Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

Download Full-text

Banana contains a diverse array of endogenous badnaviruses

Journal of General Virology ◽

10.1099/vir.0.80261-0 ◽

2005 ◽

Vol 86 (2) ◽

pp. 511-520 ◽

Cited By ~ 74

Author(s):

Andrew D. W. Geering ◽

Neil E. Olszewski ◽

Glyn Harper ◽

Benham E. L. Lockhart ◽

Roger Hull ◽

...

Keyword(s):

Nuclear Genome ◽

Synonymous Substitution ◽

Selective Constraint ◽

Musa Balbisiana ◽

Reading Frame ◽

B Genome ◽

Species Analysis ◽

Breeding Programmes ◽

Distinct Sequence ◽

High Degree

Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus. Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.) breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation. This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown. In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars ‘Obino l'Ewai’ and ‘Klue Tiparot’, were cloned. In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other. There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species. Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event.

Download Full-text

Use of Wild Arachis Species/Introgression of Genes into A. hypogaea L.

Peanut Science ◽

10.3146/i0095-3679-28-2-12 ◽

2001 ◽

Vol 28 (2) ◽

pp. 114-116 ◽

Cited By ~ 49

Author(s):

C. E. Simpson

Keyword(s):

North Carolina ◽

Chromosome Number ◽

Wild Species ◽

Diploid Species ◽

Breeding Lines ◽

B Genome ◽

Improvement Programs ◽

Selection For ◽

Direct Dna Delivery ◽

No Releases

Abstract The use of wild Arachis L. in cultivar improvement programs has been considered an option for more than 50 yr. Both A. Krapovickas and W.C. Gregory, independently, made interspecific hybridizations in the 1940s. However, only three cultivars have been released as a result of interspecific hybridizations, and only one of those has a clearly identifiable genetic component from the wild species. Several breeding lines have been reported and several germplasm releases are documented from Texas, North Carolina, and ICRISAT. At least four potential options exist for transferring genes from wild Arachis to the cultigen: a) The hexaploid pathway consists of crossing a diploid wild species directly with A. hypogaea, doubling the chromosome number to the hexaploid level, then backcrossing for several generations to restore the tetraploid condition. Several options are possible in this pathway involving various crossing schemes prior to crossing a diploid hybrid with A. hypogaea. North Carolina and ICRISAT have had success with this pathway. b) The diploid/tetraploid pathway has been the most successful in Texas to date. This pathway involves crossing diploid species (two to several), doubling the chromosome number of the hybrid, then crossing to A. hypogaea and backcrossing with selection for the desired character. This pathway is most successful when both A-and B-genome species are involved. Germplasm lines and a cultivar have been released in Texas using this pathway. c) Another diploid/tetraploid pathway could be to double chromosome numbers of diploid species and cross the amphiploids directly with A. hypogaea. Several attempts have been made with this technique, but no germplasm releases have been reported, in large part because sterility is too great when both A and B genomes are not included in the hybrid. Many of the sections/species of wild Arachis are so greatly isolated from A. hypogaea that plant transformation will be the likely method to introduce genes into the cultigen. d) Molecular methods of “inserting” genes into peanut that have been modestly successful and include use of Agrobacterium spp., electroporation, and direct DNA delivery techniques such as the gene gun, whiskers, and sonication. No releases have resulted.

Download Full-text

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.

Download Full-text

Insights on the process of reciprocal gene loss in the duplicate DPL genes of rice

10.21203/rs.2.19306/v1 ◽

2019 ◽

Author(s):

Xun Xu ◽

Song Ge ◽

Fu-min Zhang

Keyword(s):

Evolutionary History ◽

Gene Loss ◽

Diploid Species ◽

Recent Common Ancestor ◽

Duplicate Genes ◽

Evolutionary Divergence ◽

Dna Transposons ◽

B Genome ◽

A Genome ◽

History Of

Abstract Background: Reciprocal gene loss (RGL) of duplicate genes is an important genetic resource of reproductive isolation, which is essential for speciation. In the past decades, various RGL patterns have been revealed, but RGL process is still poorly understood. The RGL of the duplicate DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2) gene can lead to BDM-type hybrid incompatibility between two rice subspecies. The evolutionary history of the duplicate genes, including their origin and mechanism of duplication as well as their evolutionary divergence after the duplication, remains unclear. In this study, we investigated the evolutionary history of the duplicate genes for gaining insights into the process of RGL.Results: We reconstructed phylogenetic relationships of DPL copies from all 15 diploid species representing six genome types of rice genus and then found that all the DPL copies from the latest diverged A- and B-genome gather into one monophyletic clade. Southern blot analysis also detected definitely two DPL copies only in A- and B-genome. High conserved collinearity can be observed between A- and B-genomic segments containing DPL1 and DPL2 respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is related to DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective constraint in DPL1 lineage but an enhancement in DPL2 lineage after DPL duplication. Sequence analysis also indicated that quite a few defective DPL1 can be found in 6 wild and cultivated species out of all 8 species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions: DPL duplication of rice originated in the recent common ancestor of A- and B-genome about 6.76 million years ago and the duplication was possibly caused by DNA transposons. The DPL1 is a redundant copy and has being in the process of pseudogenization, suggesting that artificial selection may play an important role in forming the RGL of DPLs between two rice subspecies during the domestication.

Download Full-text

Pervasive hybridizations in the history of wheat relatives

Science Advances ◽

10.1126/sciadv.aav9188 ◽

2019 ◽

Vol 5 (5) ◽

pp. eaav9188 ◽

Cited By ~ 17

Author(s):

Sylvain Glémin ◽

Celine Scornavacca ◽

Jacques Dainat ◽

Concetta Burgarella ◽

Véronique Viader ◽

...

Keyword(s):

Methodological Approach ◽

Diploid Species ◽

Phylogenomic Analysis ◽

D Genome ◽

B Genome ◽

Hybridization Event ◽

History Of ◽

Complex Scenario ◽

Ancient Hybridization

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

Download Full-text

SCAR Marker for the A Genome of Bananas (Musa spp. L.) Supports Lack of Differentiation between the A and B Genomes

Journal of Agricultural Science ◽

10.5539/jas.v9n6p64 ◽

2017 ◽

Vol 9 (6) ◽

pp. 64

Author(s):

Lloyd Mabonga ◽

Michael Pillay

Keyword(s):

Scar Marker ◽

Agronomic Traits ◽

Random Amplified Polymorphic Dna ◽

Diploid Species ◽

Specific Marker ◽

Correct Identification ◽

Musa Spp ◽

B Genome ◽

A Genome ◽

Putative Marker

Bananas (Musa spp. L.) are grouped on the basis of their genomic origins in relation to Musa acuminata (A genome) and M. balbisiana (B genome). The two ancestral wild seeded diploid species evolved in vastly different geographical areas and contributed several agronomic traits towards the present genetic composition of cultivated bananas. Most cultivated bananas are triploid (AAA, AAB and ABB), some are diploid (AA, BB and AB) and a few are tetraploids (AAAA, AAAB, AABB and ABBB). Limitations on the correct identification of the A and B genomes in Musa have generated need for the development of new and more reliable techniques. Distinguishing the A and the B genome remains practically and theoretically important for banana breeders. The aim of the research was to develop a DNA based A genome specific marker for the identification of the A genome in bananas. A putative marker (600 bp) specific to the A genome was identified by Random Amplified Polymorphic DNA (RAPD) technique. A sequence characterised amplified region (SCAR) marker was developed from the RAPD amplicon. The SCAR primers annealed a 500 bp fragment specific to the A genome in a sample of 22 randomly selected homo- and heterogenomic A genome containing accessions representing different genome combinations. The 500 bp SCAR marker is useful for the identification of the A genome. However an additional 700 bp fragment annealed in all M. balbisiana genotypes and in five of the eight heterogenomic accessions, suggesting lack of differentiation between the A and B genome. This study has provided a 500 bp A genome SCAR marker and recent evidence that the A and B genomes of banana may not be as differentiated as previously considered.

Download Full-text

Chromosome painting in cultivated banana and their wild relatives (Musa spp.) reveals differences in chromosome structure

10.1101/2020.08.01.232207 ◽

2020 ◽

Author(s):

D Šimoníková ◽

A Němečková ◽

J Čížková ◽

A Brown ◽

R Swennen ◽

...

Keyword(s):

Chromosome Structure ◽

Diploid Species ◽

Musa Acuminata ◽

Cross Hybridization ◽

B Genome ◽

A Genome ◽

Structural Chromosome ◽

Cytogenetic Characterization ◽

Hybrid Clones ◽

Painting Probes

AbstractEdible banana cultivars are diploid, triploid or tetraploid hybrids which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid M. balbisiana. Participation of two other wild diploid species M. schizocarpa and M. textilis was also indicated by molecular studies. Fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. FISH with chromosome-arm specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure discriminating individual accessions. These results permitted identification of putative progenitors of cultivated clones and clarified genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in selection of appropriate parents for cross hybridization.HighlightOligo painting FISH revealed chromosomal translocations in subspecies of Musa acuminata (A genome), their intra-specific hybrids as well as in M. balbisiana (B genome) and in interspecific hybrid clones originating from cross hybridization between M. acuminata and M. balbisiana

Download Full-text

Variability in wheat based on low-copy DNA sequence comparisons

Genome ◽

10.1139/g95-125 ◽

1995 ◽

Vol 38 (5) ◽

pp. 951-957 ◽

Cited By ~ 15

Author(s):

L. E. Talbert ◽

N. K. Blake ◽

E. W. Storlie ◽

M. Lavin

Keyword(s):

Dna Sequence ◽

Diploid Species ◽

Sequence Variability ◽

D Genome ◽

Sequence Comparisons ◽

Molecular Analyses ◽

B Genome ◽

Hybridization Event ◽

Copy Dna ◽

Diploid Ancestor

The chromosomes of the B genome of hexaploid wheat (AABBDD) do not pair completely with those of any of the diploid species with genomes similar to B. Various biochemical and molecular analyses have suggested that each of the five diploid species in section Sitopsis of Triticum are ancestral to B. These observations have led to the hypothesis that the B genome may be polyphyletic, descending from more than one diploid ancestor. This hypothesis may account for differences between the wheat B genome and the diploids and also for variability that currently exists among different wheat accessions. In this study, we cloned and compared nucleotide sequences for three low-copy DNA fragments from the B and D genomes of several wheat accessions and from diploid relatives of the B and D genomes. Our results suggested that the amount of DNA sequence variability in wheat is low, although somewhat more variability existed in the B genome than in the D genome. The B genome of wheat was significantly diverged from all the Sitopsis diploid species, and Triticum speltoides was closer to B than to other members of this section. The D genome of wheat was very similar to that of its progenitor, Triticum tauschii. No evidence for a polyphyletic origin of the B genome was found. A more parsimonious hypothesis is that the wheat B genome diverged from its diploid ancestor after the original hybridization event occurred.Key words: wheat, low-copy DNA, phylogenetics.

Download Full-text

HYBRIDS BETWEEN A DIPLOID AGROPYRON ELONGATUM AND AEGILOPS SQUARROSA

Canadian Journal of Genetics and Cytology ◽

10.1139/g71-013 ◽

1971 ◽

Vol 13 (1) ◽

pp. 90-94 ◽

Cited By ~ 8

Author(s):

J. Dvořák

Keyword(s):

Chromosome Pairing ◽

Agropyron Elongatum ◽

B Genome ◽

Hybrid Plants ◽

Aegilops Squarrosa ◽

High Degree

Hybrids were obtained in crosses between Aegilops squarrosa and Agropyron elongatum (2x) but not in crosses between Ag. elongatum and Ae. speltoides and T. boeoticum, respectively. Chromosome pairing revealed a rather high degree of homoeology between the genomes of Ae. squarrosa and Ag. elongatum. The average pairing was 10.7′ + 1.5″ + 0.027″′ per cell with a range of from 0 to 5 pairs. All F1 hybrid plants were sterile with very low pollen fertility.It is proposed that the A and D genomes of wheat are more closely related to the genomes of section Elytrigia of the genus Agropyron than is the B genome.

Download Full-text