Isolation and identification of Triticeae chromosome 1 receptor-like kinase genes (Lrk10) from diploid, tetraploid, and hexaploid species of the genus Avena

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 119-127 ◽  
Author(s):  
D W Cheng ◽  
K C Armstrong ◽  
G Drouin ◽  
A McElroy ◽  
G Fedak ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Chromosome 1 ◽  
Isolation And Identification ◽  
Genome Species ◽  
A Genome ◽  
Receptor Like Kinase ◽  
C Genome ◽  
Multiple Copies ◽  
Genome Group

The DNA sequence of an extracellular (EXC) domain of an oat (Avena sativa L.) receptor-like kinase (ALrk10) gene was amplified from 23 accessions of 15 Avena species (6 diploid, 6 tetraploid, and 3 hexaploid). Primers were designed from one partial oat ALrk10 clone that had been used to map the gene in hexaploid oat to linkage groups syntenic to Triticeae chromosome 1 and 3. Cluster (phylogenetic) analyses showed that all of the oat DNA sequences amplified with these primers are orthologous to the wheat and barley sequences that are located on chromosome 1 of the Triticeae species. Triticeae chromosome 3 Lrk10 sequences were not amplified using these primers. Cluster analyses provided evidence for multiple copies at a locus. The analysis divided the ALrk EXC sequences into two groups, one of which included AA and AABB genome species and the other CC, AACC, and CCCC genome species. Both groups of sequences were found in hexaploid AACCDD genome species, but not in all accessions. The C genome group was divided into 3 subgroups: (i) the CC diploids and the perennial autotetraploid, Avena macrostachya (this supports other evidence for the presence of the C in this autotetraploid species); (ii) a sequence from Avena maroccana andAvena murphyi and several sequences from different accessions of A.sativa; and (iii) A. murphyi and sequences from A. sativa andAvena sterilis. This suggests a possible polyphyletic origin for A. sativa from the AACC progenitor tetraploids or an origin from a progenitor of the AACC tetraploids. The sequences of the A genome group were not as clearly divided into subgroups. Although a group of sequences from the accession 'SunII' and a sequence from line Pg3, are clearly different from the others, the A genome diploid sequences were interspersed with tetraploid and hexaploid sequences.Key words: phylogeny, genome evolution, speciation, oat.

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.

Inferences on the origins of polyploid Turnera species (Passifloraceae) based on molecular data

Botany ◽  
2013 ◽  
Vol 91 (3) ◽  
pp. 167-175 ◽  
Author(s):  
Alicia López ◽  
Aveliano Fernández ◽  
Joel S. Shore
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Diploid Species ◽  
Nuclear Genome ◽  
Molecular Data ◽  
Genome Donor ◽  
A Genome ◽  
Cytogenetic Studies ◽  
C Genome ◽  
Nuclear Its

We explore the evolution of polyploids in subseries Turnera, testing hypotheses on their origins using DNA sequences (partial ndhF and trnT-L) from the plastid genome, as well as sequences of the nuclear ribosomal internal transcribed spacer (ITS). We construct phylogenies (with both Bayesian and maximum parsimony methods) using both the plastid and ITS sequences. We test hypotheses concerning the genome contributors to polyploids where previous cytogenetic studies had designated various diploid species as possessing A or C genomes and had proposed various genomic constitutions for the polyploids. Our analyses support the occurrence of a C genome clade of species and the origin of autooctoploid T. fernandezii Arbo from T. grandiflora (Urb.) Arbo (a C genome diploid). Nuclear ITS data support the hypothesis that T. concinna Arbo (an A genome species) contributed a genome to the segmental allotetraploid T. grandidentata (Urb.) Arbo, whereas analyses of ndhF and trnT-L sequences did not lead to identification of the plastid (or additional nuclear genome) donor. Our analyses support the origins of allooctoploids T. aurelii Arbo and T. cuneiformis Poir. from hexaploid T. orientalis (Urb.) Arbo. We found no evidence that hexaploid T. velutina Presl. possesses a C genome. We provide evidence, using Bayes factors, supporting the hypothesis that the segmental allohexaploids have had independent origins.

Further hybrids involving the perennial autotetraploid oat Avena macrostachya

Genome ◽  
1992 ◽  
Vol 35 (2) ◽  
pp. 273-275 ◽  
Author(s):  
J. M. Leggett
Keyword(s):  
Chromosome Pairing ◽  
Triploid Hybrid ◽  
Genome Species ◽  
A Genome ◽  
C Genome

Chromosome pairing in the triploid hybrid Avena damascena × A. macrostachya is very similar to the chromosome pairing observed in previously reported triploid hybrids involving the A genome diploid taxa A. atlantica and A. prostrata, indicating that little more than residual homology remains between these A genome diploids and either of the genomes of A. macrostachya. The chromosome pairing in the hybrid between A. macrostachya and the C genome diploid A. ventricosa is similar to that observed in the previously reported hybrid A. eriantha × A. macrostachya. In both these hybrids, the frequency of trivalents is greater than that observed in hybrids involving the A genome species and A. macrostachya, which is indicative of closer homology of A. macrostachya to the C genome diploids than the A genome diploids.Key words: Avena, hybrids, interspecific chromosome pairing, phylogeny.

Giemsa C-banded karyotypes of Avena species

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 627-632 ◽  
Author(s):  
A. Fominaya ◽  
C. Vega ◽  
E. Ferrer
Keyword(s):  
Interspecific Hybrids ◽  
Chromatin Condensation ◽  
Diploid Species ◽  
Divergent Evolution ◽  
Intercalary Heterochromatin ◽  
Banding Patterns ◽  
Genome Species ◽  
C Banding ◽  
A Genome ◽  
C Genome

Giemsa C-banding was used to identify individual somatic chromosomes in eight diploid species of Avena. Two patterns of heterochromatin distribution were found. The chromosomes of five A genome species (A. strigosa, A. hirtula, A. longiglumis, A. damascena, and A. canariensis) possessed mainly telomeric bands, whereas those from three C genome species (A. clauda, A. pilosa, and A. ventricosa) were characterized by higher chromatin condensation and several intercalary heterochromatin bands. The divergent evolution between the two groups is confirmed after C-banding. The unique C-banding patterns of several chromosomes in each species will be a useful tool for the study of meiotic behaviour in interspecific hybrids among Avena spp.Key words: C-banding, Avena, heterochromatin.

ELECTROPHORETIC PATTERNS OF OAT PROLAMINES AND SPECIES RELATIONSHIPS IN AVENA

1979 ◽  
Vol 21 (3) ◽  
pp. 309-318 ◽  
Author(s):  
S. I. Kim ◽  
J. Mossé
Keyword(s):  
Intraspecific Variation ◽  
Evolutionary Process ◽  
Species Relationships ◽  
D Genome ◽  
Genome Species ◽  
Electrophoretic Patterns ◽  
A Genome ◽  
C Genome ◽  
Starch Gel

Starch gel electrophoretic studies on seed prolamines of 17 different di-, tetra-, and hexaploid Avena species were undertaken to determine species relationships and the evolutionary process of the polyploids. Significant intraspecific variation was observed. Electrophoregrams of each species were obtained by superposing all the bands found in the same species and in total, 17 bands were observed. Clear differences were found between species in their patterns, which allowed determination of the bands specific to three genomes (A, C and D). Like the diploids, the tetraploids can be divided into two groups on the basis of electrophoretic patterns: A. barbata and A. magna-A. murphyi. It is evident that A. magna-murphyi group is derived from both the A and C genome species of diploids while A. barbata is derived from the A genome species only. The similarity between A. magna and A. murphyi was also confirmed. The hexaploids were derived from A. magna-murphyi group and a D genome ancestor although the last one is not discovered yet.

scholarly journals The Use of DNA Sequences from the β-Amylase Gene to Determine the Genetic Relationship among Sweetpotato, I. batatas and Other Ipomoea Species in Series Batatas (Convolvulaceae)

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1121E-1122
Author(s):  
Sriyani Rajapakse ◽  
Janice Ryan-Bohac ◽  
Sasanda Nilmalgoda ◽  
Robert Ballard ◽  
Daniel F. Austin
Keyword(s):  
Dna Sequences ◽  
Ipomoea Batatas ◽  
Dna Flow Cytometry ◽  
Amylase Gene ◽  
Genome Species ◽  
B Genome ◽  
A Genome ◽  
Nucleotide Sequence Variation ◽  
In Series ◽  
True Hybrid

The sweet potato Ipomoea batatas (L.) Lam. is classified in series Batatas (Choisy) in Convolvulaceae, with 12 other species and an interspecific true hybrid. The phylogenetic relationships of a sweetpotato cultivar and 13 accessions of Ipomoeas in the series Batatas were investigated using the nucleotide sequence variation of the nuclear-encoded β-amylase gene. First, flowers were examined to identify the species, and DNA flow cytometry used to determine their ploidy. The sweetpotato accession was confirmed as a hexaploid, I. tabascana a tetraploid, and all other species were diploids. A 1.1–1.3 kb fragment of the β-amylase gene spanning two exons separated by a long intron was PCR-amplified, cloned, and sequenced. Exon sequences were highly conserved, while the intron yielded large sequence differences. Intron analysis grouped species currently recognized as A and B genome types into separate clades. This grouping supported the prior classification of all the species, with one exception. The species I. tiliacea was previously classified as a B genome species, but this DNA study classifies it as an A genome species. From the intron alignment, sequences specific to both A and B genome species were identified. Exon sequences indicated that I. ramosissima and I. umbraticola were quite different from other A genome species. Placement of I. littoralis was questionable: its introns were similar to other B genome species, but exons were quite different. Exon evolution indicated the B genome species evolved faster than A genome species. Both intron and exon results indicated the B genome species most closely related to sweetpotato (I. batatas) were I. trifida and I. tabascana.

scholarly journals Epigenetic Variation at a Genomic Locus Affecting Biomass Accumulation under Low Nitrogen in Arabidopsis thaliana

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 636 ◽  
Author(s):  
Markus Kuhlmann ◽  
Rhonda C. Meyer ◽  
Zhongtao Jia ◽  
Doreen Klose ◽  
Lisa-Marie Krieg ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Genome Wide Association Study ◽  
Biomass Accumulation ◽  
Snp Markers ◽  
Growth Patterns ◽  
Production Costs ◽  
Chromosome 1 ◽  
Genomic Locus ◽  
A Genome

Nitrogen (N) is a macronutrient determining crop yield. The application of N fertilisers can substantially increase the yield, but excess use also causes the nitrate pollution of water resources and increases production costs. Increasing N use efficiency (NUE) in crop plants is an important step to implement low-input agricultural systems. We used Arabidopsis thaliana as model system to investigate the natural genetic diversity in traits related to NUE. Natural variation was used to study adaptive growth patterns and changes in gene expression associated with limited nitrate availability. A genome-wide association study revealed an association of eight SNP markers on Chromosome 1 with shoot growth under limited N. The identified linkage disequilibrium (LD) interval includes the DNA sequences of three cysteine/histidine-rich C1 domain proteins in tandem orientation. These genes differ in promoter structure, methylation pattern and expression level among accessions, correlating with growth performance under N deficiency. Our results suggest the involvement of epigenetic regulation in the expression of NUE-related traits.

The genomes of Glycine canescens F.J. Herm., and G. tomentella Hayata of Western Australia and their phylogenetic relationships in the genus Glycine Willd.

Genome ◽  
1998 ◽  
Vol 41 (5) ◽  
pp. 669-679 ◽  
Author(s):  
Ram J Singh ◽  
Krishna P Kollipara ◽  
Theodore Hymowitz
Keyword(s):  
Western Australia ◽  
Phylogenetic Relationships ◽  
Diploid Species ◽  
South Australia ◽  
Its Region ◽  
Genomic Diversity ◽  
Complex Species ◽  
Genome Species ◽  
A Genome ◽  
Genome Group

A multidisciplinary approach is an extremely powerful tool for determining genomic diversity and establishing genomic relationships within and among species. This study used cytogenetics and a molecular method (ITS of the rDNA) to uncover genomic diversity in Glycine canescens and Glycine tomentella and to establish their phylogenetic relationships with the other diploid species of the genus Glycine. Cytogenetics revealed that G. canescens accessions (PIs 583944, 583946, 583953, and 591575) from Western Australia were genomically similar. However, they were differentiated by a paracentric inversion from the standard G. canescens (PI 440932) collected from South Australia. By contrast, G. tomentella (2n = 40) accessions from Western Australia were highly diverse genomically. Cytogenetics and ITS investigations separated the diploid G. tomentella accessions in Australia into four distinct groups. The genome symbols DD (isozyme group D3; PI 505222), D1D1 (isozyme group D5; PI 505301), D2D2 (isozyme group D5; PI 505203), and D3D3 (isozyme group D4; PI 441000) are being assigned to these four groups. The D1 and D2 genome group accessions are distributed in Western Australia. The D3-genome group of G. tomentella accessions are morphologically similar neither to A-genome species nor to the D-, D1-, or D2-genome groups. However, the D3-genome group was phylogenetically grouped with the A-genome species, while the D-, D1-, and D2-genome groups showed a close relationship with E-, H-, and I-genome species. This study demonstrates that diploid G. tomentella of Western Australia is a complex species, and from an evolutionary viewpoint, it is actively radiating out into several genomic variants.Key words: Glycine spp., soybean, genome, cytogenetics, ITS region.

scholarly journals Phylogenetic Relationships of Tetraploid AB-Genome Avena Species Evaluated by Means of Cytogenetic (C-Banding and FISH) and RAPD Analyses

2010 ◽  
Vol 2010 ◽  
pp. 1-13 ◽  
Author(s):  
E. D. Badaeva ◽  
O. Yu. Shelukhina ◽  
S. V. Goryunova ◽  
I. G. Loskutov ◽  
V. A. Pukhalskiy
Keyword(s):  
Diploid Species ◽  
5S Rdna ◽  
Banding Technique ◽  
Diploid Progenitor ◽  
Genome Species ◽  
C Banding ◽  
A Genome ◽  
Different Types ◽  
Genome Group

Tetraploid oat species Avena abyssinica, A. vaviloviana, A. barbata, and A. agadiriana were studied using C-banding technique, in situ hybridization with the 45S and 5S rDNA probes, and RAPD analysis in comparison with the diploid species carrying different types of the A-genome (A. wiestii, As; A. longiglumis, Al; A. canariensis, Ac; A. damascena, Ad, A. prostrata, Ap). The investigation confirmed that all four tetraploids belong to the same AB-genome group; however A. agadiriana occupies distinct position among others. The C-banding, FISH, and RAPD analyses showed that Avena abyssinica, A. vaviloviana, and A. barbata are very similar; most probably they originated from a common tetraploid ancestor as a result of minor translocations and alterations of C-banding polymorphism system. AB-genome species are closely related with the A-genome diploids, and an As-genome species may be regarded as the most probable donor of their A-genome. Although their second diploid progenitor has not been identified, it seems unlikely that it belongs to the As-genome group. The exact diploid progenitors of A. agadiriana have not been determined; however our results suggest that at least one of them could be related to A. damascena.

scholarly journals Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 545
Author(s):  
Gédéon Prince Manouana ◽  
Paul Alvyn Nguema-Moure ◽  
Mirabeau Mbong Ngwese ◽  
C.-Thomas Bock ◽  
Peter G. Kremsner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Preventive Measures ◽  
Phylogenetic Analyses ◽  
Enteric Viruses ◽  
Study Cohort ◽  
Viral Agent ◽  
A Genome ◽  
Stool Samples ◽  
Pcr Techniques ◽  
High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

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