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PubMed2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide associations between hybrid sterility QTL and marker transmission ratio distortion.

Marker transmission ratio distortion (TRD) in genetic mapping populations is frequently ascribed to selection against allelic combinations that cause hybrid incompatibility. Accordingly, genomic regions of TRD should be nonrandomly associated (colocated) with loci that underlie hybrid incompatibility. To directly test this hypothesis, we evaluated the genome-wide qualitative and quantitative agreement between chromosomal regions exhibiting marker TRD and those known to contain hybrid incompatibility quantitative trait locus (QTL). Incompatibility data came from a near-isogenic line (NIL) analysis of pollen and seed sterility in a cross between two Solanum (formerly Lycopersicon) species. We assessed (1) whether these incompatibility loci are colocated with markers that show significant TRD in two earlier generations preceding these introgression lines and (2) whether the magnitude of marker distortion quantitatively matches the estimated strength of selection against each incompatibility locus. We found evidence that TRD regions are chromosomally colocated with hybrid incompatibility loci more frequently than is expected by chance: pollen sterility QTLs were most closely associated with distorted heterozygote frequencies in later-generation backcrosses. Nonetheless, there was no evidence for an association between TRD and seed sterility and little evidence of a quantitative association between the magnitude of marker TRD and the fitness effects of heterospecific alleles at each chromosomal location. We propose and test a model (the "dance partner" model) to explain several cases where regions of TRD are not associated with hybrid incompatibility loci. Under this model, some NILs containing greater than one heterospecific introgression may not express hybrid incompatibility phenotypes because they carry both appropriate genetic dance partners required for a fully functional interaction. Accordingly, negative interactions expressed in earlier backcross generations are masked in these double-introgression NILs. Based on this model, we identify the location of several new putative pairwise interactors underlying hybrid incompatibility in this species cross.

Chromosome Mapping↗

PubMed2002

Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia.

Populations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long-term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.

Alleles↗

PubMed2004

Geographic origin and taxonomic status of the invasive Privet, Ligustrum robustum (Oleaceae), in the Mascarene Islands, determined by chloroplast DNA and RAPDs.

Information concerning the area of origin, genetic diversity and possible acquisition of germplasm through hybridisation is fundamental to understanding the evolution, ecology and possible control measures for an introduced invasive plant species. Among the most damaging of alien plants that are invading and degrading native vegetation in the Mascarene Islands of the Indian Ocean is the Tree Privet, Ligustrum robustum. Exact information about the geographic source of introduced material of this species is lacking, in part because Ligustrum is a taxonomically difficult genus. Native material of L. robustum ssp. walkeri from Sri Lanka, L. robustum ssp. robustum from northeastern India, and the closely related L. perrottetii from southern India was compared with introduced material from La Réunion and Mauritius using chloroplast DNA RFLP markers and random amplified polymorphic DNA (RAPDs). Sri Lankan and introduced material was monomorphic for the same cpDNA haplotype that was absent from south and northeast Indian Ligustrum. Sri Lankan and introduced material was also clearly distinguished from Indian Ligustrum by RAPDs. It was concluded that material introduced and established in the Mascarene Islands is derived from the Sri Lankan subspecies L. robustum ssp. walkeri. No geographic structuring of genetic variation within Sri Lanka was detected for this taxon, so the location(s) within Sri Lanka from which introduced material is derived could not be pinpointed. RAPDs indicate that L. robustum ssp. walkeri in Sri Lanka is more similar to south Indian L. perrottetii than to northeast Indian L. robustum ssp. robustum. Moreover, RAPDs showed that introduced material in La Réunion has undergone little or no loss of genetic diversity since introduction. However, there was no evidence that it is introgressed with germplasm from two other alien Ligustrum species present on La Réunion.

Chloroplasts↗

PubMed2002

Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp.

BACKGROUND: The cosmopolitan moon jelly Aurelia is characterized by high degrees of morphological and ecological plasticity, and subsequently by an unclear taxonomic status. The latter has been revised repeatedly over the last century, dividing the genus Aurelia in as many as 12 or as little as two species. We used molecular data and phenotypic traits to unravel speciation processes and phylogeographic patterns in Aurelia. RESULTS: Mitochondrial and nuclear DNA data (16S and ITS-1/5.8S rDNA) from 66 world-wide sampled specimens reveal star-like tree topologies, unambiguously differentiating 7 (mtDNA) and 8 (ncDNA) genetic entities with sequence divergences ranging from 7.8 to 14% (mtDNA) and 5 to 32% (ncDNA), respectively. Phylogenetic patterns strongly suggest historic speciation events and the reconstruction of at least 7 different species within Aurelia. Both genetic divergences and life history traits showed associations to environmental factors, suggesting ecological differentiation forced by divergent selection. Hybridization and introgression between Aurelia lineages likely occurred due to secondary contacts, which, however, did not disrupt the unambiguousness of genetic separation. CONCLUSIONS: Our findings recommend Aurelia as a model system for using the combined power of organismic, ecological, and molecular data to unravel speciation processes in cosmopolitan marine organisms.

Animals↗

PubMed2004

Determination and evaluation of the sequence and textural effects of the puroindoline a and puroindoline b genes in a population of synthetic hexaploid wheat.

Aegilops tauschii (2 n=2 x=14, DD) is a rich source of genetic variability for hexaploid wheat ( Triticum aestivum, 2 n=6 x=42, AABBDD) improvement. This variability can be accessed through utilizing synthetic hexaploid wheat lines, which contain genomes from Ae. tauschii and T. turgidum (2 n=4 x=28, AABB). Numerous desirable characteristics can and have been introgressed into common hexaploid wheat with this germplasm. In this work, the genetic variability in the two puroindoline genes (a and b) contained on the D genome, and the relationship that sequence polymorphisms in these genes have on endosperm texture among a population of 75 CIMMYT synthetic hexaploid accessions is described. Kernel texture was evaluated using the single kernel characterization system (SKCS). Kernel texture differed significantly ( P<or=0.0001) among the synthetic hexaploid accessions (range 2.6-40.9) and the parent types, durum or Ae. tauschii. The interaction term between parent types was also a significant effect ( P<or=0.0001). In addition to the 'wild-type' protein sequences of the puroindoline genes (those present in 'Chinese Spring' and all other soft wheats), three other translated sequences were identified in puroindoline a and two others in puroindoline b. These protein sequences were associated with significantly ( P<or=0.0001) softer endosperm textures than the wild-type protein sequences. As the softer alleles are expressed in a hexaploid background, they are immediately available to wheat breeding programs.

Agriculture↗

PubMed2000

Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone.

Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization-related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows (Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD-based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter- and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered.

Crosses, Genetic↗

PubMed1999

Structure and dynamics of experimentally introduced and naturally occurring laccaria sp. Discrete genotypes in a douglas fir plantation

Ectomycorrhizal fungi have been introduced in forest nurseries to improve seedling growth. Outplanting of inoculated seedlings to forest plantations raises the questions about inoculant persistence and its effects on indigenous fungal populations. We previously showed (M.-A. Selosse et al. Mol. Ecol. 7:561-573, 1998) that the American strain Laccaria bicolor S238N persisted 10 years after outplanting in a French Douglas fir plantation, without introgression or selfing and without fruiting on uninoculated adjacent plots. In the present study, the relevance of those results to sympatric strains was assessed for another part of the plantation, planted in 1985 with seedlings inoculated with the French strain L. bicolor 81306 or left uninoculated. About 720 Laccaria sp. sporophores, collected from 1994 to 1997, were typed by using randomly amplified polymorphic DNA markers and PCR amplification of the mitochondrial and nuclear ribosomal DNAs. All plots were colonized by small spontaneous discrete genotypes (genets). The inoculant strain 81306 abundantly fruited beneath inoculated trees, with possible introgression in indigenous Laccaria populations but without selfing. In contrast to our previous survey of L. bicolor S238N, L. bicolor 81306 colonized a plot of uninoculated trees. Meiotic segregation analysis verified that the invading genet was strain 81306 (P < 0.00058), implying a vegetative growth of 1.1 m. year-1. This plot was also invaded in 1998 by strain S238N used to inoculate other trees of the plantation. Five other uninoculated plots were free of these inoculant strains. The fate of inoculant strains thus depends less on their geographic origin than on unknown local factors.

Journal Article↗

PubMed1999

Plant genetic resources: what can they contribute toward increased crop productivity?

To feed a world population growing by up to 160 people per minute, with >90% of them in developing countries, will require an astonishing increase in food production. Forecasts call for wheat to become the most important cereal in the world, with maize close behind; together, these crops will account for approximately 80% of developing countries' cereal import requirements. Access to a range of genetic diversity is critical to the success of breeding programs. The global effort to assemble, document, and utilize these resources is enormous, and the genetic diversity in the collections is critical to the world's fight against hunger. The introgression of genes that reduced plant height and increased disease and viral resistance in wheat provided the foundation for the "Green Revolution" and demonstrated the tremendous impact that genetic resources can have on production. Wheat hybrids and synthetics may provide the yield increases needed in the future. A wild relative of maize, Tripsacum, represents an untapped genetic resource for abiotic and biotic stress resistance and for apomixis, a trait that could provide developing world farmers access to hybrid technology. Ownership of genetic resources and genes must be resolved to ensure global access to these critical resources. The application of molecular and genetic engineering technologies enhances the use of genetic resources. The effective and complementary use of all of our technological tools and resources will be required for meeting the challenge posed by the world's expanding demand for food.

Agriculture↗

PubMed1987

Alcohol-preferring (AA) and alcohol-avoiding (ANA) lines of rats after introgression of alien genes.

Outcrossing has been used as a method for introducing new genetic variability into the high-drinking AA and low-drinking ANA rat lines that had reached their selection limits and were suffering of poor fertility and decreased litter size. The response to the renewed selection for differential alcohol consumption, and the effect of outcrossing upon the components of productivity are reported.

Alcohol Drinking↗

PubMed2001

Population history of Eresus cinnaberinus (Araneae: Eresidae) colour variants at a putative species transition.

Comparative population genetic and phylogenetic analyses were used to study historical and recent gene flow between two colour variants of the spider Eresus cinnaberinus, in order to explain variant distributions in Northern and Central Europe. Recently, the colour variants have been assigned to two species, E. cinnaberinus and E. sandaliatus, the latter found isolated in Denmark and in Bavaria. Explaining Eresus's distributions thus poses a twofold problem: (i) clarifying species limits at a population-species transition and (ii) explaining noncontinuous distributions in a postglacially colonized area. Combined allozyme and mtDNA data suggest that disjunct distributions of E. sandaliatus in Bavaria and Denmark were caused by introgression of E. cinnaberinus into a E. sandaliatus background, giving rise to E. cinnaberinus phenotypes, rather than competitive exclusion of a genetically independent species by the other. Introgression caused mtDNA paraphyly of the derived E. sandaliatus whereas paraphyly of E. cinnaberinus outside the putative introgression zone may be associated with lineage sorting. Allozymes reveal local and extant gene flow processes better than mtDNA, but, because of the divided population structure, allozymes have limited power in making inferences about historical gene flow and the speed of postglacial colonization. Mitochondrial DNA distributions indicate that postglacial colonization of Northern Europe occurred rapidly and in several waves from different source populations.

Animals↗

PubMed2003

QTLs for resistance to powdery mildew in pepper under natural and artificial infections.

Epidemics of powdery mildew due to Leveillula taurica is an increasing problem in pepper production areas, particularly in coastal regions or greenhouse cultivation. The highly resistant genitor 'H3' was submitted to genetic analysis and QTL mapping in order to promote the introgression of its oligogenic resistance into large and sweet-fruited cultivars. The doubled-haploid progeny from the cross 'H3' (resistant) by 'Vania' (susceptible) was tested for resistance under both natural field infection and artificial inoculation tests, and QTL detection was compared for those two methods. Seven genomic regions including additive QTLs and epistatic interactions were detected, explaining altogether the major part of genotypic variance. Two genomic regions were common to both the evaluation methods, whereas other QTLs were method-specific, reflecting the environment dependence of powdery mildew epidemics. Orthologies with tomato genomic regions carrying resistance genes to L. taurica and Oidium lycopersicum were revealed by comparative mapping with pepper. Tight linkages between the detected QTLs and virus resistance or fruit color traits in pepper were also shown, which adds to the agronomic importance of these regions in pepper breeding programs.

Ascomycota↗

PubMed2006

Phylogenetic divisions among Collared peccaries (Pecari tajacu) detected using mitochondrial and nuclear sequences.

The Collared peccary (Pecari tajacu) is one of the three extant recognised species of the family Tayassuidae, living in the Americas. To understand phylogenetic relationships among Collared peccaries, the entire mitochondrial DNA control region and cytochrome b as well as partial nuclear GPIP and PRE-1 P27, PRE-1 P642 and TYR sequences from specimens from Colombia, Argentina, Bolivia, Mexico, United States and Australian zoo animals of unknown origin were analysed. Separate and combined analyses of the mitochondrial sequences provided good resolution of Collared peccary relationships. Nuclear sequences were partially informative when combined sequence analyses were performed. Maximum Likelihood analyses of mitochondrial sequences showed that Collared peccaries clustered in two major clades, representing North-Central American and South American specimens. Collared peccaries from Colombia are paraphyletic. Statistical Parsimony analysis of combined nuclear sequences showed a distribution of DNA variants consistent with mitochondrial sequence analyses. However, there is an uncoupling of nuclear and mitochondrial sequence variation in two specimens from Colombia. The present study suggests the recent contact of isolated populations within Colombia and possible mitochondrial introgression between the North/Central clade and the South clade. Pairwise genetic distances comparison of mitochondrial sequences show that divergence between the two major clades of the Collared peccary was higher and comparable respectively with that within and between the other two recognised peccary species. Divergence between the two major clades of the Collared peccary was also higher than that observed within and even between recognised species of the Suidae family. The divergence within the major clades of the Collared peccary showed comparable values with those observed within the other two species of Tayassuidae and within six species of Suidae. The results show that the geographically widespread and phenotypically diverse Collared peccary consists of two species or at least subspecies with implications for management of wild, zoo and captive populations.

Americas↗

PubMed2002

[Populus nigra L. in the Garonne valley: legacy of the past and present constraints].

This study used documents from archives and historical maps to follow the simultaneous change of the riparian woodlands (where Populus nigra is dominant) and the poplar plantations. Results showed that the riparian woodland decreased by 81% over the two last centuries. Each period was characterised by the dominance of only a few number of clones. The risk of introgression due to the massive presence of such a restricted genetic material around P. nigra was discussed. The impact of river management on poplar regeneration was examined as well.

Climate↗

PubMed2005

Genetics of female functional virginity in the parthenogenesis-Wolbachia infected parasitoid wasp Telenomus nawai (Hymenoptera: Scelionidae).

A lepidopteran egg parasitoid species Telenomus nawai consists of two distinct populations with different reproductive modes. One is a completely thelytokous population consisting of females only, whereas the other displays arrhenotokous reproduction where fertilized eggs develop into diploid females and unfertilized eggs into haploid males. Thelytoky in T. nawai is caused by a bacterial symbiont, the parthenogenesis-inducing (PI) Wolbachia. Recent theoretical studies have shown that when a PI-Wolbachia is spreading in a population, mutations that allow uninfected females to produce more male offspring will spread rapidly eventually becoming fixed. The consequence of such a mutation is that sexual reproduction is no longer successful in infected females. Here we determine the genetic basis of the females' inability to reproduce sexually by introgressing the genome of a thelytokous line into an arrhenotokous line. The results suggest that the mutations are recessive and inherited either as a single-locus major gene with some modifiers, or as two partially linked loci.

Animals↗

PubMed2025

Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.

Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models have been developed in the multispecies coalescent (MSC) framework to infer gene flow from genomic data, assuming either constant-rate continuous migration (MSC-M) or discrete introgression/hybridization (MSC-I). The extreme simplicity of these models raises concerns about their usefulness as they represent misspecified models when applied to real data. Here, we study inference of gene flow under the MSC-M model, considering mis-assignment of gene flow onto incorrect parental or daughter lineages, misspecification of the direction of gene flow, and misspecification of the mode of gene flow. Mis-assignment of gene flow to an incorrect lineage causes large biases in the estimated rates. The Bayesian test has high power for inferring both recent and ancient gene flow, between either sister lineages or nonsister lineages, although misspecification of the direction of gene flow may make it hard to distinguish early divergence with gene flow from recent complete isolation. Misspecification of the mode of gene flow (MSC-I versus MSC-M) has small local effects, and gene flow is detected with high power despite the misspecification. We analyze a genomic dataset from the purple cone spruce (Picea spp., Pinaceae), which putatively arose through homoploid hybrid speciation, to demonstrate practical implications of our theoretical analyses. Overall, we find that the extremely idealized models of gene flow (in particular the discrete MSC-I model) are very effective for extracting information about species divergence and gene flow from genomic data.

Gene Flow↗

PubMedDate not supplied

[New morphological marker for chromosomes of the fourth homologous group of Triticinae].

The character "hairy leaf sheath" was studied in two groups of introgressive common wheat lines. The first group involves lines containing genetic material of Aegilops sharonensis, the second one includes lines with chromatin of Triticum miguschovae. The gene controlling hairy leaf sheath, Hs, was located by us on chromosomes 4S1 (Ae. sharonensis) and 4D (T. miguschovae) due to its joint transfer with beta-Amy-S(1)1, beta-Amy-D1, Acph-S(1)1 and Acph-D1 genes situated on the and 4D chromosomes. The possibility to use the identified gene as a morphological marker for these chromosomes was shown.

Chromosome Mapping↗

PubMed2000

SHR.BN-congenic strains for genetic analysis of multifactorially determined traits.

The laboratory rat is an important laboratory animal with multiple well-defined inbred strains, including some of the most widely used animal models of human diseases. Recent advances in the development of rat genetic resources will enable the exploitation of the full potential of rat models of human diseases and, in addition, the rat can provide useful information for comparative genomics of humans and mice. In the current review, we describe the development of congenics strains by introgression of differential chromosome segments from the Brown Norway (BN) rat to the genetic background of the spontaneously hypertensive rat (SHR). These SHR.BN-congenic strains and recombinant sublines derived from them were developed as a model system for genetic analysis of multifactorially determined pathophysiological and morphological conditions.

Animals↗

PubMed2007

Analysis of an introgressed Nicotiana tomentosa genomic region affecting leaf number and correlated traits in Nicotiana tabacum.

Germplasm from closely related diploid relatives of tobacco (Nicotiana tabacum L.) could be of value for continued genetic modification of this species and for mapping quantitative trait loci (QTLs). We examined near isogenic tobacco lines and hybrids differing for an introgressed genomic region from N. tomentosa Ruiz and Pavon designated as Many Leaves that exhibits a large influence on leaf number and correlated traits. Within a 'Red Russian' genetic background, the region acted in an additive to partially dominant fashion to delay flowering time, and increase leaf number, plant height, and green leaf yield. Evidence of epistasis was observed as the region affected these traits to varying degrees in diverse near isogenic hybrids. Fifteen amplified fragment length polymorphism (AFLP) markers of N. tomentosa origin were mapped within a single linkage group of 34.5 cM using a population of 207 BC(1)F(1) individuals segregating for Many Leaves. Composite interval mapping produced 2-LOD confidence intervals for likely QTL positions influencing leaf number (3.1 cM region), plant height (2.9 cM region), and days to flowering (3.3 cM region). These intervals were overlapping. Results demonstrate that genomic regions with large genetic effects can be transferred to tobacco from closely related diploid relatives, and that sufficient recombination within these regions may permit mapping of genes controlling quantitative traits. Materials and results described here may be useful in future research to gain insight on the genetic control of the transition from vegetative to reproductive development in Nicotiana.

Amplified Fragment Length Polymorphism Analysis↗