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PubMed2003

The maintenance of reproductive isolation in a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata.

Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 x 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.

Animal Migration↗
PubMed2006

Analysis of sugarcane mosaic virus resistance in maize in an isogenic dihybrid crossing scheme and implications for breeding potyvirus-resistant maize hybrids.

The gene action of 2 sugarcane mosaic virus (SCMV) resistance loci in maize, Scmv1 and Scmv2, was evaluated for potyvirus resistance in an isogenic background. All 4 homozygous and 5 heterozygous isogenic genotypes were produced for introgressions of the resistant donor (FAP1360A) alleles at both loci into the susceptible parent (F7) genetic background using simple sequence repeat markers. For SCMV and maize dwarf mosaic virus (MDMV), virus symptoms appeared rapidly in the 3 homozygous genotypes, with susceptibility alleles fixed at 1 or both loci. Although the 9 isogenic genotypes revealed a high level of resistance to Zea mosaic virus (ZeMV), the same 3 homozygous genotypes were only partially resistant. This indicates that 1 resistance gene alone is not sufficient for complete resistance against SCMV, MDMV, and ZeMV. Scmv1 showed strong early and complete dominant gene action to SCMV, but it gradually became partially dominant. Scmv2 was not detected at the beginning, showing dominant gene action initially and additive gene action at later stages. Both genes interacted epistatically (for a high level of resistance, at least 1 resistance allele at each of both loci is required). This implies that double heterozygotes at the 2 loci are promising for producing SCMVresistant hybrids. Results are discussed with respect to prospects for isolation of SCMV and MDMV resistance genes.

Breeding↗
PubMed2004

Nucleotide diversity of the ZmPox3 maize peroxidase gene: relationships between a MITE insertion in exon 2 and variation in forage maize digestibility.

BACKGROUND: Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility. RESULTS: Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated pi was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE). The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion. CONCLUSION: These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using specific allele introgressions.

Base Sequence↗
PubMed2005

A 14-gene region of rat chromosome 8 in SHR-derived polydactylous congenic substrain affects muscle-specific insulin resistance, dyslipidaemia and visceral adiposity.

The SHR and the PD/Cub are two established rodent models of human metabolic syndrome. Introgression of a ca 30 cM region of rat chromosome 8 from PD/Cub onto the genetic background of SHR was previously shown to influence several of the metabolic syndrome-related traits along with causing the PLS in the SHR-Lx congenic strain. In the process of identification of the causative alleles, we have produced several congenic sublines. The differential segment of SHR-Lx PD5 congenic substrain [SHR.PD(D8Rat42-D8Arb23)/Cub] spans approximately 1.4 Mb encompassing only 14 genes. When comparing the metabolic, morphometric and gene expression profiles of the SHR-Lx PD5 vs. SHR, the polydactyly and several distinct metabolic features observed in the original SHR-Lx congenic were still manifested, suggesting that the responsible genes were "trapped" within the relatively short differential segment of PD/Cub origin in SHR-Lx PD5. Particularly, the SHR-Lx PD5 displayed substantial reduction of insulin sensitivity confined to skeletal muscle. Among the candidate genes, the promyelocytic leukaemia zinc-finger Plzf (Zbtb16) transcription repressor is most likely responsible for the Lx mutation resulting in PLS and could also be involved in the alteration of metabolic pathways. The sequence analysis of the Plzf gene revealed a SNP leading to a threonine to serine substitution in SHR at aminoacid position 208 (T208S). In summary, we have isolated a 1.4 Mb genomic region syntenic to human chromosome 11q23, which, apart from causing polydactyly-luxate syndrome (PLS), affects total body weight, adiposity, lipid profile, insulin sensitivity of skeletal muscle and related gene expression as shown in the SHR-Lx PD5 congenic substrain.

Adipose Tissue↗
PubMed2006

Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population.

In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.

Arabidopsis↗
PubMed2006

Establishment of transgenic herbicide-resistant creeping bentgrass (Agrostis stolonifera L.) in nonagronomic habitats.

Concerns about genetically modified (GM) crops include transgene flow to compatible wild species and unintended ecological consequences of potential transgene introgression. However, there has been little empirical documentation of establishment and distribution of transgenic plants in wild populations. We present herein the first evidence for escape of transgenes into wild plant populations within the USA; glyphosate-resistant creeping bentgrass (Agrostis stolonifera L.) plants expressing CP4 EPSPS transgenes were found outside of cultivation area in central Oregon. Resident populations of three compatible Agrostis species were sampled in nonagronomic habitats outside the Oregon Department of Agriculture control area designated for test production of glyphosate-resistant creeping bentgrass. CP4 EPSPS protein and the corresponding transgene were found in nine A. stolonifera plants screened from 20,400 samples (0.04 +/- 0.01% SE). CP4 EPSPS-positive plants were located predominantly in mesic habitats downwind and up to 3.8 km beyond the control area perimeter; two plants were found within the USDA Crooked River National Grassland. Spatial distribution and parentage of transgenic plants (as confirmed by analyses of nuclear ITS and chloroplast matK gene trees) suggest that establishment resulted from both pollen-mediated intraspecific hybridizations and from crop seed dispersal. These results demonstrate that transgene flow from short-term production can result in establishment of transgenic plants at multi-kilometre distances from GM source fields or plants. Selective pressure from direct application or drift of glyphosate herbicide could enhance introgression of CP4 EPSPS transgenes and additional establishment. Obligatory outcrossing and vegetative spread could further contribute to persistence of CP4 EPSPS transgenes in wild Agrostis populations, both in the presence or absence of herbicide selection.

Agriculture↗
PubMed1999

Microsatellite polymorphism and genetic impact of restocking in mediterranean brown trout (Salmo trutta L.)

The genetic impact of restocking Mediterranean brown trout populations with hatchery stocks was investigated in the Orb River drainage (France), using genetic data from three microsatellite loci. We sampled two wild populations, the main river which is restocked each year and one of its tributaries which has not been restocked for 6 years. Each sample was divided into two age groups (juveniles/adults). Introgression of each native population by hatchery stocks was previously estimated using allele frequencies from two diagnostic protein-coding loci and one mtDNA haplotype. The genetic structure and allelic frequency at three microsatellite loci in native populations were compared with two hatchery samples belonging to stocks usually used for restocking this drainage. High levels of polymorphism (23-27 alleles per locus) were detected for two loci, whereas the third was less polymorphic. Polymorphism was significantly higher in the restocked population than in the now undisturbed population. Significant differences between age groups were observed in the main river, but not in its tributary. The introgression estimates using microsatellites were compared to those obtained from proteins and mtDNA. The different possible origins of alleles common to hatcheries and wild populations (homoplasy, ancestral polymorphism or introgression) are discussed.

Journal Article↗
PubMed2005

Stocking impact and temporal stability of genetic composition in a brackish northern pike population (Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples.

During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from the three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and <1% introgression of stocked freshwater pike into the brackish pike population. Furthermore, pairwise F(ST) estimates between samples demonstrated close genetic relationship among temporal samples from Stege Nor, indicating temporal stability over the last 45 years. We also estimated the effective population size (N(e)) of pike in Stege Nor and applied a test for recent population bottlenecks. The harmonic mean of N(e) was relatively high (>250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding to historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation.

Animals↗
PubMed2002

Genetic differences among three colour morphotypes of the black rockfish, Sebastes inermis, inferred from mtDNA and AFLP analyses.

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.

Animals↗
PubMed2002

Metabolic characterization of insulin resistance syndrome feature loci in three brown Norway-derived congenic strains.

Studies on genetic determination of the insulin resistance syndrome in rat models revealed several susceptibility loci for features of this complex phenotype, i.e. dyslipidemia, insulin resistance and obesity. We analysed the influence of introgression of the RNO4, RNO20 segments of SHR origin and RNO8 segment of PD/Cub origin (all previously shown to be involved in (dys)regulation of carbohydrate and lipid metabolism) onto the genetic background of a common progenitor, the Brown Norway (BN/Cub) rat. The differential segments were genetically characterized in the BN.PD-D8Rat39/D8Rat35 (BN-Lx, RNO8 congenic), BN.SHR-Il6/Cd36 (BN.SHR4, RNO4 congenic) and BN.PD-D8Rat39/D8Rat3, SHR-D4Mgh2/Cd36,SHR-D20Wox3/D20Mgh5 (BN-Lx 1K, RNO4, 8, 20 triple congenic) strains and their metabolic profiling was performed. After one week of high-sucrose diet, all congenic strains showed substantially higher levels of serum triglycerides and free fatty acids as well as impaired glucose tolerance in comparison with the BN/Cub progenitor strain. The BN-Lx 1K triple congenic strain displayed the most profound dyslipidemia, glucose intolerance and highest increase of triglyceridemia in response to high-sucrose diet overall, though accompanied with the significantly lowest adiposity index. These results further support the role of genes present within the studied chromosomal regions in observed metabolic disturbances. Furthermore, these findings point to the studied loci within the gene-gene and gene-environment interactions involved in pathogenesis of the insulin resistance syndrome. The set of defined congenic strains provides a possibility of assessing individual features of such a complex phenotype.

Animals↗
PubMed1993

An autosomal factor from Drosophila arizonae restores normal spermatogenesis in Drosophila mojavensis males carrying the D. arizonae Y chromosome.

Males of Drosophila mojavensis whose Y chromosome is replaced by the Y chromosome of the sibling species Drosophila arizonae are sterile. It is shown that genetic material from the fourth chromosome of D. arizonae is necessary and sufficient, in single dose, to restore fertility in these males. In introgression and mapping experiments this material segregates as a single Mendelian factor (sperm motility factor, SMF). Light and electron microscopy studies of spermatogenesis in D. mojavensis males whose Y chromosome is replaced by introgression with the Y chromosome of D. arizonae (these males are symbolized as mojYa) revealed postmeiotic abnormalities all of which are restored when the SMF of D. arizonae is co-introgressed (these males are symbolized as mojYaSMFa). The number of mature sperm per bundle in mojYaSMFa is slightly less than in pure D. mojavensis and is even smaller in males whose fertility is rescued by introgression of the entire fourth chromosome of D. arizonae. These observations establish an interspecific incompatibility between the Y chromosome and an autosomal factor (or more than one tightly linked factors) that can be useful for the study of the evolution of male hybrid sterility in Drosophila and the genetic control of spermatogenesis.

Animals↗
PubMed2004

Extensive sharing of chloroplast haplotypes among European birches indicates hybridization among Betula pendula, B. pubescens and B. nana.

Extensive sharing of chloroplast haplotypes among the silver birch, Betula pendula Roth., the downy birch, B. pubescens Ehrh., and the dwarf birch, B. nana L., was discovered using polymerase chain reaction-restriction fragment length polymporphism markers. The geographical component of the genetic variation was stronger than the species component: the species were not significantly different while 11% of the variation could be attributed to differentiation between the two main regions studied, Scandinavia and western Russia. All haplotypes occurring in more than 2% of the individuals were shared among the species and the introgression ratios were quite large: 0.79 between B. pubescens and B. pendula and 0.67 between B. pubescens and B. nana. The data also indicate that B. pendula individuals are more similar to sympatric B. pubescens than to B. pendula individuals from nearby forests. However, this trend is not as pronounced when B. pubescens is considered, suggesting that introgression is not symmetrical. The haplotype sharing among the three Betula species is most likely caused by hybridization and subsequent cytoplasmic introgression.

Betula↗
PubMed2002

Proteinuria and glomerulosclerosis in the Sabra genetic rat model of salt susceptibility.

In search of an experimental model that would simulate the association between proteinuria and salt sensitivity in humans, we studied protein excretion in the Sabra rat model of salt susceptibility. Monthly measurements of urinary protein excretion in animals fed standard rat chow revealed that normotensive salt-sensitive SBH/y developed proteinuria that averaged 65 +/- 7 mg/day (n = 10) at 9 mo, whereas proteinuria in normotensive salt-resistant SBN/y was 39 +/- 4 mg/day (n = 10) (P < 0.01). Histopathological evaluation revealed focal and segmental glomerulosclerosis (FSGS) lesions grade 2 in SBH/y and normal histology in SBN/y. To amplify the differences between the strains, uninephrectomy was performed. At 9 mo, proteinuria in SBH/y with one kidney (SBH/y-1K) was 195 +/- 12 mg/day (n = 10) and in SBN/y was 128 +/- 10 mg/day (n = 10) (P < 0.001); histopathology revealed FSGS grade 3 in SBH/y-1K and grade 1-2 in SBN/y-1K. To determine the effect of salt loading, animals were provided with 8% NaCl in chow, causing hypertension in SBH/y but not in SBN/y. Proteinuria markedly increased in both SBH/y with two kidneys (SBH/y-2K) and SBH/y-1K, but not in SBN/y; histopathology revealed FSGS grade 1-2 in SBH/y-2K, grade 2 in SBH/y-1K, no lesions in SBN/y-2K, and grade 0-1 in SBN/y-1K. We concluded that the SBH/y strain is more susceptible to develop proteinuria and glomerulosclerosis than SBN/y. In search for the genetic basis of this phenomenon, we investigated the role of candidate proteinuric gene loci. Consomic strains were constructed by introgressing chromosome 1 (which harbors the rf-1 and rf-2 proteinuric loci) or chromosome 17 (which harbors rf-5) from SBH/y onto the SBN/y genomic background. The resulting consomic strains developed marked proteinuria that was severalfold higher than in SBN/y-1K; histopathological evaluation, however, revealed FSGS lesions grade 1-2, similar to those found in SBN/y-1K and less severe than in SBH/y-1K. These results suggest a functional role of gene systems located on chromosomes 1 and 17 in inducing proteinuria in the salt-susceptible Sabra rat strain. These genetic loci do not appear to harbor major genes for glomerulosclerosis.

Age Factors↗
PubMed2004

Effect of Add1 gene transfer on blood pressure in reciprocal congenic strains of Milan rats.

Genetic variants of alpha adducin (ADD1) taken alone or in interaction with those of beta (ADD2) and gamma (ADD3) subunits have been associated with primary hypertension in humans and in Milan hypertensive (MHS) rats. In this study, we report the dissection of the individual contribution of each rat Add gene to blood pressure, by congenic substitution mapping. Congenic strains were developed by introgressing Add1, Add2, and Add3 genes (and chr14, chr4, and chr1 associated segments) of MHS in the Milan normotensive rat (MNS) genetic background (MNS.H-Add1, MNS.H-Add2, and MNS.H-Add3) and vice versa (MHS.N-Add1, MHS.N-Add2, and MHS.N-Add3). Systolic blood pressure (SBP) of MNS.H-Add1 rats was significantly higher (+10 mmHg) than that of MNS, whereas SBP of MHS.N-Add1 was significantly lower (-10 mmHg) than that of MHS. The differences account for 43% of the blood pressure differences between MHS and MNS. In contrast, SBPs of Add2 and Add3 congenic strains were not different from those of the correspondent recipient parental strain. The fine mapping of chr14 congenic segment supports the identity of blood pressure QTL with Add1 gene.

Animals↗
PubMed2002

[Phylogenetic relationship of mitochondrial DNA in salmonids of the subfamily Salmoninae: analysis of the cytochrome b gene sequences].

On the basis of comparison of the cytochrome b gene nucleotide sequences from genetic databases, the possible phylogenetic relationships of mitochondrial DNA (mtDNA) among all major lineages of Salmoninae (Brachymystax, Parahucho, Salvelinus, Salmo, Parasalmo, and Oncorhynchus) were examined. Three different phylogenetic methods (UPGMA, NJ, and ML) yielded phylogenetic trees of essentially the same topology: (((Brachymystax, Parahucho), Salvelinus, Salmo), (Parasalmo, Oncorhynchus)). The results obtained using the maximum parsimony method were less clear. Apparently, the divergence of the main salmonid lineages occurred during a relatively short time period; hence, the number of synapomorphs marking the order of their divergence was extremely low. This may account for the relative failure to use the maximum parsimony method of phylogenetic reconstruction. The problem of concordance of mtDNA and species phylogenetic schemes is discussed. Their discrepancy in salmonids may be caused by interspecific introgressive hybridization.

Animals↗
PubMed2005

A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica.

Lack of introgression or divergent selection may be responsible for the maintenance of phenotypic differences between sympatric populations of crops and their wild progenitors. To distinguish between these hypotheses, amplified fragment length polymorphism markers were located on a molecular linkage map of Phaseolus vulgaris relative to genes for the domestication syndrome and other traits. Diversity for these same markers was then analyzed in two samples of wild and domesticated populations from Mesoamerica. Differentiation between wild and domesticated populations was significantly higher in parapatric and allopatric populations compared to sympatric populations. It was also significantly higher near genes for domestication compared to those away from these genes. Concurrently, the differences in genetic diversity between wild and domesticated populations were strongest around such genes. These data suggest that selection in the presence of introgression appears to be a major evolutionary factor maintaining the identity of wild and domesticated populations in sympatric situations. Furthermore, alleles from domesticated populations appear to have displaced alleles in sympatric wild populations, thus leading to a reduction in genetic diversity in such populations. These results also provide a possible experimental framework for assessing the long-term risk of transgene escape and the targeting of transgenes inside the genome to minimize the survival of these transgenes into wild populations following introduction by gene flow.

Chromosome Mapping↗
PubMed2006

Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus).

Hybrid zones provide an excellent opportunity for studying the consequences of genetic changes between closely related taxa. Here we investigate patterns of genetic variability and gene flow at four X-linked loci within and between the two subspecies of European rabbit (Oryctolagus cuniculus cuniculus and O. c. algirus). Two of these genes are located near the centromere and two are located near the telomeres. We observed a deep split in the genealogy of each gene with the root located along the deepest branch in each case, consistent with the evolution of these subspecies in allopatry. The two centromeric loci showed low levels of variability, high levels of linkage disequilibrium, and little introgression between subspecies. In contrast, the two telomeric loci showed high levels of variability, low levels of linkage disequilibrium, and considerable introgression between subspecies. These data are consistent with suppression of recombination near the centromere of the rabbit X chromosome. These observations support a view of speciation where genomic incompatibilities at different loci in the genome create localized differences in levels of gene flow between nascent species.

Animals↗