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Results for “Genetic Introgression”

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PubMed2006

Congenic strains confirm aerobic running capacity quantitative trait loci on rat chromosome 16 and identify possible intermediate phenotypes.

We previously identified two inbred rat strains divergent for treadmill aerobic running capacity (ARC), the low-performing Copenhagen (COP) and the high-performing DA rats, and used an F(2)(COPxDA) population to identify ARC quantitative trait loci (QTLs) on rat chromosome 16 (RNO16) and the proximal portion of rat chromosome 3 (RNO3). Two congenic rat strains were bred to further investigate these ARC QTLs by introgressing RNO16 and the proximal portion of RNO3 from DA rats into the genetic background of COP rats and were named COP.DA(chr 16) and COP.DA(chr 3), respectively. COP.DA(chr 16) rats had significantly greater ARC compared with COP rats (696.7 +/- 38.2 m vs. 571.9 +/- 27.5 m, P = 0.03). COP.DA(chr 3) rats had increased, although not significant, ARC compared with COP rats (643.6 +/- 40.9 m vs. 571.9 +/- 27.5 m). COP.DA(chr 16) rats had significantly greater subcutaneous abdominal fat, as well as decreased fasting triglyceride levels, compared with COP rats (P < 0.05), indicating that genes responsible for strain differences in fat metabolism are also located on RNO16. While this colocalization of QTLs may be coincidental, it is also possible that these differences in energy balance may be associated with the superior running performance of COP.DA(chr 16) consomic rats.

Adipose Tissue↗

PubMed2003

Isolation of a chromosome 1 region affecting blood pressure and vascular disease traits in the stroke-prone rat model.

Recently, a genome-wide screen has shown a major quantitative trait locus (QTL) for a stroke-associated phenotype on rat chromosome 1 (RNO1) independent of QTL for blood pressure (BP) in the stroke-prone spontaneously hypertensive rat (SHRSP) of a Heidelberg colony. However, it remains to be elucidated whether these observations reflect the existence of different genes predisposing to each of the disorders. To address this issue, we performed comprehensive approaches in a Japanese colony, Izm, as follows. First, we undertook genome-wide searches in F1(SHRSP/IzmxWKY/Izm)xSHRSP/Izm back-cross (n=63) to pursue a causal relation between hypertension and stroke. Although the strongest linkage to BP (LOD score of 3.4) was identified on RNO1, its relevance to stroke was not supported in the F1 back-cross studied. Second, we also investigated linkage to BP in F2 progeny (n=175) involving the stroke-resistant (or normal) spontaneously hypertensive rat (SHR). In F2 studies of SHR/Izm, this locus did not appear to constitute a principal BP QTL. Third, we constructed congenic animals with detailed phenotype characterization. Transfer of a chromosomal fragment between markers Klk1 and D1Rat116 from WKY/Izm onto the SHRSP/Izm background lowered systolic BP by 20 to 80 mm Hg, prevented development of apparent stroke, and exaggerated impaired glucose tolerance. In conclusion, we have successfully isolated an RNO1 region affecting BP, stroke, and glucose tolerance in SHRSP/Izm-derived congenic rats. The size of the introgressed region is large, but our novel congenic strain should help delineate complex, genetic impairments underlying BP and associated vascular disease phenotypes.

Animals↗

PubMed2006

Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato.

The efficiency of marker-assisted backcross for the introgression of a quantitative trait locus (QTL) from a donor line into a recipient line depends on the stability of QTL expression. QTLs for six quality traits in tomato (fruit weight, firmness, locule number, soluble solid content, sugar content and titratable acidity) were studied in order to investigate their individual effect and their stability over years, generations and genetic backgrounds. Five chromosome regions carrying fruit quality QTLs were transferred following a marker-assisted backcross scheme from a cherry tomato line into three modern lines with larger fruits. Three sets of genotypes corresponding to three generations were compared: (1) an RIL population, which contained 50% of each parental genome, (2) three BC3S1 populations which segregated simultaneously for the five regions of interest but were almost fully homozygous for the recipient genome on the eight chromosomes carrying no QTL and (3) three sets of QTL-NILs (BC3S3 lines) which differed from the recipient line only in one of the five regions. QTL detection was performed in each generation, in each genetic background and during 2 successive years for QTL-NILs. About half of the QTLs detected in QTL-NILs were detected in both years. Eight of the ten QTLs detected in RILs were recovered in the QTL-NILs with the genetic background used for the initial QTL mapping experiment, with the exception of two QTLs for fruit firmness. Several new QTLs were detected. In the two other genetic backgrounds, the number of QTLs in common with the RILs was lower, but several new QTLs were also detected in advanced generations.

Fruit↗

PubMed2005

Genetic diversity of the Andean tetraploid cultivated potato (Solanum tuberosum L. subsp. andigena Hawkes) evaluated by chloroplast and nuclear DNA markers.

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are native farmer-selected important cultivars that form a primary gene pool of the common potato (Solanum tuberosum L. subsp. tuberosum). The genetic diversity of 185 Andigena accessions and 6 Chilean native potatoes (S. tuberosum subsp. tuberosum) was studied using chloroplast DNA (ctDNA) microsatellites and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Andigena potatoes had 14 ctDNA haplotypes and showed higher variability in the central Andes, particularly in Bolivia, whereas those in the northern regions of the distribution area were remarkably uniform with A1 ctDNA and Chilean subsp. tuberosum with T ctDNA. Most of 123 clearly scored RFLP bands using 30 single-copy probes were randomly distributed throughout the distribution area and proved the same gene pool shared among these widely collected accessions. Nevertheless, the geographic trend of the nDNA differentiation from north to south along the Andes and the correlated differentiation between nDNA and ctDNA (r = 0.120) could also be revealed by canonical variates analysis. These results suggest that the genetic diversity in Andigena was brought about primarily from cultivated diploid species but considerably modified through sexual polyploidization and intervarietal and (or) introgressive hybridization and long-distance dispersal of seed tubers by humans.

Cell Nucleus↗

PubMed2002

Natural and artificial secondary contact in brown trout (Salmo trutta, L.) in the French western Pyrenees assessed by allozymes and microsatellites.

Analysis of allozyme polymorphism in brown trout (Salmo trutta) populations from south-western France shows that two genetically differentiated wild forms (characterised by the LDH-C1*100 and 90 alleles) introgress in this area. As allozymes could not evaluate the impact of stocking in the Atlantic basin, microsatellites have been necessary to detect the influence of hatchery fish and to confirm that the observed structure was natural. Microsatellites confirm the distinctness of the two wild forms based on allozyme loci. This situation provides a new example of secondary contact for this species in the Atlantic basin, with various levels of mixing being seen between the two population groups. The origin of these forms is discussed in the light of previous studies concerning modern and ancestral Atlantic trout (Hamilton et al, 1989) and lineages stemming from different glacial refuges (Garcia Marin et al, 1999; Weiss et al, 2000). This local analysis provides new insights in defining the evolutionary history of this species and confirms the important role of glaciation events in this history.

Animals↗

PubMed2006

Contrasting hybridization rates between sympatric three-spined sticklebacks highlight the fragility of reproductive barriers between evolutionarily young species.

Three-spined sticklebacks (Gasterosteus aculeatus) are a powerful evolutionary model system due to the rapid and repeated phenotypic divergence of freshwater forms from a marine ancestor throughout the Northern Hemisphere. Many of these recently derived populations are found in overlapping habitats, yet are reproductively isolated from each other. This scenario provides excellent opportunities to investigate the mechanisms driving speciation in natural populations. Genetically distinguishing between such recently derived species, however, can create difficulties in exploring the ecological and genetic factors defining species boundaries, an essential component to our understanding of speciation. We overcame these limitations and increased the power of analyses by selecting highly discriminatory markers from the battery of genetic markers now available. Using species diagnostic molecular profiles, we quantified levels of hybridization and introgression within three sympatric species pairs of three-spined stickleback. Sticklebacks within Priest and Paxton lakes exhibit a low level of natural hybridization and provide support for the role of reinforcement in maintaining distinct species in sympatry. In contrast, our study provides further evidence for a continued breakdown of the Enos Lake species pair into a hybrid swarm, with biased introgression of the 'limnetic' species into that of the 'benthic'; a situation that highlights the delicate balance between persistence and breakdown of reproductive barriers between young species. A similar strategy utilizing the stickleback microsatellite resource can also be applied to answer an array of biological questions in other species' pair systems in this geographically widespread and phenotypically diverse model organism.

Animals↗

PubMed2001

Distribution of donor genome composition and its application in marker aided backcrossing.

Conditional distribution was derived for the genome composition given the marker genotype of individuals from a backcross population. Genome size from donor was predicted by the mean. The precision of the prediction, indicated by the correlation with the unknown actual genome size from donor, was formulated by the variance and expressed as a function of the marker density. Results indicated that although high correlation can be obtained with a moderate marker density, say 40 cM per marker, the best individual in a large population has to be identified through a map of high density, say 10 to 20 cM per marker. For the best use of marker information in a marker aided backcrossing program for gene introgression, a stepwise marker genotyping and individual selection were suggested. That is, a preliminary selection can be made among all individuals but only on a few markers for each individual, and a fine selection would then be made among a few individuals but on more markers for each individual. This would be a very efficient method to increase the selection intensity in a large population but with a manageable number of marker genotyping for a gene introgression experiment.

Crosses, Genetic↗

PubMed2026

Comparative Population Genomics of Relictual Caribbean Island Gossypium hirsutum.

Gossypium hirsutum is the world's most important source of cotton fibre, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilisation of wild diversity in G. hirsutum.

Genetics, Population↗

PubMed2002

Reciprocal rat chromosome 2 congenic strains reveal contrasting blood pressure and heart rate QTL.

Evidence exists implying multiple blood pressure quantitative trait loci (QTL) on rat chromosome 2. To examine this possibility, four congenic strains and nine substrains were developed with varying size chromosome segments introgressed from the spontaneously hypertensive rat (SHR/lj) and normotensive Wistar-Kyoto rat (WKY/lj) onto the reciprocal genetic background. Cardiovascular phenotyping was conducted with telemetry over extended periods during standard salt (0.7%) and high-salt (8%) diets. Our results are consistent with at least three independent pressor QTL: transfer of SHR/lj alleles to WKY/lj reveals pressor QTL within D2Rat21-D2Rat27 and D2Mgh10-D2Rat62, whereas transfer of WKY/lj D2Rat161-D2Mit8 to SHR/lj reveals a depressor locus. Our results also suggest a depressor QTL in SHR/lj located within D2Rat161-D2Mgh10. Introgressed WKY/lj segments also reveal a heart rate QTL within D2Rat40-D2Rat50 which abolished salt-induced bradycardia, dependent upon adjoining SHR/lj alleles. This study confirms the presence of multiple blood pressure QTL on chromosome 2. Taken together with our other studies, we conclude that rat chromosome 2 is rich in alleles for cardiovascular and behavioral traits and for coordinated coupling between behavior and cardiovascular responses.

Animals↗

PubMed2001

The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation.

Phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA (mtDNA) variation were used to infer the temporal dynamics of distributional and demographic history of brown trout (Salmo trutta). Both new and previously published data were analyzed for 1,794 trout from 174 populations. This combined analysis improved our knowledge of the complex evolutionary history of brown trout throughout its native Eurasian and North African range of distribution in many ways. It confirmed the existence of five major evolutionary lineages that evolved in geographic isolation during the Pleistocene and have remained largely allopatric since then. These should be recognized as the basic evolutionarily significant units within brown trout. Finer phylogeographic structuring was also resolved within major lineages. Contrasting temporal juxtaposition of different evolutionary factors and timing of major demographic expansions were observed among lineages. These unique evolutionary histories have been shaped both by the differential latitudinal impact of glaciations on habitat loss and potential for dispersal, as well as climatic impacts and landscape heterogeneity that translated in a longitudinal pattern of genetic diversity and population structuring at more southern latitudes. This study also provided evidence for the role of biological factors in addition to that of physical isolation in limiting introgressive hybridization among major trout lineages.

Animals↗

PubMed2005

Genetic entities and mating system in hermaphroditic Fucus spiralis and its close dioecious relative F. vesiculosus (Fucaceae, Phaeophyceae).

To date, molecular markers have not settled the question of the specific status of the closely related, but phylogenetically unresolved, brown seaweeds, hermaphroditic Fucus spiralis and dioecious Fucus vesiculosus, nor their propensity for natural hybridization. To test the degree of species integrity and to assess effect of the mating system on the population genetic structure, 288 individuals coming from parapatric (discontinuous) and sympatric (contiguous) spatial configurations at two sites were genotyped with five microsatellite loci. Using a Bayesian admixture analysis, our results show that F. spiralis and F. vesiculosus comprise clearly distinct genetic entities (clusters) generally characterized by cosexual and unisexual individuals, respectively. Genetic diversity within each entity suggests that F. spiralis reproduces primarily through selfing while F. vesiculosus is characterized by an endogamous breeding regime. Nevertheless, aberrant sexual phenotypes were observed in each cluster, no diagnostic alleles were revealed and 10% of study individuals were intermediate between the two genetic entities. This pattern can be explained by recent divergence of two taxa with retention of ancestral polymorphism or asymmetrical, introgressive hybridization. However, given (i) coincident monomorphism at three loci in spiralis clusters and (ii) that significantly more intermediates were observed in sympatric stations than in parapatric stations, we argue that interspecific gene flow has occurred after divergence of the two taxa. Finally, we show that whether recently separated or recently introgressive, the divergent breeding systems probably contribute to species integrity in these two taxa.

Bayes Theorem↗

PubMed1975

Gene flow versus selection pressure and ancestral differentiation in the composition of species: analysis of population variation of Juniperus ashei Buch. using terpenoid data.

Twenty-four populations of Juniperus ashei were sampled throughout the range of this taxon and the terpenoids of the foliage were analyzed by gas/liquid chromatography. Population differentiation was investigated by analysis of variance and numerical taxonomy. Three south Texas and one Mexican population clustered together with the rest of the taxon appearing fairly uniform. No evidence was found of hybridization or introgression with other taxa. Disjunct populations in Oklahoma and the Ozarks, which have been genetically isolated from the central population for thousands of years, showed no signs of differentiation nor genetic drift. The present pattern of distribution probably dates from the Pleistocene. The south Texas and Mexican populations appear to be the primitive elements of the species. Populational differences have apparently been maintained in adjacent populations in spite of seemingly large gene flow and conversely, chemical uniformity is being maintained in many disjunct populations where there is little or no gene flow.

Biological Evolution↗

PubMed2003

Pedigree-based assignment tests for reversing coyote (Canis latrans) introgression into the wild red wolf (Canis rufus) population.

The principal threat to the persistence of the endangered red wolf (Canis rufus) in the wild is hybridization with the coyote (Canis latrans). To facilitate idengification and removal of hybrids, assignment tests are developed which use genotype data to estimate identity as coyote, 1/4, 1/2, 3/4 or full red wolf. The tests use genotypes from the red wolves that founded the surviving population and the resulting pedigree, rather than a contemporary red wolf sample. The tests are evaluated by analysing both captive red wolves at 18 microsatellite loci, and data simulated under a highly parameterized, biologically reasonable model. The accuracy of assignment rates are generally high, with over 95% of known red wolves idengified correctly. There are, however, tradeoffs between ambiguous assignments and misassignments, and between misidengifying red wolves as hybrids and hybrids as red wolves. These result in a compromise between limiting introgression and avoiding demographic losses. The management priorities and level of introgression determine the combination of test and removal strategy that best balances these tradeoffs. Ultimately, we conclude that the use of the assignment tests has the capacity to arrest and reverse introgression. To our knowledge, the presented approach is novel in that it accounts for genetic drift when the genotypes under analysis are temporally separated from the reference populations to which they are being assigned. These methods may be valuable in cases where reference databases for small populations have aged substantially, pedigree information is available or data are generated from historical samples.

Animals↗

PubMed2000

Microsatellite analysis reveals substantial genetic differentiation between contemporary New World and Old World Holstein Friesian populations.

Genotypic data from 39 microsatellite loci typed in 211 animals were used to assess the genetic differentiation between Old World and New World Holstein Friesian cattle populations. Gene diversities were similar in all five Holstein Friesian populations surveyed, ranging from 0.43 to 0.48. A tree of individuals based on the proportion of shared alleles indicated a clear distinction between Old World and New World Holstein Friesian populations. Similarly, genetic differentiation between populations, as measured by FST, was highly significant. Using the split decomposition method, we were able to visualize the significant introgression of New World Holstein Friesian into European Holstein Friesian populations.

Alleles↗

PubMed2001

A fertile amphiploid between durum wheat (Triticum turgidum) and the x Agroticum amphiploid (Agropyron cristatum x T. tauschii).

Agropyron (Gaertn) is a genus of Triticeae which includes the crested wheatgrass complex, i.e. A. cristatum (L.) as representative species containing the P genome. This species is an important source for increase the genetic variability of both durum and bread wheat. Among the possible interesting features to be introgressed into wheat are resistance to wheat streak mosaic virus, rust diseases, and tolerance to drought, cold and moderate salinity. By crossing tetraploid wheat (Triticum turgidum conv durum, 2n = 4x = 28; AABB) with a fertile allotetraploid (2n = 4x = 28; DDPP) between diploid wheat (T. tauschii) and crested wheatgrass (A. cristatum L.), amphiploid plants were obtained. Fluorescence in situ hybridization (FISH) using both genomic DNA from A. cristatum and the repetitive probe pAs1, proved that the plants were true amphiploids with a chromosome number 2n = 8x = 56 and genomic constitution AABBDDPP. Using total genomic in situ hybridization (GISH) to study meiotic metaphase I, data on allosyndetic and autosyndetic chromosome pairing were obtained. The amphiploids were perennial like the male parent but their morphology was close to that of the wheat parent. They were resistant to wheat leaf rust and powdery mildew under field conditions.

Chimera↗

PubMed1986

Possible derivation of the laboratory mouse genome from multiple wild Mus species.

Laboratory strains of mice are thought to be derived from wild populations of Mus domesticus. Many instances of non-domesticus genetic information fixed in these strains have been described, however, and the amount of strain-to-strain genetic variation exceeds that found in wild domesticus populations. In order to estimate the extent of the non-domesticus contribution to laboratory mouse genomes, and to determine whether it could account for observed variation, we have used computer simulations to investigate the properties of genetically marked chromosomal segments and the distribution of residual allogenicity at various times during inbreeding. A locus or chromosomal segment is allogenic if it is unfixed within a lineage at a given time. The odds of fixation of a foreign chromosome segment are predicted to be an exponentially decreasing function of its length. The median segment length is predicted to be 17 centimorgans. Available data for markers of chromosomes 1, 9 and 12 in recombinant inbred strain sets conform to these predictions. Together, the results suggest that introgression of non-domesticus chromosomes and segregation of residual allogenicity are sufficient to account for the genetic diversity observed among inbred mouse strains and substrains.

Alleles↗

PubMed2003

Mapping of Rym14Hb, a gene introgressed from Hordeum bulbosum and conferring resistance to BaMMV and BaYMV in barley.

Hordeum bulbosum represents the secondary gene pool of barley and constitutes a potential source of various disease resistances in barley breeding. Interspecific crosses of H. vulgare x H. bulbosum resulted in recombinant diploid-barley progeny with immunity to BaMMV after mechanical inoculation. Tests on fields contaminated with different viruses demonstrated that resistance was effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed that resistance was dominantly inherited. Marker analysis in a F5 mapping family was performed to map the introgression in the barley genome and to estimate its size after several rounds of recombination. RFLP anchor-marker alleles indicative of an H. bulbosum introgression were found to cover an interval 2.9 cM in length on chromosome 6HS. The soil-borne virus resistance locus harboured by this introgressed segment was designated Rym14(Hb). For marker-assisted selection of Rym14(Hb) carriers, a diagnostic codominant STS marker was derived from an AFLP fragment amplified from leaf cDNA of homozygous-resistant genotypes inoculated with BaMMV.

Chromosome Mapping↗

PubMed2006

Allozyme diversity and morphometrics of Melocactus paucispinus (Cactaceae) and evidence for hybridization with M. concinnus in the Chapada Diamantina, North-eastern Brazil.

BACKGROUND AND AIMS: Melocacatus paucispinus (Cactaceae) is endemic to the state of Bahia, Brazil, and due to its rarity and desirability to collectors it has been considered threatened with extinction. This species is usually sympatric and inter-fertile with M. concinnus, and morphological evidence for hybridization between them is present in some populations. Levels of genetic and morphological variation and sub-structuring in populations of these species were assessed and an attempt was made to verify the occurrence of natural hybridization between them. METHODS: Genetic variability was surveyed using allozymes (12 loci) and morphological variability using multivariate morphometric analyses (17 vegetative characters) in ten populations of M. paucispinus and three of M. concinnus occurring in the Chapada Diamantina, Bahia. KEY RESULTS: Genetic variability was low in both species (P = 0.0-33.3, A = 1.0-1.6, H(e) = 0.000-0.123 in M. paucispinus; P = 0.0-25.0, A = 1.0-1.4, H(e) = 0.000-0.104 in M. concinnus). Deficit of heterozygotes within the populations was detected in both species, with high values of F(IS) (0.732 and 0.901 in M. paucispinus and M. concinnus, respectively). Evidence of hybridization was detected by the relative allele frequency in the two diaphorase loci. High levels of genetic (F(ST) = 0.504 in M. paucispinus and 0.349 in M. concinnus) and morphological (A = 0.20 in M. paucispinus and 0.17 in M. concinnus) structuring among populations were found. CONCLUSIONS: The Melocactus spp. displayed levels of genetic variability lower than the values reported for other cactus species. The evidence indicates the occurrence of introgression in both species at two sites. The high F(ST) values cannot be explained by geographical substructuring, but are consistent with hybridization. Conversely, morphological differentiation in M. paucispinus, but not in M. concinnus, is probably due to isolation by distance.

Brazil↗