A Chromosomal Region Promoting Outcrossing in a Conifer

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1283-1289
Author(s):  
Claire G Williams ◽  
Yi Zhou ◽  
Sarah E Hall
Keyword(s):  
Linkage Group ◽  
Chromosomal Region ◽  
Expressed Sequence Tag ◽  
Balancing Selection ◽  
Lethal Factor ◽  
Genetic Mechanism ◽  
Heterozygote Advantage ◽  
Experimental Profile ◽  
Gametic Selection ◽  
Pinus Taeda L

Abstract Prefertilization mechanisms influencing selfing rates are thought to be absent in conifers. Outcrossing in conifers is promoted via an embryo-lethal system, but the genetic mechanism is poorly understood. This study is the first experimental profile of the genetic mechanism promoting outcrossing in conifers. Molecular dissection of a Pinus taeda L. selfed pedigree detected a chromosomal region identified as PtTX3020-RPtest9. Within this region, a semilethal factor was tightly linked (r = 0.0076) to a polymorphic expressed sequence tag (EST). The linkage group flanking the lethal factor showed strong heterozygote advantage. Using genotypic frequencies for the linkage group, three hypotheses about the semilethal factor could be tested: (1) the presence of a balanced lethal system, i.e., a lethal factor present in each of the two marker intervals; (2) gametic selection operative prior to fertilization; and (3) a stage-specific lethal factor. Selection acted via the embryo-lethal system. No support for a genetic mechanism operating prior to fertilization was found. The semilethal factor exerted no effect after embryo maturity. The genetic mechanism promoting outcrossing in P. taeda L. appears to have a balancing selection system due to either pseudo-overdominance or true overdominance.

Anchored Reference Loci in Loblolly Pine (Pinus taeda L.) for Integrating Pine Genomics

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 799-809 ◽  
Author(s):  
Garth R Brown ◽  
Edward E Kadel ◽  
Daniel L Bassoni ◽  
Kristine L Kiehne ◽  
Berhanu Temesgen ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Comparative Mapping ◽  
Expressed Sequence Tag ◽  
Single Species ◽  
Douglas Fir ◽  
Genetic Maps ◽  
Multiple Sources ◽  
Primer Sets ◽  
Pinus Taeda L

Abstract Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37–61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a “generic” pine map and serving as a foundation for studies on genome organization and evolution.

scholarly journals Molecular-marker-based Genetic Analysis of Tepary Bean-derived Common Bacterial Blight Resistance in Different Developmental Stages of Common Bean

1997 ◽  
Vol 122 (3) ◽  
pp. 329-337 ◽  
Author(s):  
Geunhwa Jung ◽  
Paul W. Skroch ◽  
Dermot P. Coyne ◽  
James Nienhuis ◽  
E. Arnaud-Santana ◽  
...  
Keyword(s):  
Linkage Group ◽  
Common Bean ◽  
Linkage Map ◽  
Recombinant Inbred ◽  
Bacterial Blight ◽  
Chromosomal Region ◽  
Bacterial Disease ◽  
Common Bacterial Blight ◽  
Group 5 ◽  
Group 1

Randomly amplified polymorphic DNA (RAPD) molecular markers were used to construct a partial genetic linkage map in a recombinant inbred population derived from the common bean (Phaseolus vulgaris L.) cross PC-50 × XAN-159 for studying the genetics of bacterial disease resistance in common bean. The linkage map spanned 426 cM and included 168 RAPD markers and 2 classical markers with 11 unassigned markers. The seventy recombinant inbred lines were evaluated for resistance to two strains of common bacterial blight [Xanthomonas campestris pv. phaseoli (Smith) Dye] (Xcp). Common bacterial blight (CBB) resistance was evaluated for Xcp strain EK-11 in later-developed trifoliolate leaves and for Xcp strains, DR-7 and EK-11, in first trifoliolate leaves, seeds, and pods. One to four quantitative trait loci (QTLs) accounted for 18% to 53% of the phenotypic variation for traits. Most significant effects for CBB resistance were associated with one chromosomal region on linkage group 5 and with two regions on linkage group 1, of the partial linkage map. The chromosomal region (a 13-cM interval) in linkage group 5 was significantly associated with resistance to Xcp strains DR-7 and EK-11 in leaves, pods, and seeds. The regions in linkage group 1 were also significantly associated with resistance to both Xcp strains in more than one plant organ. In addition, a seedcoat pattern gene (C) and a flower color gene (vlae) were mapped in linkage groups 1 and 5, respectively, of the partial linkage map. The V locus was found to be linked to a QTL with a major effect on CBB resistance.

scholarly journals HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation

2019 ◽  
Vol 37 (3) ◽  
pp. 639-650 ◽  
Author(s):  
Jatin Arora ◽  
Federica Pierini ◽  
Paul J McLaren ◽  
Mary Carrington ◽  
Jacques Fellay ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Human Leukocyte ◽  
Hla Class I ◽  
T Cell Response ◽  
Cytotoxic T Cell ◽  
Heterozygote Advantage ◽  
Hla Alleles ◽  
Relative Contribution ◽  
Peptide Presentation ◽  
Hiv 1

Abstract Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual’s HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.

scholarly journals Transition from background selection to associative overdominance promotes diversity in regions of low recombination

2019 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Fanny Pouyet ◽  
Laurent Excoffier ◽  
Stephan Peischl
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Purifying Selection ◽  
Heterozygote Advantage ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Recombination Rates ◽  
Locus Model ◽  
Genome Wide ◽  
Linked Selection

SummaryLinked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworth et al. 1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyet et al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.

scholarly journals Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae)

2020 ◽  
Vol 7 (3) ◽  
pp. 191720 ◽  
Author(s):  
Kristen Côté ◽  
Andrew M. Simons
Keyword(s):  
Genetic Variation ◽  
Balancing Selection ◽  
Rank Order ◽  
Empirical Test ◽  
Heterozygote Advantage ◽  
Environment Interaction ◽  
Fluctuating Selection ◽  
Long Term Study ◽  
Genotype Environment Interaction ◽  
Lobelia Inflata

High levels of genetic variation are often observed in natural populations, suggesting the action of processes such as frequency-dependent selection, heterozygote advantage and variable selection. However, the maintenance of genetic variation in fitness-related traits remains incompletely explained. The extent of genetic variation in obligately self-fertilizing populations of Lobelia inflata (Campanulaceae L.) strongly implies balancing selection. Lobelia inflata thus offers an exceptional opportunity for an empirical test of genotype-environment interaction (G × E) as a variance-maintaining mechanism under fluctuating selection: L. inflata is monocarpic and reproduces only by seed, facilitating assessment of lifetime fitness; genome-wide homozygosity precludes some mechanisms of balancing selection, and microsatellites are, in effect, genotypic lineage markers. Here, we find support for the temporal G × E hypothesis using a manipulated space-for-time approach across four environments: a field environment, an outdoor experimental plot and two differing growth-chamber environments. High genetic variance was confirmed: 83 field-collected individuals consisted of 45 distinct microsatellite lineages with, on average, 4.5 alleles per locus. Rank-order fitness, measured as lifetime fruit production in 16 replicated multilocus genotypes, changed significantly across environments. Phenotypic differences among microsatellite lineages were detected. Results thus support the G × E hypothesis in principle. However, the evaluation of the effect size of this mechanism and fitness effects of life-history traits will require a long-term study of fluctuating selection on labelled genotypes in the field.

Resolving the paradox of common, harmful, heritable mental disorders: Which evolutionary genetic models work best?

2006 ◽  
Vol 29 (4) ◽  
pp. 385-404 ◽  
Author(s):  
Matthew C. Keller ◽  
Geoffrey Miller
Keyword(s):  
Mental Disorders ◽  
Mental Disorder ◽  
Human Behavior ◽  
Behavior Genetics ◽  
Balancing Selection ◽  
Paternal Age ◽  
Heterozygote Advantage ◽  
Psychiatric Genetics ◽  
Apparent Paradox ◽  
Evolutionary Genetic

Given that natural selection is so powerful at optimizing complex adaptations, why does it seem unable to eliminate genes (susceptibility alleles) that predispose to common, harmful, heritable mental disorders, such as schizophrenia or bipolar disorder? We assess three leading explanations for this apparent paradox from evolutionary genetic theory: (1) ancestral neutrality (susceptibility alleles were not harmful among ancestors), (2) balancing selection (susceptibility alleles sometimes increased fitness), and (3) polygenic mutation-selection balance (mental disorders reflect the inevitable mutational load on the thousands of genes underlying human behavior). The first two explanations are commonly assumed in psychiatric genetics and Darwinian psychiatry, while mutation-selection has often been discounted. All three models can explain persistent genetic variance in some traits under some conditions, but the first two have serious problems in explaining human mental disorders. Ancestral neutrality fails to explain low mental disorder frequencies and requires implausibly small selection coefficients against mental disorders given the data on the reproductive costs and impairment of mental disorders. Balancing selection (including spatio-temporal variation in selection, heterozygote advantage, antagonistic pleiotropy, and frequency-dependent selection) tends to favor environmentally contingent adaptations (which would show no heritability) or high-frequency alleles (which psychiatric genetics would have already found). Only polygenic mutation-selection balance seems consistent with the data on mental disorder prevalence rates, fitness costs, the likely rarity of susceptibility alleles, and the increased risks of mental disorders with brain trauma, inbreeding, and paternal age. This evolutionary genetic framework for mental disorders has wide-ranging implications for psychology, psychiatry, behavior genetics, molecular genetics, and evolutionary approaches to studying human behavior.

The role of infectious disease, inbreeding and mating preferences in maintaining MHC genetic diversity: an experimental test

1994 ◽  
Vol 346 (1317) ◽  
pp. 369-378 ◽  
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Natural Populations ◽  
House Mice ◽  
Heterozygote Advantage ◽  
Immune Recognition ◽  
Mating Preferences ◽  
Conventional View ◽  
Mhc Genes ◽  
Allele Specific

In house mice, and probably most mammals, major histocompatibility complex (MHC) gene products influence both immune recognition and individual odours in an allele-specific fashion. Although it is generally assumed that some form of pathogen-driven balancing selection is responsible for the unprecedented genetic diversity of MHC genes, the MHC-based mating preferences observed in house mice are sufficient to account for the genetic diversity of MHC genes found in this and other vertebrates. These MHC disassortative mating preferences are completely consistent with the conventional view that pathogen-driven MHC heterozygote advantage operates on MHC genes. This is because such matings preferentially produce MHC-heterozygours progeny, which could enjoy enhanced disease resistance. However, such matings could also function to avoid genome-wide inbreeding. To discriminate between these two hypotheses we measured the fitness consequences of both experimentally manipulated levels of inbreeding and MHC homozygosity and heterozygosity in semi-natural populations of wild-derived house mice. We were able to measure a fitness decline associated with inbreeding, but were unable to detect fitness declines associated with MHC homozygosity. These data suggest that inbreeding avoidance may be the most important function of MHC-based mating preferences and therefore the fundamental selective force diversifying MHC genes in species with such mating patterns. Although controversial, this conclusion is consistent with the majority of the data from the inbreeding and immunological literature.

scholarly journals Genetic organization of the unc-60 region in Caenorhabditis elegans.

Genetics ◽  
1988 ◽  
Vol 118 (1) ◽  
pp. 49-59
Author(s):  
K S McKim ◽  
M F Heschl ◽  
R E Rosenbluth ◽  
D L Baillie
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Gene Order ◽  
Chromosomal Region ◽  
Essential Genes ◽  
Ethyl Methanesulfonate ◽  
Induced Mutations ◽  
Nematode Caenorhabditis Elegans ◽  
Genetic Organization ◽  
Muscle Structure

Abstract We have investigated the chromosomal region around unc-60 V, a gene affecting muscle structure, in the nematode Caenorhabditis elegans. The region studied covers 3 map units and lies at the left end of linkage group (LG) V. Compared to the region around dpy-11 (at the center of LGV), the unc-60 region has relatively few visible genes per map unit. We found the same to be true for essential genes. By screening simultaneously for recessive lethals closely linked to either dpy-11 or unc-60, we recovered ethyl methanesulfonate-induced mutations in 10 essential genes near dpy-11 but in only two genes near unc-60. Four deficiency breakpoints were mapped to the unc-60 region. Using recombination and deficiency mapping we established the following gene order: let-336, unc-34, let-326, unc-60, emb-29, let-426. Regarding unc-60 itself, we compared the effect of ten alleles (including five isolated during this study) on hermaphrodite mobility and fecundity. We used intragenic mapping to position eight of these alleles. The results show that these alleles are not distributed uniformly within the gene, but map to two groups approximately 0.012 map unit apart.

scholarly journals Supergene formation is associated with a major shift in genome-wide patterns of diversity in a butterfly

2021 ◽  
Author(s):  
María Ángeles Rodríguez de Cara ◽  
Paul Jay ◽  
Mathieu Chouteau ◽  
Annabel Whibley ◽  
Barbara Huber ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Mate Preferences ◽  
Heterozygote Advantage ◽  
Effective Population ◽  
Adaptive Introgression ◽  
Continental Scale ◽  
Geographic Structure ◽  
Genome Wide ◽  
Genetic Diversity And Structure

AbstractSelection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Adaptive introgression provides a way to assess how adaptive evolution at one locus impacts whole-genome biology. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform subclade. H. numata is known to have evolved a supergene via the introgression of an adaptive inversion about 2.2 million years ago, triggering a polymorphism maintained by balancing selection. This locus controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics, and butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages in a phylogenetic framework. We show that H. numata populations which carry the introgressed inversions in a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest diversity and demographic estimates in the entire clade, as well as a remarkably low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show the lowest effective population sizes and genetic diversity in the clade, and higher levels of geographical structure across the continent. This suggests that the large effective population size of polymorphic populations could be a property associated with harbouring the supergene. Our results are consistent with the hypothesis that the adaptive introgression of the inversion triggered a shift from directional to balancing selection and a change in gene flow due to disassortative mating, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

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