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.

Fluorescence in situ hybridization mapping of Avena sativa L. cv. SunII and its monosomic lines using cloned repetitive DNA sequences

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1230-1237 ◽  
Author(s):  
M L Irigoyen ◽  
C Linares ◽  
E Ferrer ◽  
A Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
D Genome ◽  
Fish Mapping ◽  
Intergenomic Translocations ◽  
A Genome ◽  
C Genome

Fluorescent in situ hybridization (FISH) employing multiple probes was used with mitotic or meiotic chromosome spreads of Avena sativa L. cv. SunII and its monosomic lines to produce physical chromosome maps. The probes used were Avena strigosa pAs120a (which hybridizes exclusively to A-genome chromosomes), Avena murphyi pAm1 (which hybridizes exclusively to C-genome chromosomes), A. strigosa pAs121 (which hybridizes exclusively to A- and D-genome chromosomes), and the wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH employing two-by-two combinations of these probes allowed the unequivocal identification and genome assignation of all chromosomes. Ten pairs were found carrying intergenomic translocations: (i) between the A and C genomes (chromosome pair 5A); (ii) between the C and D genomes (pairs 1C, 2C, 4C, 10C, and 16C); and (iii) between the D and C genomes (pairs 9D, 11D, 13D, and 14D). The existence of a reciprocal intergenomic translocation (10C–14D) is also proposed. Comparing these results with those of other hexaploids, three intergenomic translocations (10C, 9D, and 14D) were found to be unique to A. sativa cv. SunII, supporting the view that 'SunII' is genetically distinct from other hexaploid Avena species and from cultivars of the A. sativa species. FISH mapping using meiotic and mitotic metaphases facilitated the genomic and chromosomal identification of the aneuploid chromosome in each monosomic line. Of the 18 analyzed, only 11 distinct monosomic lines were actually found, corresponding to 5 lines of the A genome, 2 lines of the C genome, and 4 lines of the D genome. The presence or absence of the 10C–14D interchange was also monitored in these lines.Key words: Avena sativa, monosomics, FISH mapping, genomic identification, intergenomic translocations.

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 New evidence concerning the genome designations of the AC(DC) tetraploid Avena species

2020 ◽  
Author(s):  
Honghai Yan ◽  
Zichao Ren ◽  
Di Deng ◽  
Kehan Yang ◽  
Chuang Yang ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Repetitive Dna Sequences ◽  
D Genome ◽  
Intergenomic Translocations ◽  
5S Rrna Gene ◽  
New Evidence ◽  
Robust Evidence

AbstractThe tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

Chromosomal distribution of a repeated DNA sequence from C-genome heterochromatin and the identification of a new ribosomal DNA locus in the Avena genus

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 548-557 ◽  
Author(s):  
Araceli Fominaya ◽  
Gregorio Hueros ◽  
Yolanda Loarce ◽  
Esther Ferrer
Keyword(s):  
In Situ Hybridization ◽  
Satellite Dna ◽  
Repeated Dna ◽  
Chromosomal Distribution ◽  
Genome Chromosome ◽  
26S Rdna ◽  
A Genome ◽  
C Genome ◽  
Repeated Dna Sequence

Satellite DNA specific to the oat C genome was sequenced and located on chromosomes of diploid, tetraploid, and hexaploid Avena ssp. using in situ hybridization. The sequence was present on all seven C genome chromosome pairs and hybridized to the entire length of each chromosome, with the exception of the terminal segments of some chromosome pairs. Three chromosome pairs belonging to the A genome showed hybridization signals near the telomeres of their long arms. The existence of intergenomic chromosome rearrangements and the deletions of the repeated units are deduced from these observations. The number of rDNA loci (18S–5.8S–26S rDNA) was determined for the tetraploid and hexaploid oat species. Simultaneous in situ hybridization with the satellite and rDNA probes was used to assign the SAT chromosomes of these species to their correct genomes.Key words: oats, satellite DNA, rDNA, in situ hybridization, genome evolution.

Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 293-306 ◽  
Author(s):  
Ekaterina D. Badaeva ◽  
Bernd Friebe ◽  
Bikram S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Dna Sequences ◽  
Aegilops Species ◽  
D Genome ◽  
C Banding ◽  
Genome Differentiation ◽  
Highly Repetitive Dna

Genome differentiation in 12 diploid Aegilops species was analyzed using in situ hybridization with the highly repetitive DNA sequences pSc119 and pAs1 and C-banding. Chromosomes of all these diploid Aegilops species hybridized with the pSc119 probe; however, the level of hybridization and labeling patterns differed among genomes. Only four species (Ae. squarrosa, Ae. comosa, Ae. heldreichii, and Ae. uniaristata) showed distinct hybridization with pAs1. The labeling patterns were species-specific and chromosome-specific. Differences in in situ hybridization (ISH) patterns, also observed by C-banding, exist between the karyotypes of Ae. comosa and Ae. heldreichii, suggesting that they are separate, although closely related, subspecies. The S genome of Ae. spelioides was most similar to the B and G genomes of polyploid wheats on the basis of both C-banding and ISH patterns, but was different from other species of section Sitopsis. These species had different C-banding patterns but they were similar to each other and to Ae. mutica in the distribution of pSc119 hybridization sites. Two types of labeling were detected in Ae. squarrosa with the pAs1 probe. The first resembled that of the D-genome chromosomes of bread wheat, Triticum aestivum L. em. Thell., while the second was similar to the D genome of some of the polyploid Aegilops species. Relationships among diploid Aegilops species and the possible mechanisms of genome differentiation are discussed. Key words : wheat, Triticum, Aegilops, in situ hybridization, C-banding, evolution.

Nonisotopic in situ hybridization and plant genome mapping: the first 10 years

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 717-725 ◽  
Author(s):  
Jiming Jiang ◽  
Bikram S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Dna Sequences ◽  
Genome Mapping ◽  
Molecular Cytogenetics ◽  
Gene Families ◽  
Single Copy ◽  
Plant Genome ◽  
Metaphase Chromosomes

Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopolyploid species. GISH also provides a powerful technique for monitoring chromatin introgession during interspecific hybridization. A sequential chromosome banding and ISH technique was developed. The sequential technique is very useful for more precise and efficient mapping as well as cytogenetic determination of genomic affinities of individual chromosomes in allopolyploid species. A critical review is made on the present resolution of the ISH technique and the future outlook of ISH research is discussed.Key words: in situ hybridization, physical mapping, genome mapping, molecular cytogenetics.

scholarly journals New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0240703
Author(s):  
Honghai Yan ◽  
Zichao Ren ◽  
Di Deng ◽  
Kehan Yang ◽  
Chuang Yang ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Repetitive Dna Sequences ◽  
D Genome ◽  
Intergenomic Translocations ◽  
5S Rrna Gene ◽  
New Evidence ◽  
Robust Evidence

The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

Amplification of DNA sequences in wheat and its relatives: the Dgas44 and R350 families of repetitive sequences

Genome ◽  
1994 ◽  
Vol 37 (2) ◽  
pp. 320-327 ◽  
Author(s):  
D. McNeil ◽  
E. S. Lagudah ◽  
U. Hohmann ◽  
R. Appels
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Tetraploid Wheat ◽  
Genomic Clone ◽  
Sequence Family ◽  
Chain Reaction ◽  
D Genome ◽  
Polymerase Chain

The sequence of a Triticum tauschii genomic clone representing a family of D-genome amplified DNA sequences, designated Dgas44, is reported. The Dgas44 sequence occurs on all chromosomes of the D genome of wheat, Triticum aestivum, and in situ hybridization revealed it to be evenly dispersed on all seven chromosome pairs. An internal HindIII fragment of Dgas44, designated Dgas44-3, defines the highly amplified region that is specific to the D genome. The polymerase chain reaction was used to amplify a 236-bp fragment within Dgas44-3 from chromosomes 1D, 2D, 3D, 4D, 5D, and 7D, and identical copies of this region of the Dgas44-3 sequence were found among the isolates from each of the chromosomes. The Dgas44-3 sequence population from specific chromosomes differed on average by 0.22% from the original Dgas44 sequence. The Dgas44 sequence was found to differentiate between the D genome present in T. aestivum, T. tauschii, hexaploid T. crassum, T. cylindricum, T. ventricosum, in which the sequence was present in a highly amplified form and T. juvenale, T. syriacum, and tetraploid T. crassum where the sequence family was difficult to detect. Another class of amplified sequences previously considered to be rye "specific." R350, was isolated from tetraploid wheat and its dispersed distribution on chromosomes was similar to the Dgas44 family in T. tauschii. In contrast with the Dgas44 sequence family, genome specificity for the remnant R350 sequence family was not evident since it was present on all wheat chromosomes.Key words: D genome, sequence amplification, in situ hybridization.

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 431-441 ◽  
Author(s):  
Evgueni V Ananiev ◽  
M Isabel Vales ◽  
Ronald L Phillips ◽  
Howard W Rines
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Repeated Sequences ◽  
C Genome ◽  
Copy Dna

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.Key words: oat, cosmid library, in situ hybridization.

Repeated DNA sequences isolated by microdissection. I. Karyotyping of barley (Hordeum vulgare L.)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1082-1090 ◽  
Author(s):  
Winfried Busch ◽  
Regina Martin ◽  
Reinhold G. Herrmann ◽  
Uwe Hohmann
Keyword(s):  
In Situ Hybridization ◽  
Hordeum Vulgare ◽  
Fluorescence In Situ Hybridization ◽  
Dna Sequences ◽  
Fish Analysis ◽  
Hordeum Vulgare L ◽  
Agropyron Elongatum ◽  
D Genome ◽  
In Situ Experiments

We report on microdissection, cloning and sequence, and Southern and fluorescence in situ hybridization (FISH) analysis of one moderately and one highly amplified repetitive DNA element, pHvMWG2314 and pHvMWG2315, respectively, isolated from barley (Hordeum vulgare L.) chromosome arm 3HL. The pHvMWG2315 sequence hybridizes to all 14 telomeric or subtelomeric regions of the barley chromosomes as determined by FISH. The 50 different hybridization sites that include intercalary signals allow the discrimination of all 14 chromosome arms and the construction of a karyotype of barley. The tandemly repeated subtelomeric element of 331 bp exists in all Triticeae species tested (H. vulgare, Agropyron elongatum, Secale cereale, Triticum tauschii, T. turgidum, and T. aestivum). It is AT rich (66%), exhibits 84% sequence homology to subfragments of the D genome "specific" 1-kb element pAsl of T. tauschii and 75% homology to the interspersed genome-specific DNA sequence pHcKB6 from H. chilense. The repetitive sequence pHvMWG2314 is moderately amplified in barley and highly amplified in hexaploid wheat. The in situ experiments revealed no distinct signals on barley chromosomes, indicating a dispersed character for the sequence. The significance of the results for the identification of chromosomes and chromosome aberrations in FISH experiments are discussed.Key words: karyotype, fluorescence in situ hybridization, FISH, DNA sequencing.

Sign in / Sign up

Export Citation Format

Share Document