Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Download Full-text

Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations

Theoretical and Applied Genetics ◽

10.1007/s00122-010-1382-x ◽

2010 ◽

Vol 121 (7) ◽

pp. 1209-1225 ◽

Cited By ~ 6

Author(s):

C. Y. Hao ◽

M. R. Perretant ◽

F. Choulet ◽

L. F. Wang ◽

E. Paux ◽

...

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Linkage Disequilibrium ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Genomic Region ◽

Chromosome 3B

Download Full-text

Variance in Estimated Pairwise Genetic Distance Under High versus Low Coverage Sequencing: the Contribution of Linkage Disequilibrium

10.1101/108928 ◽

2017 ◽

Author(s):

Max Shpak ◽

Yang Ni ◽

Jie Lu ◽

Peter Müller

Keyword(s):

Linkage Disequilibrium ◽

Genetic Distance ◽

Low Frequency ◽

Allele Frequencies ◽

High Coverage ◽

Pairwise Linkage Disequilibrium ◽

Pairwise Genetic Distance ◽

Linkage Disequilibria ◽

The Mean ◽

Low Coverage

AbstractThe mean pairwise genetic distance among haplotypes is an estimator of the population mutation rate θ and a standard measure of variation in a population. With the advent of next-generation sequencing (NGS) methods, this and other population parameters can be estimated under different modes of sampling. One approach is to sequence individual genomes with high coverage, and to calculate genetic distance over all sample pairs. The second approach, typically used for microbial samples or for tumor cells, is sequencing a large number of pooled genomes with very low individual coverage. With low coverage, pairwise genetic distances are calculated across independently sampled sites rather than across individual genomes. In this study, we show that the variance in genetic distance estimates is reduced with low coverage sampling if the mean pairwise linkage disequilibrium weighted by allele frequencies is positive. Practically, this means that if on average the most frequent alleles over pairs of loci are in positive linkage disequilibrium, low coverage sequencing results in improved estimates of θ, assuming similar per-site read depths. We show that this result holds under the expected distribution of allele frequencies and linkage disequilibria for an infinite sites model at mutation-drift equilibrium. From simulations, we find that the conditions for reduced variance only fail to hold in cases where variant alleles are few and at very low frequency. These results are applied to haplotype frequencies from a lung cancer tumor to compute the weighted linkage disequilibria and the expected error in estimated genetic distance using high versus low coverage.

Download Full-text

Faculty Opinions recommendation of Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1088665.542769 ◽

2007 ◽

Author(s):

Julin Maloof

Keyword(s):

Genetic Diversity ◽

Arabidopsis Thaliana ◽

Sequence Polymorphisms ◽

Common Sequence

Download Full-text

Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations

Genetics ◽

10.1093/genetics/157.2.899 ◽

2001 ◽

Vol 157 (2) ◽

pp. 899-909

Author(s):

Rongling Wu ◽

Zhao-Bang Zeng

Keyword(s):

Linkage Disequilibrium ◽

Complex Traits ◽

Positional Cloning ◽

Genome Structure ◽

Natural Populations ◽

Linkage Disequilibrium Mapping ◽

Linkage Disequilibria ◽

Time Simulation ◽

New Strategy ◽

Fisher Scoring Algorithm

Abstract A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the information about the linkage of the markers (as measured by recombination fraction) and the degree of their linkage disequilibrium created at a historic time. Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and positional cloning of the genes underlying both simple and complex traits.

Download Full-text

The Arabidopsis thaliana plasma membrane H(+)-ATPase multigene family. Genomic sequence and expression of a third isoform.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)77391-2 ◽

1990 ◽

Vol 265 (23) ◽

pp. 13601-13608

Author(s):

J.F. Harper ◽

L. Manney ◽

N.D. DeWitt ◽

M.H. Yoo ◽

M.R. Sussman

Keyword(s):

Arabidopsis Thaliana ◽

Plasma Membrane ◽

Multigene Family ◽

Genomic Sequence

Download Full-text

Distribution of the number of alleles in multigene families

Journal of Applied Probability ◽

10.1017/s0021900200043655 ◽

1992 ◽

Vol 29 (04) ◽

pp. 759-769

Author(s):

R. C. Griffiths

Keyword(s):

Stochastic Model ◽

Gene Conversion ◽

Lower Bounds ◽

Multigene Families ◽

Expected Number ◽

Allele Type ◽

The Mean

The distribution of the number of alleles in samples from r chromosomes is studied. The stochastic model used includes gene conversion within chromosomes and mutation at loci on the chromosomes. A method is described for simulating the distribution of alleles and an algorithm given for computing lower bounds for the mean number of alleles. A formula is derived for the expected number of samples from r chromosomes which contain the allele type of a locus chosen at random.

Download Full-text

The variance of linkage disequilibrium between three loci in a finite population

Canadian Journal of Genetics and Cytology ◽

10.1139/g83-026 ◽

1983 ◽

Vol 25 (2) ◽

pp. 139-145 ◽

Cited By ~ 3

Author(s):

C. Strobeck ◽

G. B. Golding

Keyword(s):

Linkage Disequilibrium ◽

Finite Population ◽

Intragenic Recombination ◽

Random Drift ◽

Third Order ◽

Linkage Disequilibria ◽

Order Of Magnitude ◽

Infinite Alleles Model

The variance of three-locus linkage disequilibria for an equilibrium infinite alleles model is solved numerically on a computer, using identity coefficients. It is shown that the variance of three-locus linkage disequilibrium created by random drift, although smaller than the variance of two-locus linkage disequilibrium, is of the same order of magnitude. Hence third-order disequilibria are not necessarily good indications of selection. The formula for the variance of linkage disequilibrium is given when there is no recombination between the genes. This model can also be interpreted as intragenic recombination between three sites within a gene.

Download Full-text

Genetic diversity of Avena strigosa Schreb. ecotypes on the basis of isoenzyme markers

Biodiversity Research and Conservation ◽

10.2478/v10119-009-0013-3 ◽

2009 ◽

Vol 15 (1) ◽

pp. 23-28 ◽

Cited By ~ 4

Author(s):

Katarzyna Kubiak

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Avena Strigosa ◽

Total Genetic Diversity ◽

Geographical Regions ◽

The World ◽

Total Variability ◽

The Mean ◽

Intrapopulation Diversity ◽

Very High

Genetic diversity ofAvena strigosaSchreb. ecotypes on the basis of isoenzyme markersGenetic diversity was analyzed in 19 ecotypes of the diploid oatA. strigosaoriginating from various geographical regions of the world. Six isoenzyme systems (AAT, ACP, EST, LAP, MDH, PX) were studied and 16 loci were identified. Only two loci (Est4andMdh2) were polymorphic. Ecotypes were characterized by the percentage of polymorphic loci (P=3.3%), the mean number of alleles per locus (A=1.04) and intrapopulation diversity (HS=0.013). Total genetic diversity (HT=0.07) and interpopulation diversity (DST=0.057) were examined as well. The value of the coefficient of gene differentiation (GST=0.821) indicated that diversity among populations was an important contributor to total variability. Genetic similarity betweenA. strigosapopulations was very high (IN=0.94). Cluster analysis did not demonstrate strongly differentiated groups among the ecotypes examined.

Download Full-text

Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

Plant Genetic Resources ◽

10.1017/s1479262114000525 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S125-S129

Author(s):

Gi-An Lee ◽

Sok-Young Lee ◽

Ho-Sun Lee ◽

Kyung-Ho Ma ◽

Jae-Gyun Gwag ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Management ◽

Underutilized Crops ◽

Crop Species ◽

Closely Related Species ◽

Polymorphic Loci ◽

Allele Number ◽

The Mean ◽

Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

Download Full-text