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

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.

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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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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.

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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

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Bali Bananas (Musa spp. L.) Genetic Relationship Based on Internal Transcribed Spacer 2 (ITS-2)

Pertanika Journal of Tropical Agricultural Science ◽

10.47836/pjtas.43.4.12 ◽

2020 ◽

Vol 43 (4) ◽

Author(s):

Fenny Martha Dwivany ◽

Muhammad Rifki Ramadhan ◽

Carolin Lim ◽

Agus Sutanto ◽

Husna Nugrahapraja ◽

...

Keyword(s):

Secondary Structure ◽

Genetic Relationship ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Resolving Power ◽

Structure Information ◽

Musa Spp ◽

Internal Transcribed Spacer 2 ◽

B Genome ◽

A Genome

Banana is one of the most essential commodities in Bali island. It is not only for nutrition sources but also for cultural and religious aspects. However, Bali banana genetic diversity has not been explored; therefore, in this study, we focused on its genetic relationship using a molecular approach. This research aimed to determine the genetic relationship of Bali banana cultivars using the internal transcribed spacer 2 (ITS-2) region as a molecular marker. A total of 39 banana samples (Musa spp. L.) were collected from Bali island. The ITS-2 DNA regions were then amplified and sequenced from both ends. ITS-2 sequences were predicted using the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). The multiple sequences alignment was performed using ClustalX for nucleotide-based tree and LocARNA to provide the secondary structure information. Phylogenetic trees were constructed using neighbor-joining (Kimura-2-parameter model, 1,000 bootstrap). The result showed that two clades were formed, one clade was abundant in A genome (AA and AAA), and the other rich in the B genome (BB and ABB). This result suggested that cultivars that had similar genomic compositions tended to be grouped within the same clade and separated with different genomic compositions. This study gives perspectives that ITS-2 sequences in bananas are quite similar and differ much compared to other families. Secondary structure has been described to provide more robust resolving power in phylogenetic analysis.

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Molecular Genotypic Diversity of Populations of Brinjal Shoot and Fruit Borer, Leucinodes Orbonalis and Development of SCAR Marker for Pesticide Resistance

10.21203/rs.3.rs-721509/v1 ◽

2021 ◽

Author(s):

Palraju Murali ◽

Karuppiah Hilda ◽

Muthusamy Ramakrishnan ◽

Arumugam Ganesh ◽

Sreeramulu Bhuvaragavan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Tamil Nadu ◽

Scar Marker ◽

Random Amplified Polymorphic Dna ◽

Pesticide Resistance ◽

Specific Marker ◽

Leucinodes Orbonalis ◽

Fruit Borer ◽

Different Populations

Abstract The brinjal shoot and fruit borer, Leucinodes orbonalis is a destructive pest of Solanum melongena. The control of L. orbonalis with extensive application of synthetic chemical insecticides resulted in the development of resistance with known genetic heterogeneity among populations. Understanding the genetic diversity of their populations is important in developing strategies for their management. The present investigation was performed to characterize populations of L. orbonalis for their genetic diversity in the entire region of Tamil Nadu, South India using random amplified polymorphic DNA (RAPD) primers as a tool of the molecular marker. Among sixty random 10-mer primers, only ten primers generated reproducible and scorable banding profile. Among the ten different random primers, the primers namely OPG 7, OPG 8, OPS 2 and OPS 7 generated the highest genetic variation with over 80% genetic polymorphism. Phylogram analysis produced 18 clusters with 8 major and 10 minor clusters. Cluster analysis, statistical fitness, population structure and analysis of molecular variance confirmed the significant genetic variation among different populations. A trait specific marker obtained through RAPD was cloned, sequenced and used to develop a stable diagnostic SCAR marker for DNA fingerprinting to distinguish the populations. Amplification of this locus in the samples of 20 different populations indicated recognition of the trait for pesticide resistance in 12 populations. The results suggest that the biochemical nature of host plant varieties of this insect pest and variation in the application of different insecticides are essential contributing factors for the genotypic variations observed among populations of L. orbonalis.

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Identification of RAPD markers linked to A and B genome sequences in Musa L.

Genome ◽

10.1139/g00-038 ◽

2000 ◽

Vol 43 (5) ◽

pp. 763-767 ◽

Cited By ~ 20

Author(s):

M Pillay ◽

D C Nwakanma ◽

A Tenkouano

Keyword(s):

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Diploid Species ◽

Morphological Characteristics ◽

Genome Composition ◽

Reliable System ◽

B Genome ◽

Wild Diploid Species

Plantains and bananas (Musa spp. sect. eumusa) originated from intra- and interspecific hybridization between two wild diploid species, M. acuminata Colla. and M. balbisiana Colla., which contributed the A and B genomes, respectively. Polyploidy and hybridization have given rise to a number of diploid, triploid, and tetraploid clones with different permutations of the A and B genomes. Thus, dessert and highland bananas are classified mainly as AAA, plantains are AAB, and cooking bananas are ABB. Classification of Musa into genomic groups has been based on morphological characteristics. This study aimed to identify RAPD (random amplified polymorphic DNA) markers for the A and B genomes. Eighty 10-mer Operon primers were used to amplify DNA from M. acuminata subsp. burmannicoides clone 'Calcutta 4' (AA genomes) and M. balbisiana clone 'Honduras' (BB genomes). Three primers (A17, A18, and D10) that produced unique genome-specific fragments in the two species were identified. These primers were tested in a sample of 40 genotypes representing various genome combinations. The RAPD markers were able to elucidate the genome composition of all the genotypes. The results showed that RAPD analysis can provide a quick and reliable system for genome identification in Musa that could facilitate genome characterization and manipulations in breeding lines.Key words: banana and plantain, A and B genomes, genomic groups, RAPD markers.

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Pathways for Introgression of Pest Resistance into Arachis hypogaea L.1

Peanut Science ◽

10.3146/i0095-3679-18-1-8 ◽

1991 ◽

Vol 18 (1) ◽

pp. 22-26 ◽

Cited By ~ 49

Author(s):

Charles E. Simpson

Keyword(s):

Arachis Hypogaea ◽

Chromosome Doubling ◽

Diploid Species ◽

Gene Introgression ◽

Diploid Hybrid ◽

B Genome ◽

Arachis Hypogaea L ◽

A Genome ◽

Bridge Species ◽

Species Hybrids

Abstract Four pathways for gene introgression into Arachis hypogaea L. were studied. Two “hexaploid routes” involved direct crosses of diploid Arachis species and diploid species hybrids with A. hypogaea (Pathways 1 and 2, respectively) and were followed by chromosome doubling with colchicine. A third pathway, a tetraploid route, involved chromosome doubling of a diploid hybrid before crossing with A. hypogaea. These first three routes involved only the A genome species, and all were unsuccessful because of lack of fertility. The fourth pathway, also a tetraploid route, utilized the B genome A. batizocoi Krap. et Greg. as a bridge species and brought about a successful (fertile) introgression. Genes from A. cardenasii Krap. et Greg. nom. nud. and A. chacoensis Krap et Greg. nom. nud. were combined into a hybrid and incorporated into A. hypogaea by using the B genome bridge species. Introgression of additional characters from these and other species through this pathway should be possible.

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A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

10.1101/681080 ◽

2019 ◽

Cited By ~ 5

Author(s):

Kumar Paritosh ◽

Satish Kumar Yadava ◽

Priyansha Singh ◽

Latika Bhayana ◽

Arundhati Mukhopadhyay ◽

...

Keyword(s):

Brassica Juncea ◽

Single Molecule ◽

Genome Assembly ◽

Diploid Species ◽

Gene Clusters ◽

Specific Gene ◽

Dry Land ◽

Gene Block ◽

B Genome ◽

A Genome

AbstractBrassica juncea (AABB; genome size ∼920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ∼100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.

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

10.21203/rs.3.rs-38569/v2 ◽

2020 ◽

Author(s):

Liuyang Fu ◽

Qian Wang ◽

Lina Li ◽

Tao Lang ◽

Junjia Guo ◽

...

Keyword(s):

Physical Mapping ◽

Tandem Repeats ◽

Genetic Research ◽

Diploid Species ◽

B Genome ◽

A Genome ◽

Genome Map ◽

Reference Sequences ◽

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. Thus, the identification of chromosomal variants in peanut remains a challenge, owing to a lack of efficient chromosomal markers. Results: A total 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 oligos were classified into 28 types, based on their positions, and overlapping signals in chromosomes. For each oligo types, a single and representative oligos was selected and modified with 6-carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA). Based on these 28 probes, a new multiplex #3 cocktail was developed with FAM-modified TIF-439, TIF-185-1, TIF-134-3, and TIF-165-3, and TAMRA-modified Ipa-1162, Ipa-1137, DP-1, and DP-5. This 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 peanut induced by radiation. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, and intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the other 15 were extensively mapped in the pericentric regions of chromosomes. Conclusions: The development of new oligo probes provides effective tools, which can be used to distinguish various chromosomes of peanut. Physical mapping reveals the genomic organization of repetitive oligos in peanut chromosomes by FISH. Following comparisons with their positions in the reference sequences, a genome map-based karyotype was established and used for the identification of chromosome variations in peanut.

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

10.21203/rs.3.rs-38569/v3 ◽

2021 ◽

Author(s):

Liuyang Fu ◽

Qian Wang ◽

Lina Li ◽

Tao Lang ◽

Junjia Guo ◽

...

Keyword(s):

Physical Mapping ◽

Tandem Repeats ◽

Genetic Research ◽

Diploid Species ◽

Reference Sequence ◽

B Genome ◽

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 oligos 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 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 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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