INCIPIENT GENOME DIFFERENTIATION IN GOSSYPIUM. III. COMPARISON OF CHROMOSOMES OF G. HIRSUTUM AND ASIATIC DIPLOIDS USING HETEROZYGOUS TRANSLOCATIONS

ABSTRACT Hybrids between upland cotton (G. hirsutum, genome constitution 2AhDh) and either A-genome or D-genome diploid species exhibit 26 paired and 13 unpaired chromosomes at metaphase I. The Ah and Dh genomes are therefore considered homoeologous with those of the respective diploids. Previous studies, nevertheless, revealed a low level of ("incipient") differentiation between Dh and various diploid D genomes. The diploid A genomes have been regarded as more closely homologous to Ah on the basis of low preferential pairing and autotetraploid segregation ratios in allohexaploids.—The present study addressed the following questions: Are the diploid A genomes differentiated from Ah in meiotic homology? If so, is the differentiation manifested equally by all 13 chromosomes or is it localized in certain chromosomes?—Three diploid A-genome lines representing G. herbaceum and G. arboreum were hybridized by in ovulo culture of embryos (1) with a standard line of G. hirsutum, which differs from G. herbaceum by two and from G. arboreum by three naturally occurring reciprocal translocations involving chromosomes 1—5, and (2) with six lines homozygous for experimental translocations involving chromosomes 6, 7, 10, 11, 12 and 13. Chiasma frequencies in hybrids were compared with those in appropriate G. hirsutum controls. In every comparison overall chiasma frequencies were slightly lower in the hybrids. Therefore Ah appears to be differentiated from the diploid A genomes. No localized differentiation was detected in chromosomes marked by experimental translocations. The differentiation may be localized mainly in chromosomes 4 and 5.

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Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽

10.1139/g99-007 ◽

1999 ◽

Vol 42 (4) ◽

pp. 706-713 ◽

Cited By ~ 10

Author(s):

Concha Linares ◽

Antonio Serna ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Diploid Species ◽

D Genome ◽

Specific Sequence ◽

Chromosomal Organization ◽

Intergenomic Translocations ◽

A Genome ◽

Slot Blot Analysis ◽

Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

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Pervasive hybridizations in the history of wheat relatives

10.1101/300848 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sylvain Glémin ◽

Celine Scornavacca ◽

Jacques Dainat ◽

Concetta Burgarella ◽

Véronique Viader ◽

...

Keyword(s):

Methodological Approach ◽

Diploid Species ◽

Phylogenomic Analysis ◽

D Genome ◽

Species Relationship ◽

B Genome ◽

Hybridization Event ◽

A Genome ◽

History Of ◽

Complex Scenario

AbstractBread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

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ABORTIVE POLLEN: A PHENOTYPIC MARKER OF MONOSOMICS IN UPLAND COTTON, GOSSYPIUM HIRSUTUM

Canadian Journal of Genetics and Cytology ◽

10.1139/g68-114 ◽

1968 ◽

Vol 10 (4) ◽

pp. 913-915 ◽

Cited By ~ 3

Author(s):

Charles R. Douglas

Keyword(s):

Gossypium Hirsutum ◽

Upland Cotton ◽

Pollen Abortion ◽

Gossypium Hirsutum L ◽

D Genome ◽

Phenotypic Marker ◽

Abortive Pollen ◽

A Genome

Plants from six different monosomic (2n-1) lines of cotton, Gossypium hirsutum L., which lack chromosomes 2, 4 and 6 of the A genome, and 16, 17 and 18 of the D genome, respectively, showed significantly higher pollen abortion than plants from a standard, highly inbred disomic (2n) line.Pollen abortion can be used to identify certain monosomic plants that otherwise lack distinctive phenotypes.

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ANALYSIS OF SPECIES RELATIONSHIPS IN AVENAE BY THIN-LAYER CHROMATOGRAPHY AND DISC ELECTROPHORESIS

Canadian Journal of Genetics and Cytology ◽

10.1139/g72-038 ◽

1972 ◽

Vol 14 (2) ◽

pp. 305-316 ◽

Cited By ~ 5

Author(s):

H. C. Dass

Keyword(s):

Thin Layer ◽

Diploid Species ◽

Disc Electrophoresis ◽

Tetraploid Species ◽

Species Relationships ◽

D Genome ◽

Genome Donor ◽

A Genome ◽

Layer Chromatography ◽

Esterase Patterns

Thin-layer chromatographic studies on flavonoids, and disc electrophoretic studies on proteins and esterase isoenzymes were conducted with Avena to determine species relationships and genome homologies. Distinctness of Avena ventricosa and A. pilosa was observed in comparison to other diploid species. Closeness of the diploid species of the A. strigosa group (including hirtula and wiestii) was evident from the similarity of their protein and esterase spectra. The tetraploid species, A. barbata and A. abyssinica, were found to be very close to A. hirtula and A. strigosa, respectively, by TLC studies. Proteins and esterases also showed that the tetraploid species are very close to the A. strigosa group of diploid species. The contribution of a genome by the A. strigosa group to the tetraploids and hexaploids was confirmed. The hexaploids showed different protein and esterase patterns. The involvement of A. ventricosa as the C genome donor to the hexaploids was shown by the protein and esterase spectra. A few extra protein bands observed may have been from the D genome.

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Comparative Functional Studies on Two Diploid Cotton Genomes Reveals Functional Differences of Basic Helix-loop-helix Proteins in Arabidopsis Trichome Initiation

Annual Research & Review in Biology ◽

10.9734/arrb/2019/v34i230146 ◽

2020 ◽

pp. 1-12

Author(s):

Anh Phu Nam Bui ◽

Vimal Kumar Balasubramanian ◽

Thuan-Anh Nguyen-Huu ◽

Tuan-Loc Le ◽

Hoang Dung Tran

Keyword(s):

Diploid Species ◽

Natural Phenomenon ◽

Tetraploid Cotton ◽

D Genome ◽

Genome Species ◽

Functional Studies ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Cotton Species ◽

A Genome

Background: The cultivated tetraploid cotton species (AD genomes) was originated from two ancestral diploid species (A and D genomes). While the ancestral A-genome species produce spinnable fibers, the D- genome species do not. Cotton fibers are unicellular trichomes originating from seed coat epidermal cells, and currently there is an immense interest in understanding the process of fiber initiation and development. Current knowledge demonstrates that there is a great of deal of resemblance in initiation mechanism between by Arabidopsis trichome and cotton fiber. Methodology: In this study, we performed comparative functional studies between A genome and D-genome species in cotton by using Arabidopsis trichome initiation as a model. Four cotton genes TTG3, MYB2, DEL61 and DEL65 were amplified from A-genome and D-genome species, and transformed into their homolog trichomeless mutants Arabidopsis ttg1, gl1, and gl3egl3, respectively. Results: Our data indicated that the transgenic plants expressing TTG3 and MYB2 genes from A-genome and D-genome species complement the ttg1 and gl1 mutants, respectively. We also discovered complete absences of two functional basic helix loop helix (bHLH) proteins (DEL65/DEL61) in D- diploid species and one (DEL65) that is functional in A-genome species, but not from D-genome species. This observation is consistent with the natural phenomenon of spinnable fiber production in A- genome species and absence in D-genome species.

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GENETIC LENGTHS AND BREAK POINTS IN TWELVE CHROMOSOMES OF GOSSYPIUM HIRSUTUM INVOLVED IN TEN RECIPROCAL TRANSLOCATIONS

Genetics ◽

10.1093/genetics/88.3.541 ◽

1978 ◽

Vol 88 (3) ◽

pp. 541-558

Author(s):

Margaret Y Menzel ◽

Meta S Brown

Keyword(s):

Genetic Mapping ◽

Gossypium Hirsutum ◽

Genome Chromosome ◽

D Genome ◽

Reciprocal Translocations ◽

A Genome ◽

Break Points ◽

Mother Cells ◽

Chromosome Regions ◽

Good Agreement

ABSTRACT Chromosome configurations were recorded in about 5500 pollen mother cells (PMC's) in 2n and 2n-1 (missing the intact A-genome chromosome) heterozygotes of ten reciprocal translocations involving six A-genome chromosomes (H1, H2, H3, H4, H6 and H7) and six D-genome chromosomes (H14, H15, H16, H19, H20 and H21) of Gossypium hirsutum. From these records, chiasma frequencies at each of six positions were determined for nine translocations and at two positions for one. These frequencies were used to calculate recombination frequencies in different chromosome regions, and from these distances the breakpoints in 15 chromosome arms were mapped relative to each other and to their respective centromeres, insofar as the data permitted. The karyotype so derived for twelve chromosomes is in reasonably good agreement with data from genetic mapping, telosome and monosome mapping, and the mitotic idiogram.

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COLD HARDINESS IN Triticum AND Aegilops SPECIES

Canadian Journal of Plant Science ◽

10.4141/cjps85-010 ◽

1985 ◽

Vol 65 (1) ◽

pp. 71-77 ◽

Cited By ~ 14

Author(s):

A. E. LIMIN ◽

D. B. FOWLER

Keyword(s):

Winter Wheat ◽

Common Wheat ◽

Cold Hardiness ◽

Diploid Species ◽

Genetic System ◽

Aegilops Species ◽

D Genome ◽

Genome Species ◽

Triticum Timopheevi ◽

A Genome

A total of 237 Triticum and Aegilops accessions were cold-acclimated and screened for cold hardiness. These included 90 A genome accessions (T. monococcum L. and T. beoticum Boiss.), 26 AG genome accessions of T. timopheevi (Zhuk.) Zhuk., 44 D genome accessions of Ae. squarrosa L., and 77 accessions made from 22 Aegilops species. The greatest degree of cold hardiness was found in the polyploid Aegilops species; particularly Ae. cylindrica Host (CD genome). One Ae. cylindrica accession was equal to the hardy winter wheat cultivar Norstar (T. aestivum L., ABD genome). Triticum timopheevi accessions possessed only poor levels of cold hardiness. Two of the diploid progenitor species of common wheat, T. monococcum and Ae. squarrosa, had poor to intermediate levels of cold hardiness. The D genome species was, on average, more hardy than the A genome species. Several polyploids have achieved a level of cold hardiness greater than that found in any of the diploid species. It is speculated that these hardiness levels have been achieved, in part, by the chance incorporation of hardy diploids in the original hybridization. However, the evolution of new genie forms or an integrated genetic system between the genomes of the polyploid was probably equally important to the development of highly cold hardy types. The utility of related species for the improvement of cold hardiness in common wheat is discussed.Key words: Triticum, Aegilops, cold hardiness, winter wheat, interspecific hybridization

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Secondary Tetrasomic Segregation of MDH-B and Preferential Pairing of Homeologues in Rainbow Trout

Genetics ◽

10.1093/genetics/145.4.1083 ◽

1997 ◽

Vol 145 (4) ◽

pp. 1083-1092 ◽

Cited By ~ 3

Author(s):

Fred W Allendorf ◽

Roy G Danzmann

Keyword(s):

Allelic Variation ◽

Male Meiosis ◽

Proximal Region ◽

Stage Model ◽

Preferential Pairing ◽

Homologous Chromosomes ◽

Tetrasomic Inheritance ◽

Segregation Ratios ◽

Homeologous Chromosomes ◽

Duplicated Loci

We examined the inheritance of allelic variation at an isozyme locus, MDH-B, duplicated by ancestral polyploidy in salmonid fishes. We detected only disomic segregation in females. Segregation ratios in males were best explained by a mixture of disomic and tetrasomic inheritance. We propose a two-stage model of pairing in male meiosis in which, first, homologous chromosomes pair and recombine in the proximal region of the chromosome. Next, homeologous chromosomes pair and recombine distally. We suggest that this type of tetrasomic inheritance in which centromeres segregate disomically should be referred to as “secondary tetrasomy” to distinguish it from tetrasomy involving entire chromosomes (i.e., “primary tetrasomy”). Differences in segregation ratios between males indicate differences between individuals in the amount of recombination between homeologous chromosomes. We also consider the implication of these results for estimation of allele frequencies at duplicated loci in salmonid populations.

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A Microsatellite Map of Wheat

Genetics ◽

10.1093/genetics/149.4.2007 ◽

1998 ◽

Vol 149 (4) ◽

pp. 2007-2023 ◽

Cited By ~ 8

Author(s):

Marion S Röder ◽

Victor Korzun ◽

Katja Wendehake ◽

Jens Plaschke ◽

Marie-Hélène Tixier ◽

...

Keyword(s):

Bread Wheat ◽

Reference Population ◽

Triticum Aestivum L ◽

Wheat Genome ◽

D Genome ◽

B Genome ◽

Microsatellite Map ◽

A Genome ◽

Polymorphic Microsatellite ◽

Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

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Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

BMC Plant Biology ◽

10.1186/s12870-021-02875-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Liuyang Fu ◽

Qian Wang ◽

Lina Li ◽

Tao Lang ◽

Junjia Guo ◽

...

Keyword(s):

In Situ Hybridization ◽

Physical Mapping ◽

Tandem Repeats ◽

Genetic Research ◽

Diploid Species ◽

Reference Sequence ◽

A Genome ◽

Genome Map ◽

Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

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