot of F1 plants produced, only five hybrids (H1–H5) were distinguished morphologically from female B. napus parents by showing low fertility and some characters of I. indigotica, and also by having different chromosome numbers. H1–H4 had similar but variable chromosome numbers in their somatic and meiotic cells (2n = 25–30), and H5 had 2n = 19, the same number as the haploid of B. napus. GISH analysis of the cells from H1 and H5 detected one I. indigotica chromosome and one or two chromosome terminal fragments. New B. napus types with phenotypic and genomic alterations were produced by H1 after pollination by B. napus and selfing for several generations, and by H5 after selfing. A progeny plant (2n = 20) was derived from H1 after pollination by I. indigotica twice and had a phenotype similar to a certain type of B. rapa, showing that hybrid H1 likely retained all chromosomes of the A genome and lost some of the C genome in parental B. napus. The reasons for the formation of the partial hybrids with unexpected chromosomal complements and for the chromosome elimination are discussed.

Latent S alleles are widespread in cultivated self-compatible Brassica napus

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 257-265 ◽  
Author(s):  
U U Ekuere ◽  
I A.P Parkin ◽  
C Bowman ◽  
D Marshall ◽  
D J Lydiate
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Self Incompatibility ◽  
S Locus ◽  
Winter Oilseed Rape ◽  
A Genome ◽  
C Genome ◽  
S Alleles ◽  
Crop Types ◽  
S Allele

The genetic control of self-incompatibility in Brassica napus was investigated using crosses between resynthesized lines of B. napus and cultivars of oilseed rape. These crosses introduced eight C-genome S alleles from Brassica oleracea (S16, S22, S23, S25, S29, S35, S60, and S63) and one A-genome S allele from Brassica rapa (SRM29) into winter oilseed rape. The inheritance of S alleles was monitored using genetic markers and S phenotypes were determined in the F1, F2, first backcross (B1), and testcross (T1) generations. Two different F1 hybrids were used to develop populations of doubled haploid lines that were subjected to genetic mapping and scored for S phenotype. These investigations identified a latent S allele in at least two oilseed rape cultivars and indicated that the S phenotype of these latent alleles was masked by a suppressor system common to oilseed rape. These latent S alleles may be widespread in oilseed rape varieties and are possibly associated with the highly conserved C-genome S locus of these crop types. Segregation for S phenotype in subpopulations uniform for S genotype suggests the existence of suppressor loci that influenced the expression of the S phenotype. These suppressor loci were not linked to the S loci and possessed suppressing alleles in oilseed rape and non-suppressing alleles in the diploid parents of resynthesized B. napus lines.Key words: self-incompatibility, B. oleracea, B. rapa, S locus, suppression.

Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1122-1131 ◽  
Author(s):  
I. A. P. Parkin ◽  
A. G. Sharpe ◽  
D. J. Keith ◽  
D. J. Lydiate
Keyword(s):  
Brassica Napus ◽  
Linkage Map ◽  
Oilseed Rape ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Resynthesized Brassica Napus ◽  
Disomic Inheritance ◽  
A Genome ◽  
C Genome ◽  
Homoeologous Chromosomes

A genetic linkage map consisting of 399 RFLP-defined loci was generated from a cross between resynthesized Brassica napus (an interspecific B. rapa × B. oleracea hybrid) and "natural" oilseed rape. The majority of loci exhibited disomic inheritance of parental alleles demonstrating that B. rapa chromosomes were each pairing exclusively with recognisable A-genome homologues in B. napus and that B. oleracea chromosomes were pairing similarly with C-genome homologues. This behaviour identified the 10 A genome and 9 C genome linkage groups of B. napus and demonstrated that the nuclear genomes of B. napus, B. rapa, and B. oleracea have remained essentially unaltered since the formation of the amphidiploid species, B. napus. A range of unusual marker patterns, which could be explained by aneuploidy and nonreciprocal translocations, were observed in the mapping population. These chromosome abnormalities were probably caused by associations between homoeologous chromosomes at meiosis in the resynthesized parent and the F1 plant leading to nondisjunction and homoeologous recombination.Key words: genetic linkage map, homoeologous recombination, Brassica rapa, Brassica oleracea, genome organization.

scholarly journals A genome in flux: homoeologous exchanges, subgenome dominance, and gene dosage balance constraints in resynthesized allopolyploid Brassica napus

2021 ◽  
Author(s):  
Kevin A Bird ◽  
J Chris Pires ◽  
Robert VanBuren ◽  
Zhiyong Xiong ◽  
Patrick P. Edger
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Genomic Rearrangements ◽  
Bias Estimation ◽  
Gene Expression Response ◽  
A Genome ◽  
Dosage Balance ◽  
The Impact

Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Frequently, allopolyploids exhibit genomic rearrangements that recombine, duplicate, or delete homoeologous regions of the newly formed genome. While decades of investigation have focused on how genome duplication leads to systematic differences in the retention and expression of duplicate genes, the impact of genomic rearrangements on genome evolution has received less attention. We used genomic and transcriptomic data for six independently resynthesized, isogenic Brassica napus lines in the first, fifth, and tenth generation to identify genomic rearrangements and assess their impact on gene expression dynamics related to subgenome dominance and gene dosage constraint. We find that dosage constraints on the gene expression response to polyploidy begin to loosen within the first ten generations of evolution and systematically differ between dominant and non-dominant subgenomes. We also show that genomic rearrangements can bias estimation of homoeolog expression bias, but fail to fully obscure which subgenome is dominantly expressed. Finally, we demonstrate that dosage-sensitive genes exhibit the same kind of coordinated response to homoeologous exchange as they do for genome duplication, suggesting constraint on dosage balance also acts on these changes to gene dosage.

Aneuploid marker assignment in hexaploid oat with the C genome as a reference for determining remnant homoeology

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 386-396 ◽  
Author(s):  
Shahryar F. Kianian ◽  
Bai-Chai Wu ◽  
Stephen L. Fox ◽  
Howard W. Rines ◽  
Ronald L. Phillips
Keyword(s):  
Dna Sequences ◽  
Chromosomal Rearrangements ◽  
Gene Families ◽  
Linkage Groups ◽  
Genome Chromosome ◽  
D Genome ◽  
Haploid Chromosome Number ◽  
Evolutionary Forces ◽  
C Genome

Nullisomic lines of hexaploid oat Avena sativa L. (2n = 6x − 2 = 40, AACCDD) cultivar Sun II were used to assign 134 DNA sequences to 10 chromosome-associated syntenic groups. A limited set of ditelosomic lines allowed localization of subsets of these sequences to six chromosome arms. Advantages of using such aneuploids in mapping are in the assignment of gene families, monomorphic RFLP sequences, and oat linkage groups to chromosomes. The published hexaploid oat RFLP linkage map has 38 linkage groups, 17 more than expected on the basis of the haploid chromosome number. Using nullisomics, eight linkage groups were assigned to five physical chromosomes; using ditelosomics, three of these linkage groups were assigned to their respective chromosome arms. The A- and D-genome chromosome sets of oat are indistinguishable from each other based on different staining and genomic in situ hybridization techniques, while C-genome chromosomes are distinct. Because chromosomal rearrangements such as translocations and inversions have played an important role in the evolution of hexaploid oat, the distinction of C-genome chromosomes can be used to determine remnant homoeologous segments that exist in the other two genomes. Among the 10 syntenic groups identified, six chromosomes showed sequence homoeology believed to represent segmental homoeologous regions. Owing to various evolutionary forces, segmental homoeology instead of whole chromosome homoeology appears to best describe the genome organization in hexaploid oat.Key words: oat, aneuploids, syntenic associations, homoeology, C genome.

scholarly journals Genome Duplication in Soybean (Glycine subgenus soja)

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 329-338 ◽  
Author(s):  
R C Shoemaker ◽  
K Polzin ◽  
J Labate ◽  
J Specht ◽  
E C Brummer ◽  
...  
Keyword(s):  
Seed Protein ◽  
Genome Duplication ◽  
Fragment Length Polymorphism ◽  
Gene Families ◽  
Soybean Genome ◽  
Seed Composition ◽  
Linkage Groups ◽  
Mapping Data ◽  
Or Gene ◽  
Average Size

Abstract Restriction fragment length polymorphism mapping data from nine populations (Glycine max × G. soja and G. max × G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

SINE-B1 Distribution and Chromosome Rearrangements in the South American Proechimys gr. goeldii (Echimyidae, Rodentia)

2021 ◽  
pp. 1-8
Author(s):  
Naiara P. Araújo ◽  
Radarane S. Sena ◽  
Cibele R. Bonvicino ◽  
Gustavo C.S. Kuhn ◽  
Marta Svartman
Keyword(s):  
Transposable Element ◽  
Genome Evolution ◽  
Significant Role ◽  
Sex Chromosomes ◽  
Chromosomal Rearrangements ◽  
Evolutionary Relationship ◽  
Chromosome Rearrangements ◽  
South American ◽  
Gross Chromosomal Rearrangements

<i>Proechimys</i> species are remarkable for their extensive chromosome rearrangements, representing a good model to understand genome evolution. Herein, we cytogenetically analyzed 3 different cytotypes of <i>Proechimys</i> gr. <i>goeldii</i> to assess their evolutionary relationship. We also mapped the transposable element SINE-B1 on the chromosomes of <i>P.</i> gr. <i>goeldii</i> in order to investigate its distribution among individuals and evaluate its possible contribution to karyotype remodeling in this species. SINE-B1 showed a dispersed distribution along chromosome arms and was also detected at the pericentromeric regions of some chromosomes, including pair 1 and the sex chromosomes, which are involved in chromosome rearrangements. In addition, we describe a new cytotype for <i>P.</i> gr. <i>goeldii</i>, reinforcing the significant role of gross chromosomal rearrangements during the evolution of the genus. The results of FISH with SINE-B1 suggest that this issue should be more deeply investigated for a better understanding of its role in the mechanisms involved in the wide variety of <i>Proechimys</i> karyotypes.

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