Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana

A local score approach improves GWAS resolution and detects minor QTL: application to Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches isolates

Quantitative trait loci (QTL) with small effects, which are pervasive in quantitative phenotypic variation, are difficult to detect in genome-wide association studies (GWAS). To improve their detection, we propose to use a local score approach that accounts for the surrounding signal due to linkage disequilibrium, by accumulating association signals from contiguous single markers. Simulations revealed that, in a GWAS context with high marker density, the local score approach outperforms single SNP p-value-based tests for detecting minor QTL (heritability of 5-10%) and is competitive with regard to alternative methods, which also aggregate p-values. Using more than five million SNPs, this approach was applied to identify loci involved in Quantitative Disease Resistance (QDR) to different isolates of the plant root rot pathogen Aphanomyces euteiches, from a GWAS performed on a collection of 174 accessions of the model legume Medicago truncatula. We refined the position of a previously reported major locus, underlying MYB/NB-ARC/tyrosine kinase candidate genes conferring resistance to two closely related A. euteiches isolates belonging to pea pathotype I. We also discovered a diversity of minor resistance QTL, not detected using p-value-based tests, some of which being putatively shared in response to pea (pathotype I and III) and/or alfalfa (race 1 and 2) isolates. Candidate genes underlying these QTL suggest pathogen effector recognition and plant proteasome as key functions associated with M. truncatula resistance to A. euteiches. GWAS on any organism can benefit from the local score approach to uncover many weak-effect QTL.

Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario

Interlocus gene conversion is a major evolutionary force that drives the concerted evolution of duplicated genomic regions. Theoretical models successfully have addressed the effects of interlocus gene conversion and the importance of crossover in the evolutionary fate of gene families and duplications but have not considered complex recombination scenarios, such as the presence of hotspots. To study the interplay between interlocus gene conversion and crossover, we have developed a forward-time simulator that allows the exploration of a wide range of interlocus gene conversion rates under different crossover models. Using it, we have analyzed patterns of nucleotide variation and linkage disequilibrium within and between duplicate regions, focusing on a neutral scenario with constant population size and validating our results with the existing theoretical models. We show that the interaction of gene conversion and crossover is nontrivial and that the location of crossover junctions is a fundamental determinant of levels of variation and linkage disequilibrium in duplicated regions. We also show that if crossover activity between duplications is strong enough, recurrent interlocus gene conversion events can break linkage disequilibrium within duplicates. Given the complex nature of interlocus gene conversion and crossover, we provide a framework to explore their interplay to help increase knowledge on molecular evolution within segmental duplications under more complex scenarios, such as demographic changes or natural selection.

Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution

The common morning glory (Ipomoea purpurea) is an annual vine native to Central and Southern Mexico. The genetics of flower color polymorphisms and interactions with the biotic environment have been extensively studied in I. purpurea and in its sister species I. nil. In this study, we examine nucleotide sequence polymorphism in 11 loci, 9 of which are known to participate in a pathway that produces floral pigments. A sample of 30 I. purpurea accessions from the native range of Central and Southern Mexico comprise the data, along with one accession from each of the two sister species I. alba and I. nil. We observe moderate levels of nucleotide sequence polymorphism of ~1%. The ratio of recombination to mutation parameter estimates (ρ/θ) of ~2.5 appears consistent with a mixed-mating system. Ipomoea resequencing data from these genic regions are noteworthy in providing a good fit to the standard neutral model of molecular evolution. The derived silent site frequency spectrum is very close to that predicted by coalescent simulations of a drift-mutation process, and Tajima's D values are not significantly different from expectations under neutrality.

Population genomics in bacteria: a case study of Staphylococcus aureus

We analyzed the genome-wide pattern of single nucleotide polymorphisms (SNPs) in a sample with 12 strains of Staphylococcus aureus. Population structure of S. aureus seems to be complex, and the 12 strains were divided into five groups, named A, B, C, D, and E. We conducted a detailed analysis of the topologies of gene genealogies across the genomes and observed a high rate and frequency of tree-shape switching, indicating extensive homologous recombination. Most of the detected recombination occurred in the ancestral population of A, B, and C, whereas there are a number of small regions that exhibit evidence for homologous recombination with a distinct related species. As such regions would contain a number of novel mutations, it is suggested that homologous recombination would play a crucial role to maintain genetic variation within species. In the A-B-C ancestral population, we found multiple lines of evidence that the coalescent pattern is very similar to what is expected in a panmictic population, suggesting that this population is suitable to apply the standard population genetic theories. Our analysis showed that homologous recombination caused a dramatic decay in linkage disequilibrium (LD) and there is almost no LD between SNPs with distance more than 10 kb. Coalescent simulations demonstrated that a high rate of homologous recombination-a relative rate of 0.6 to the mutation rate with an average tract length of about 10 kb-is required to produce patterns similar to those observed in the S. aureus genomes. Our results call for more research into the evolutionary role of homologous recombination in bacterial populations.

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

INTRODUCTION

Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR).

RESULTS

Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (d (S) = 0.029, d (N) = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (d (S) = 0.069 vs. 0.029, d (N) = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r (2) = 0.5 to r (2) = 0.1 within a 2-kb span.

CONCLUSION

These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.

Application of association mapping to understanding the genetic diversity of plant germplasm resources

Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.

The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms

BACKGROUND

Despite its role as a generator of haplotypic variation, little is known about how the rates of recombination evolve across taxa. Recombination is a very labile force, susceptible to evolutionary and life trait related processes, which have also been correlated with general levels of genetic diversity. For example, in plants, it has been shown that long-lived outcrossing taxa, such as trees, have higher heterozygosity (He) at SSRs and allozymes than selfing or annual species. However, some of these tree taxa have surprisingly low levels of nucleotide diversity at the DNA sequence level, which points to recombination as a potential generator of genetic diversity in these organisms. In this study, we examine how genome-wide and within-gene rates of recombination evolve across plant taxa, determine whether such rates are influenced by the life-form adopted by species, and evaluate if higher genome-wide rates of recombination translate into higher He values, especially in trees.

RESULTS

Estimates of genome-wide (cM/Mb) recombination rates from 81 higher plants showed a significant phylogenetic signal. The use of different comparative phylogenetic models demonstrated that there is a positive correlation between recombination rate and He (0.83 +/- 0.29), and that trees have higher rates of genome-wide recombination than short-lived herbs and shrubs. A significant taxonomic component was further made evident by our models, as conifers exhibited lower recombination rates than angiosperms. This trend was also found at the within-gene level.

CONCLUSIONS

Altogether, our results illustrate how both common ancestry and life-history traits have to be taken into account for understanding the evolution of genetic diversity and genomic rates of recombination across plant species, and highlight the relevance of species life forms to explain general levels of diversity and recombination.

Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in approximately 10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have approximately 45% higher recombination per kilobase than outcrossing A. lyrata.

Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations

Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is "association mapping" in populations, which is widely hoped to help find genes that influence genetic diseases (Carlson et al., 2004; Clark, 2003). Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to single-crossover recombination. However, gene-conversion is an important, and more common, form of (two-crossover) recombination which has been much less investigated in the algorithms literature. In this paper, we explicitly incorporate gene-conversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossing-over and gene-conversion (along with single-nucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of gene-conversion into recently developed discrete methods (Myers and Griffiths, 2003; Song et al., 2005) that compute lower and upper-bound information on the amount of needed recombination without gene-conversion. We first examine the most natural extension of the lower bound methods from Myers and Griffiths (2003), showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integer-linear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed single-crossovers and gene-conversions, along with explicit networks showing a putative history of mutations, single-crossovers and gene-conversions. Both lower and upper bound methods can handle data with missing entries, and the upper bound method can be used to infer missing entries with high accuracy. We validate the significance of these methods by showing that they can be effectively used to distinguish simulation-derived sequences generated without gene-conversion from sequences that were generated with gene-conversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified (Plagnol et al., 2006), where gene-conversion may have played a significant role. Demonstration software is available at www.csif.cs.ucdavis.edu/~gusfield.

Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata

BACKGROUND

Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.

PRINCIPAL FINDINGS

We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.

CONCLUSIONS

Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.

Demographic history of european populations of Arabidopsis thaliana

The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east approximately 10,000 years ago, with a rate of westward spread of approximately 0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition.

Local patterns of nucleotide polymorphism are highly variable in the selfing species Arabidopsis thaliana

Neighboring genes predictably share similar evolutionary histories to an extent delineated by recombination. This correlation should extend across multiple linked genes in a selfing species such as Arabidopsis thaliana due to its low effective recombination rate. To test this prediction, we performed a molecular population genetics analysis of nucleotide polymorphism and divergence in chromosomal regions surrounding four low-diversity loci. Three of these loci, At1g67140, At3g03700, and TERMINAL FLOWER1 (TFL1), have been previously implicated as targets of selection and we would predict stronger correlations in polymorphism between neighboring loci due to genetic hitchhiking around these loci. The remaining locus, At1g04300, was identified in a study of linkage disequilibrium surrounding the CRYPTOCHROME2 (CRY2) locus. Although we found broad valleys of reduced nucleotide variation around two of our focal genes, At1g67140 and At3g03700, all chromosomal regions exhibited extreme variation in the patterns of polymorphism and evolution between neighboring loci. Although three of our four regions contained potential targets of selection, application of the composite-likelihood-ratio test of selection in conjunction with a goodness-of-fit test supports the selection hypothesis only for the region containing At3g03700. The degree of discordance in evolutionary histories between linked loci within each region generally correlated with estimates of recombination and linkage disequilibrium for that region, with the exception of the region containing At1g04300. We discuss the implications of these data for future population genetics analyses and genomics studies in A. thaliana.

Recombination and linkage disequilibrium in Arabidopsis thaliana

Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and 'hide-the-SNP' simulations suggest that genome-wide association mapping will require only 40%-50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome-wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms.

Recombination: an underappreciated factor in the evolution of plant genomes

Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.

The road to crossovers: plants have their say

Crossovers involve the reciprocal exchange of large fragments of genetic material between homologous chromosomes during meiosis. In this way, crossovers are the basis of genetics. Remarkably, the number and distribution of crossovers on chromosomes are closely controlled. Data from various model organisms (notably Saccharomyces cerevisiae) show that the distribution of crossovers results from a series of tightly regulated events involving the formation and repair of double-strand breaks and interference. Recent advances in genetic and cytological tools, particularly for studying Arabidopsis thaliana, have enabled crossover control in plants to be studied in more detail. In this article, we discuss the contribution of plant studies to meiosis research, particularly to our understanding of crossover control and interference, and we evaluate models of interference.

Insights into recombination from population genetic variation

Patterns of genetic variation in natural populations are shaped by, and hence carry valuable information about, the underlying recombination process. In the past five years, the increasing availability of large-scale population genetic data on dense sets of markers, coupled with advances in statistical methods for extracting information from these data, have led to several important advances in our understanding of the recombination process in humans. These advances include the identification of large numbers of 'hotspots', where recombination appears to take place considerably more frequently than in the surrounding sequence, and the identification of DNA sequence motifs that are associated with the locations of these hotspots.

Meiotic recombination hotspots in plants

Many studies have demonstrated that the distribution of meiotic crossover events along chromosomes is non-random in plants and other species with sexual reproduction. Large differences in recombination frequencies appear at several scales. On a large scale, regions of high and low rates of crossover have been found to alternate along the chromosomes in all plant species studied. High crossover rates have been reported to be correlated with several chromosome features (e.g. gene density and distance to the centromeres). However, most of these correlations cannot be extended to all plant species. Only a few plant species have been studied on a finer scale. Hotspots of meiotic recombination (i.e. DNA fragments of a few kilobases in length with a higher rate of recombination than the surrounding DNA) have been identified in maize and rice. Most of these hotspots are intragenic. In Arabidopsis thaliana, we have identified several DNA fragments (less than 5 kb in size) with genetic recombination rates at least 5 times higher than the whole-chromosome average [4.6 cM (centimorgan)/Mb], which are therefore probable hotspots for meiotic recombination. Most crossover breakpoints lie in intergenic or non-coding regions. Major efforts should be devoted to characterizing meiotic recombination at the molecular level, which should help to clarify the role of this process in genome evolution.

Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity

Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter (rho) relative to estimates of the mutation parameter (theta) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of rho/theta are much greater than expected, with a mean rho/theta approximately 1.5, similar to estimates from outcrossing species. We also estimate rho with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination.

Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis

Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.

Inferring population parameters from single-feature polymorphism data

This article is concerned with a statistical modeling procedure to call single-feature polymorphisms from microarray experiments. We use this new type of polymorphism data to estimate the mutation and recombination parameters in a population. The mutation parameter can be estimated via the number of single-feature polymorphisms called in the sample. For the recombination parameter, a two-feature sampling distribution is derived in a way analogous to that for the two-locus sampling distribution with SNP data. The approximate-likelihood approach using the two-feature sampling distribution is examined and found to work well. A coalescent simulation study is used to investigate the accuracy and robustness of our method. Our approach allows the utilization of single-feature polymorphism data for inference in population genetics.