Recombination and Selection at Brassica Self-Incompatibility Loci

Abstract In Brassica species, self-incompatibility is controlled genetically by haplotypes involving two known genes, SLG and SRK, and possibly an as yet unknown gene controlling pollen incompatibility types. Alleles at the incompatibility loci are maintained by frequency-dependent selection, and diversity at SLG and SRK appears to be very ancient, with high diversity at silent and replacement sites, particularly in certain “hypervariable portions of the genes. It is important to test whether recombination occurs in these genes before inferences about function of different parts of the genes can be made from patterns of diversity within their sequences. In addition, it has been suggested that, to maintain the relationship between alleles within a given S-haplotype, recombination is suppressed in the S-locus region. The high diversity makes many population genetic measures of recombination inapplicable. We have analyzed linkage disequilibrium within the SLG gene of two Brassica species, using published coding sequences. The results suggest that intragenic recombination has occurred in the evolutionary history of these alleles. This is supported by patterns of synonymous nucleotide diversity within both the SLG and SRK genes, and between domains of the SRK gene. Finally, clusters of linkage disequilibrium within the SLG gene suggest that hypervariable regions are under balancing selection, and are not merely regions of relaxed selective constraint.

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Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus

Genetics Research ◽

10.1017/s0016672303006347 ◽

2003 ◽

Vol 82 (2) ◽

pp. 89-99 ◽

Cited By ~ 64

Author(s):

ADAM D. RICHMAN ◽

L. GERARDO HERRERA ◽

DEANNA NASH ◽

MIKKEL H. SCHIERUP

Keyword(s):

Linkage Disequilibrium ◽

Mhc Class Ii ◽

Peromyscus Maniculatus ◽

De Novo ◽

Class Ii ◽

Intragenic Recombination ◽

Allelic Polymorphism ◽

Sequence Motifs ◽

Cell Surface Antigens ◽

History Of

The MHC class II loci encoding cell surface antigens exhibit extremely high allelic polymorphism. There is considerable uncertainty in the literature over the relative roles of recombination and de novo mutation in generating this diversity. We studied class II sequence diversity and allelic polymorphism in two populations of Peromyscus maniculatus, which are among the most widespread and abundant mammals of North America. We find that intragenic recombination (or gene conversion) has been the predominant mode for the generation of allelic polymorphism in this species, with the amount of population recombination per base pair exceeding mutation by at least an order of magnitude during the history of the sample. Despite this, patchwork motifs of sites with high linkage disequilibrium are observed. This does not appear to be consistent with the much larger amount of recombination versus mutation in the history of the sample, unless the recombination rate is highly non-uniform over the sequence or selection maintains certain sites in linkage disequilibrium. We conclude that selection is most likely to be responsible for preserving sequence motifs in the presence of abundant recombination.

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Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes

Genetics ◽

10.1093/genetics/159.4.1833 ◽

2001 ◽

Vol 159 (4) ◽

pp. 1833-1844 ◽

Cited By ~ 1

Author(s):

Mikkel H Schierup ◽

Anders M Mikkelsen ◽

Jotun Hein

Keyword(s):

Major Histocompatibility Complex ◽

Phylogenetic Tree ◽

Balancing Selection ◽

Nucleotide Sequences ◽

Recombination Process ◽

Self Incompatibility ◽

Selection Coefficient ◽

Histocompatibility Complex ◽

A Site ◽

Possible Cause

AbstractUsing a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

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Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽

10.1093/genetics/155.2.863 ◽

2000 ◽

Vol 155 (2) ◽

pp. 863-872 ◽

Cited By ~ 14

Author(s):

Helmi Kuittinen ◽

Montserrat Aguadé

Keyword(s):

Nucleotide Diversity ◽

Direct Relationship ◽

Selective Sweep ◽

Balancing Selection ◽

Neutral Theory ◽

Low Frequency ◽

The Other ◽

Nucleotide Variation ◽

Rapid Population Growth ◽

History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

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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.

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A Postal Survey of Hereditary Hemorrhagic Telangectasia in the Northeast of England

Allergy & Rhinology ◽

10.2500/ar.2015.6.0114 ◽

2015 ◽

Vol 6 (1) ◽

pp. ar.2015.6.0114 ◽

Cited By ~ 2

Author(s):

Yujay Ramakrishnan ◽

Isma Z. Iqbal ◽

Mark Puvanendran ◽

Mohamed Reda ElBadawey ◽

Sean Carrie

Keyword(s):

Family History ◽

Treatment Plan ◽

Positive Family History ◽

Tertiary Hospital ◽

Postal Survey ◽

History Of ◽

Unknown Gene ◽

Specific Education ◽

Nose And Throat

The aim of this study is to identify the demographics and epistaxis burden of hereditary hemorrhagic telangiectasia (HHT). A questionnaire was sent to participants with HHT who were recruited from a prospectively maintained respiratory clinic data base in a tertiary hospital. Details on demographics, HHT symptoms, family history, epistaxis severity, and treatment received were recorded. There were 34 of 60 responses (57%). Two responses were from families of the deceased. Of the 32 evaluable patients (men, 14; women 18), the average age was 51 years (range, 23–78 years). The average age of HHT diagnosis was 31 years (range, 3–61 years). The diagnosis of HHT was made by the respiratory team in 13 patients; neurologist (2); ear, nose, and throat (ENT) specialist (4); general practitioner (5); hematologist (4); gastroenterologist (1); and not mentioned in two patients. Twenty-seven of 32 patients (84%) had a positive family history of HHT. Only 13 patients had formal genetic testing (4 endoglin, 1 activin receptor–like kinase, 8 unknown gene). All patients who presented to the respiratory clinic had a background of epistaxis, which was noted on presentation. The average age at initial epistaxis was 14 years (range, 2–50 years). The frequency of epistaxis was daily 63% (n = 20), weekly 9% (3), monthly 16% (5), and a few times a year 10% (3), and unstated in one patient. Nine of 32 patients (28%) required a transfusion. Six patients thought that they were unable to perform daily activities due to epistaxis. Only 15 of 32 patients (47%) were under the care of an ENT specialist. The treatment plan for epistaxis management was deemed good by 7 patients, adequate in 8, poor in 6, and not stated by 11 patients. In conclusion, this survey is the first to quantify the epistaxis burden within the northeast of England. The management of epistaxis needs specific education and treatment to optimize the quality of life among these patients.

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Molecular Characterization of S Locus Genes, SLG and SRK, in a Pollen-Recessive Self-Incompatibility Haplotype of Brassica rapa L

Genetics ◽

10.1093/genetics/149.3.1587 ◽

1998 ◽

Vol 149 (3) ◽

pp. 1587-1597 ◽

Cited By ~ 5

Author(s):

Katsunori Hatakeyama ◽

Takeshi Takasaki ◽

Masao Watanabe ◽

Kokichi Hinata

Keyword(s):

Brassica Rapa ◽

Genomic Dna ◽

Transmembrane Domain ◽

Brassica Species ◽

Self Incompatibility ◽

S Locus ◽

Intron Sequence ◽

High Degree ◽

Degree Of Similarity

Abstract In Brassica species that exhibit self-incompatibility, two genes, SLG and SRK, at the S locus are involved in the recognition reaction with self and non-self pollen. From a pollen-recessive S29 haplotype of Brassica rapa, both cDNA and genomic DNA clones for these two genes were isolated and characterized. The nucleotide sequence for the S domain of SRK29 showed a high degree of similarity with that of SLG29, and they belong to Class II type. RNA gel blot analysis showed that the transcript of SLG29 consisted of the first and second exons, and no other transcript containing any part of the intron sequence was detected. Because no transmembrane domain was encoded by the second exon of SLG29, SLG29 was designated a secreted type glycoprotein. SLGs of two other pollen-recessive haplotypes, S40 and S44, of B. rapa also had a similar structure to that of SLG29. Previously, SLG2 from a pollen-recessive haplotype, S2, of Brassica oleracea was found to produce two different transcripts, one for the secreted type glycoprotein and the other for a putative membrane-anchored form of SLG. Therefore, the nature of these SLGs from pollen-recessive haplotypes of B. rapa is different from that of SLG2 of B. oleracea.

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Sequence Diversity and Molecular Evolution of the Leukotoxin (lktA) Gene in Bovine and Ovine Strains ofMannheimia (Pasteurella)haemolytica

Journal of Bacteriology ◽

10.1128/jb.183.4.1394-1404.2001 ◽

2001 ◽

Vol 183 (4) ◽

pp. 1394-1404 ◽

Cited By ~ 40

Author(s):

Robert L. Davies ◽

Thomas S. Whittam ◽

Robert K. Selander

Keyword(s):

Molecular Evolution ◽

Allelic Diversity ◽

Pasteurella Haemolytica ◽

Intragenic Recombination ◽

Allelic Variants ◽

Amino Acid Divergence ◽

History Of ◽

Nucleotide Divergence ◽

Pasteurella Trehalosi ◽

Different Sources

ABSTRACT The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella)haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains representing the various evolutionary lineages and serotypes of the species. Eight major allelic variants (1.4 to 15.7% nucleotide divergence) were identified; these have mosaic structures of varying degrees of complexity reflecting a history of horizontal gene transfer and extensive intragenic recombination. The presence of identical alleles in strains of different genetic backgrounds suggests that assortative (entire gene) recombination has also contributed to strain diversification in M. haemolytica. Five allelic variants occur only in ovine strains and consist of recombinant segments derived from as many as four different sources. Four of these alleles consist of DNA (52.8 to 96.7%) derived from the lktA gene of the two related species Mannheimia glucosida andPasteurella trehalosi, and four contain recombinant segments derived from an allele that is associated exclusively with bovine or bovine-like serotype A2 strains. The two major lineages of ovine serotype A2 strains possess lktA alleles that have very different evolutionary histories and encode divergent leukotoxins (5.3% amino acid divergence), but both contain segments derived from the bovine allele. Homologous segments of donor and recipient alleles are identical or nearly identical, indicating that the recombination events are relatively recent and probably postdate the domestication of cattle and sheep. Our findings suggest that host switching of bovine strains from cattle to sheep, together with inter- and intraspecies recombinational exchanges, has played an important role in generating leukotoxin diversity in ovine strains. In contrast, there is limited allelic diversity of lktA in bovine strains, suggesting that transmission of strains from sheep to cattle has been less important in leukotoxin evolution.

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Inferring the evolutionary history of outcrossing populations through computing a multiallelic linkage–linkage disequilibrium map

Methods in Ecology and Evolution ◽

10.1111/2041-210x.12428 ◽

2015 ◽

Vol 6 (11) ◽

pp. 1259-1269 ◽

Cited By ~ 6

Author(s):

Xuli Zhu ◽

Fang Xu ◽

Shu Zhao ◽

Wenhao Bo ◽

Libo Jiang ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Evolutionary History ◽

History Of ◽

Linkage Disequilibrium Map

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Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data

Molecular Biology and Evolution ◽

10.1093/molbev/msz258 ◽

2019 ◽

Vol 37 (4) ◽

pp. 1193-1201 ◽

Cited By ~ 2

Author(s):

Mathieu Genete ◽

Vincent Castric ◽

Xavier Vekemans

Keyword(s):

De Novo ◽

Balancing Selection ◽

Methodological Approach ◽

Natural Populations ◽

Sequence Divergence ◽

Reference Database ◽

Self Incompatibility ◽

Sequencing Data ◽

Allelic Series ◽

S Alleles

Abstract Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.

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