Influence of genetic background and heterozygosity on meiotic recombination in Arabidopsis thaliana

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 971-978 ◽  
Author(s):  
Susanne Barth ◽  
Albrecht E Melchinger ◽  
Beate Devezi-Savula ◽  
Thomas Lübberstedt
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variability ◽  
Plant Breeding ◽  
Meiotic Recombination ◽  
Genetic Background ◽  
Chromosome 3 ◽  
Breeding Strategies ◽  
Strong Negative Correlation ◽  
Adjacent Marker ◽  
Genomic Regions

Plant breeding relies on genetic variability generated by meiotic recombination. Control of recombination frequencies is not yet possible, but would significantly extend the options for plant-breeding strategies. A prerequisite would be variability of recombination frequencies. In this study, 15 transgenic kanamycin (KR) and hygromycin (HR) resistance gene insertions mapping to the five Arabidopsis thaliana chromosomes were used as genetic markers. Recombination frequencies were determined from the frequencies of resistance phenotypes within populations segregating for linked KR and HR markers. Recombination frequencies of marker pairs were compared among these four ecotypes, among F1s in both reciprocal forms derived from these ecotypes, and between F1s and their parent lines. On average, the recombination frequencies in F1 crosses were substantially higher (up to 2-fold) than in the homozygous parental ecotypes. A strong negative correlation between genetic similarities of ecotypes and recombination frequencies was detected for two adjacent marker pairs located on the long arm of chromosome 3, but not for marker pairs in other genomic regions. Our results suggest that heterozygosity influences recombination in plant breeding, and cannot be ignored in genetic mapping of genomes.Key Words: meiotic recombination, Arabidopsis, genetic background, heterozygosity, homozygosity.

Influence of genetic background and heterozygosity on meiotic recombination in Arabidopsis thaliana

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 971-978 ◽  
Author(s):  
Susanne Barth ◽  
Albrecht E. Melchinger ◽  
Beate Devezi-Savula ◽  
Thomas Lübberstedt
Keyword(s):  
Arabidopsis Thaliana ◽  
Meiotic Recombination ◽  
Genetic Background

Effects of Genetic Background on Response to Selection in Experimental Populations of Arabidopsis thaliana

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 277-286
Author(s):  
Mark C Ungerer ◽  
C Randal Linder ◽  
Loren H Rieseberg
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Background ◽  
Negative Selection ◽  
Genetic Data ◽  
Selection Response ◽  
Response To Selection ◽  
Genome Wide ◽  
Experimental Populations ◽  
Genomic Regions ◽  
Evolutionary Consequences

Abstract The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.

scholarly journals Rearrangements of the DNA in Carbon Ion-Induced Mutants of Arabidopsis thaliana

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 379-387 ◽  
Author(s):  
Naoya Shikazono ◽  
Atsushi Tanaka ◽  
Hiroshi Watanabe ◽  
Shigemitsu Tano
Keyword(s):  
Arabidopsis Thaliana ◽  
Nonhomologous End Joining ◽  
Chromosome 3 ◽  
Chromosome 2 ◽  
Carbon Ions ◽  
Induced Mutations ◽  
End Joining ◽  
Carbon Ion ◽  
Induced Mutants ◽  
Dna Strand

Abstract To elucidate the nature of structural alterations in plants, three carbon ion-induced mutations in Arabidopsis thaliana, gl1-3, tt4(C1), and ttg1-21, were analyzed. The gl1-3 mutation was found to be generated by an inversion of a fragment that contained GL1 and Atpk7 loci on chromosome 3. The size of the inverted fragment was a few hundred kilobase pairs. The inversion was found to accompany an insertion of a 107-bp fragment derived from chromosome 2. The tt4(C1) mutation was also found to be due to an inversion. The size of the intervening region between the breakpoints was also estimated to be a few hundred kilobase pairs. In the case of ttg1-21, it was found that a break occurred at the TTG1 locus on chromosome 5, and reciprocal translocation took place between it and chromosome 3. From the sequences flanking the breakpoints, the DNA strand breaks induced by carbon ions were found to be rejoined using, if present, only short homologous sequences. Small deletions were also observed around the breakpoints. These results suggest that the nonhomologous end-joining (NHEJ) pathway operates after plant cells are exposed to ion particles.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals My Project

2018 ◽  
Author(s):  
K K VINOD
Keyword(s):  
Plant Breeding ◽  
Breeding Strategies ◽  
Crop Varieties ◽  
Nutrient Use ◽  
The Future

Breeding nutrient use efficient crop varieties has become a contemporary necessity to arm against the future threats in agriculture. This article comments on the necessity and ways to contemplate newer plant breeding strategies for this endeavor.

scholarly journals Sardinians Genetic Background Explained by Runs of Homozygosity and Genomic Regions under Positive Selection

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e91237 ◽  
Author(s):  
Cornelia Di Gaetano ◽  
Giovanni Fiorito ◽  
Maria Francesca Ortu ◽  
Fabio Rosa ◽  
Simonetta Guarrera ◽  
...  
Keyword(s):  
Positive Selection ◽  
Genetic Background ◽  
Runs Of Homozygosity ◽  
Genomic Regions

scholarly journals Haplotype threading: accurate polyploid phasing from long reads

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Sven D. Schrinner ◽  
Rebecca Serra Mari ◽  
Jana Ebler ◽  
Mikko Rautiainen ◽  
Lancelot Seillier ◽  
...  
Keyword(s):  
Open Source ◽  
Evolutionary History ◽  
State Of The Art ◽  
Regions Of Interest ◽  
Breeding Strategies ◽  
Polyploid Species ◽  
Two Stage ◽  
Long Reads ◽  
History Of ◽  
Genomic Regions

Abstract Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase, a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

scholarly journals Genetic Variability of Natural Populations of Grapevine leafroll-associated virus 2 in Pacific Northwest Vineyards

2010 ◽  
Vol 100 (7) ◽  
pp. 698-707 ◽  
Author(s):  
Sridhar Jarugula ◽  
Olufemi J. Alabi ◽  
Robert R. Martin ◽  
Rayapati A. Naidu
Keyword(s):  
Genetic Variability ◽  
Pacific Northwest ◽  
Current Knowledge ◽  
Natural Populations ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymorphism Analysis ◽  
Nonsynonymous Site ◽  
Genomic Regions

Genetic variability of field populations of Grapevine leafroll-associated virus 2 (GLRaV-2) in Pacific Northwest (PNW) vineyards was characterized by sequencing the entire coat protein (CP) and a portion of the heat-shock protein-70 homolog (HSP70h) genes. Phylogenetic analysis of CP and HSP70h nucleotide sequences obtained in this study and corresponding sequences from GenBank revealed segregation of GLRaV-2 isolates into six lineages with virus isolates from PNW distributed in ‘PN’, ‘H4’, and ‘RG’ lineages. An estimation of the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated that different selection pressures may be acting on the two genomic regions encoding proteins with distinct functions. Multiple alignments of CP amino acid sequences showed lineage-specific differences. Enzyme-linked immunosorbent assay results indicated that GLRaV-2-specific antibodies from a commercial source are unable to reliably detect GLRaV-2 isolates in the RG lineage, thereby limiting antibody-based diagnosis of all GLRaV-2 isolates currently found in PNW vineyards. A protocol based on reverse-transcription polymerase chain reaction and restriction fragment length polymorphism analysis was developed for differentiating GLRaV-2 isolates belonging to the three lineages present in the region. The taxonomic status of GLRaV-2 is discussed in light of the current knowledge of global genetic diversity of the virus.

Phylogeny and Polymorphism in the Long Control Region, E6, and L1 of Human Papillomavirus Types 53, 56, and 66 in Central Brazil

2011 ◽  
Vol 21 (2) ◽  
pp. 222-229 ◽  
Author(s):  
Patrícia Soares Wyant ◽  
Daniela Marreco Cerqueira ◽  
Daniella Sousa Moraes ◽  
José Paulo Gagliardi Leite ◽  
Cláudia Renata Fernandes Martins ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Variability ◽  
Binding Sites ◽  
Long Control Region ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Central Brazil ◽  
Hpv Types ◽  
Genomic Regions

Introduction:Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates.Methods:The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases.Results:Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants.Conclusions:The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

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