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PubMed2003

The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis.

The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well-understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but approximately 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.

Alleles↗
PubMed2000

Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: a tool for gene mapping and gene discovery.

A novel population consisted of a set of 99 near isogenic lines (NILs) and backcross recombinant inbred lines (BCRILs) derived from a cross between the cultivated tomato Lycopersicon esculentum cv. E6206 and L. hirsutum accession LA1777 is presented. Most of the lines contain a single defined introgression from L. hirsutum in the L. esculentum genetic background and together, the lines provide a coverage of more than the 85% of the L. hirsutum genome. These lines represent a new tool to uncover the genetic resources hidden in L. hirsutum as well as to study the genes responsible of its unique biology. Furthermore, the study of the allelic frequency and heterozygosity among BCRILs showed that specific genomic regions were likely subjected to unintentional selection pressures during the stock development. Genes involved in the reproductive behavior and (or) pollen viability are hypothesized to be responsible for these alterations.

Breeding↗
PubMed1992

Detection of polymorphic loci in Arachis germplasm using random amplified polymorphic DNAs.

The development of easily scoreable genetic markers in Arachis will facilitate the introgression of desirable traits from wild species into adapted germplasm. We have used random amplified polymorphic DNAs (RAPDs) to identify polymorphic molecular markers in a range of wild and cultivated Arachis species. From a total of sixty 10-mer oligonucleotide primers, 49 polymorphic loci were identified between cultivated A. hypogaea type (TMV-2) and a synthetic amphidiploid (B x C)2 created from a A. batizocoi and A. chacoense cross. The inheritance of polymorphic markers, both in the amphidiploid and in the F1 progeny in a TMV-2 x (B x C)2 cross, has also been demonstrated. The potential exploitation of RAPD markers in groundnut improvement programs is discussed.

Arachis↗
PubMed2003

Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages.

Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridization events and locally infesting fields. Using a chloroplastic marker and a set of nuclear microsatellite loci, the occurrence of crop-to-wild gene flow was investigated in the French sugar beet production area within a 'contact-zone' in between coastal wild populations and sugar beet fields. The results did not reveal large pollen dispersal from weed to wild beets. However, several pieces of evidence clearly show an escape of weedy lineages from fields via seed flow. Since most studies involving the assessment of transgene escape from crops to wild outcrossing relatives generally focused only on pollen dispersal, this last result was unexpected: it points out the key role of a long-lived seed bank and highlights support for transgene escape via man-mediated long-distance dispersal events.

Beta vulgaris↗
PubMed1998

Analysis of the mesotelencephalic dopamine system by quantitative-trait locus introgression.

One of the significant factors that affect brain dopamine function is the activity of tyrosine hydroxylase (TH), the first and rate-limiting enzyme in catecholamine biosynthesis. For the analysis of the genetically determined role of dopamine function and TH in behavior and in the regulatory mechanisms of the mesotelencephalic dopamine system we devised a novel genetic strategy (Vadasz; Mouse Genome 88:16-18; 1990). We hypothesized that phenotypic introgression and recombinant fixation could ensure the transfer of Quantitative Trait Loci (QTL) from one strain onto the genetic background of another strain, and new, genetically very similar quasi-congenic strains could be created that would carry individual QTLs, or QTLs in various combinations. Here we summarize the construction of the first set of QTL Introgression strains, and present evidence that QTLs that are responsible for the continuous variation of mesencephalic tyrosine hydroxylase activity (TH/MES), have been transferred onto the C57BL/6By (B6) strain background from BALB/cJ (C) and CXBI (I) donor strains with high and low TH/MES, respectively. The QTL transfer was carried out in two directions by repeated backcross-intercross cycles with concomitant selection for the extreme high and low expressions of TH/MES in replicates, resulting in four QTL Introgression lines. Analysis of regional brain TH activities in the course of the QTL introgression indicated that (a) TH activity in B6.I lines showed quite limited heritability, (b) TH/MES was not highly correlated with striatal TH, and (c) the control of hypothalamic and olfactory tubercle TH activities was largely independent from that of TH/MES. Examination of the open-field (OF) behavior data demonstrated that TH activity did not correlate significantly with OF behavior. After 5 backcross-intercross cycles, TH/MES in each replicate line was still significantly different from that of the B6 background strain. A genomewide scanning of microsatellite markers in the QTL introgression lines demonstrated that about 96% of the markers were of background (B6) type. These results indicate the successful transfer of TH/MES QTLs. After the QTL transfer phase of the experiment altogether more than 100 new RQI strains were initiated in the QTL Introgression lines by strict brother x sister mating. After fixing the introgressed QTLs, ten of the inbred RQI strains were tested for TH/MES. The results showed that in one of the new RQI strains TH/MES was restored to a level that is characteristic to the C donor strain, while TH/MES values in some other strains were between those of the background and donor strains, confirming our hypothesis that phenotypic introgression and recombinant fixation can ensure a virtually complete transfer of QTLs. We conclude from this study that complex, continuously distributed neural traits can successfully be subjected to QTL introgression, and the results raise the possibility that the RQI method can be efficiently applied for gene mapping of complex neural and behavioral traits even if their phenotypic expression is sensitive to confounding developmental and environmental variations, genetic interactions, and genotype-environment interactions.

Animals↗
PubMed2001

Development of a set of Triticum aestivum-Aegilops tauschii introgression lines.

New wheat introgression lines were obtained which contain different segments of individual chromosomes of Aegilops tauschii in the Triticum aestivum cv. 'Chinese Spring' background. The introgression lines were developed to examine various subsets of alleles from the wild grass in the genetic background of common wheat. As starting point substitution lines of 'Chinese Spring' in which single chromosomes of the D genome had been replaced by homologous chromosomes of a synthetic wheat were used. Synthetic wheat had been obtained earlier from a cross between the tetraploid emmer (genomes AABB) and wild grass Aegilops tauschii (genome DD). The seven wheat chromosome substitution lines carrying different chromosomes of Ae. tauschii were crossed twice to T. aestivum cv. 'Chinese Spring' and 259 BC1-progeny plants were analysed. Phenotypic evaluation was carried out for different traits such as plant height, spikelet number, peduncle length, flowering time, spike length, tiller number, grain weight per ear, fertility and thousand kernel weight. Genotypic analysis was performed using a set of 65 microsatellite markers previously mapped on the chromosomes of the D genome of wheat. During this analysis recombinant lines carrying different segments of Ae. tauschii chromosomes were detected. Plants containing small introgressions of the alien genetic material were selfed to get homozygous lines and plants carrying large pieces of the donor chromosome were backcrossed again to get smaller introgressions. Further microsatellite analysis of selected BC1F2-progeny plants resulted in detection of a first set of 36 homozygous lines carrying different pieces of Ae. tauschii genome.

Alleles↗
PubMed1991

Pollen-mediated introgression and hybrid speciation in Louisiana irises.

Populations of the "Louisiana iris" species Iris fulva, I. hexagona, and I. nelsonii were examined genetically to test for interspecific gene flow between I. fulva and I. hexagona, for pollen- versus seed-mediated introgression between these species, and for the presumed hybrid origin of I. nelsonii. Genetic markers were identified by using both a polymerase chain reaction-like method that allows the identification of random, nuclear markers and standard polymerase chain reaction experiments involving specific chloroplast DNA (cpDNA) oligonucleotides. Restriction endonuclease digestions of the cpDNA amplification products resolved diagnostic restriction site differences for I. fulva and I. hexagona. The distribution of the species-specific nuclear markers supports a hypothesis of bidirectional introgression between I. fulva and I. hexagona. Thus, individuals analyzed from a contemporary hybrid population demonstrate multilocus genotypes that are indicative of advanced-generation hybrid individuals. Furthermore, several markers from the alternate species were present in low frequency in one allopatric population each of I. fulva and I. hexagona. Data from the nuclear analysis also support the hypothesized hybrid origin of I. nelsonii from the interaction of I. fulva and I. hexagona. Finally, cpDNA data support the hypothesis that the localized and the dispersed introgression are largely due to pollen transfer. In addition to the biological implications, this study demonstrates the power of the polymerase chain reaction methodology for the rapid identification of random and specific genetic markers for testing evolutionary genetic hypotheses.

Journal Article↗
PubMed2000

Congenic strains developed for alcohol- and drug-related phenotypes.

Quantitative trait loci (QTLs) for many alcohol- and drug-related traits have been mapped using well-accepted mapping techniques. The ultimate goal of gene identification necessitates confirmation of the QTL and reduction of the interval surrounding the QTL; both can be accomplished in congenic strains. These strains carry a chromosomal region introgressed from a donor strain onto the genetic background of a second, recipient strain. Multiple generations of backcrossing reduce the unlinked donor genome to less than 0.1%. Then, phenotypic comparisons between mice congenic for the donor region and controls from the recipient strain allow confirmation of the QTL effect. Animals with recombinations in the donor region can be used to generate interval-specific congenic recombinant lines. Numerous congenic strains are currently being developed in which chromosomal regions carrying QTLs for alcohol- and drug-related traits have been transferred from one strain onto a second strain. The purpose of this review is to summarize the chromosomal regions, donor and recipient strains, and results obtained from these congenics. Most researchers developing such strains are willing to share these resources to facilitate localization of the genetic bases of other phenotypes.

Alcoholism↗
PubMed2003

Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites.

Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.

Animals↗
PubMed1998

Culicoides variipennis (Diptera: Ceratopogonidae) complex in Virginia.

Immature Culicoides variipennis (Coquillett) were sampled from aquatic habitats throughout Virginia, reared to adults, and examined by isozyme electrophoresis to assess their taxonomic status. Data from 22 counties showed that C. v. variipennis is widespread and common, the predominant taxon throughout Virginia, and genetically similar to C. v. variipennis in Maryland. Because C. v. variipennis is considered an inefficient vector of the bluetongue viruses, this observation is consistent with the low seroprevalence of bluetongue in indigenous livestock of the mid-Atlantic region. Culicoides v. sonorensis Wirth & Jones, considered to be the primary North American vector of the bluetongue viruses, was recovered in large numbers only from a wastewater lagoon at a dairy in southeastern Virginia, but also was detected at low levels in 6 other counties. Comparison of genetic distances and patterns of discriminating alleles among Virginia populations of C. v. variipennis and C. v. sonorensis showed that respective subspecies are genetically distinct and show no evidence of introgression, irrespective of geographic- and habitat-level sympatry. The persistence of a pure C. v. sonorensis population in a dairy wastewater lagoon may reflect physico-chemical factors that influence the distribution of immature C. variipennis complex populations. A better understanding of the distribution of the C. variipennis complex will benefit regionalization of U.S. exports of livestock and livestock germplasm to bluetongue-free countries.

Animals↗
PubMed2001

barren inflorescence2 regulates axillary meristem development in the maize inflorescence.

Organogenesis in plants is controlled by meristems. Shoot apical meristems form at the apex of the plant and produce leaf primordia on their flanks. Axillary meristems, which form in the axils of leaf primordia, give rise to branches and flowers and therefore play a critical role in plant architecture and reproduction. To understand how axillary meristems are initiated and maintained, we characterized the barren inflorescence2 mutant, which affects axillary meristems in the maize inflorescence. Scanning electron microscopy, histology and RNA in situ hybridization using knotted1 as a marker for meristematic tissue show that barren inflorescence2 mutants make fewer branches owing to a defect in branch meristem initiation. The construction of the double mutant between barren inflorescence2 and tasselsheath reveals that the function of barren inflorescence2 is specific to the formation of branch meristems rather than bract leaf primordia. Normal maize inflorescences sequentially produce three types of axillary meristem: branch meristem, spikelet meristem and floral meristem. Introgression of the barren inflorescence2 mutant into genetic backgrounds in which the phenotype was weaker illustrates additional roles of barren inflorescence2 in these axillary meristems. Branch, spikelet and floral meristems that form in these lines are defective, resulting in the production of fewer floral structures. Because the defects involve the number of organs produced at each stage of development, we conclude that barren inflorescence2 is required for maintenance of all types of axillary meristem in the inflorescence. This defect allows us to infer the sequence of events that takes place during maize inflorescence development. Furthermore, the defect in branch meristem formation provides insight into the role of knotted1 and barren inflorescence2 in axillary meristem initiation.

Chromosome Mapping↗
PubMed1990

Genetic polymorphism of urine deoxyribonuclease I isomerases of subterranean mole rats, Spalax ehrenbergi superspecies, in Israel: ecogeographical patterns and correlates.

Genetic polymorphism of urine deoxyribonuclease I (DNase I) of mole rats was analyzed by isoelectric focusing in a thin-layer polyacrylamide gel (IEF-PAGE). One hundred and three subterranean mole rats, comprising 13 populations belonging to the four chromosomal species (2n = 52, 54, 58, 60) of the actively speciating Spalax ehrenbergi superspecies in Israel, were tested. The following results were indicated. (i) Spalax DNase I consisted of 6-12 major isozymes. (ii) Four phenotypes (numbers in parentheses) were 1 (92), 1-2 (5), 1-3 (4), and 2 (1). The decreasing order of genetic diversity, He, in the four species was 0.37, 0.13, 0.10, and 0.0 for 2n = 58, 52, 54, and 60, respectively. (iii) Spearman rank correlations and multiple regression analyses indicated associations of allele frequencies and genetic diversity with climatic and vegetation factors. We concluded that (a) climatic selection, either directly or indirectly through plant (i.e., food resources) diversity, plays an important role in DNase genetic differentiation and (b) no gene flow and introgression occur between the recent derivative of speciation (2n = 60) and its ancestor (2n = 58), suggesting the operation of reproductive isolation between both species despite natural hybridization.

Animals↗
PubMed2001

Genetic verification of the role of CCK-AR in pancreatic proliferation and blood glucose and insulin regulation using a congenic rat carrying CCK-AR null allele.

A number of studies have indicated that cholecystokinin type A receptor (CCK-AR) plays a crucial role in postnatal pancreatic proliferation and blood glucose regulation through stimulating insulin secretion. The Otsuka Long-Evans Tokushima Fatty (OLETF) rat has been shown to possess poor pancreatic proliferation (PPP) capability after pancreatectomy (Px). Here we have constructed a congenic strain which introgressed an OLETF-derived 18.5 cM genomic fragment identified in our previous quantitative trait locus (QTL) analysis as a locus responsible for PPP into normoglycemic F344 genetic background The introgressed region includes CCK-AR null mutation. After Px, the congenic rat showed weak pancreatic proliferation equivalent to that of the OLETF rat. Furthermore, post-surgery non-fasting blood glucose levels for the congenic rats are significantly higher in comparison with the F344 rats. At 28 days after Px, the congenic rats also showed lower blood insulin levels than the F344 rats. These results further provide the genetic evidence that 1) CCK-AR is essential for pancreatic regeneration; 2) impaired pancreatic proliferation mediates the development of hyperglycemia.

Alleles↗
PubMed2026

A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.

Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant <&#x2009;50&#x2009;bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319&#x2009;bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.

Animals↗
PubMed2002

Wind-dispersed pollen mediates postglacial gene flow among refugia.

A long-term genetic legacy of refugial isolation has been postulated and was demonstrated for maternal refugial lineages for numerous plant and animal species. The lineages were assumed to have remained separated from each other for several glacial periods. The conifer Abies alba Miller, silver fir, is an excellent model to test whether pollen-mediated gene flow may eliminate the genetic imprints of Pleistocene refugial isolation. Two DNA markers with contrasting modes of inheritance were applied to 100 populations covering the entire range of silver fir in Europe. The markers exhibited each two highly conserved alleles based on an insertion/deletion of 80 bp in the fourth intron of the mitochondrial nad5 gene and on a synonymous substitution in the chloroplast psbC gene. The geographical distribution of the maternally inherited mitochondrial variation supported the existence of at least two refugia with two recolonizing maternal lineages remaining largely separated throughout the range. The cline of the nad5 allele frequencies was much steeper than the one of the two psbC alleles. The psbC cline was as wide as the whole range of the species. Our results provide striking evidence that even a species with very long generation times and heavy pollen grains was able to establish a highly efficient pollen-mediated gene flow between refugia. Therefore we postulate that an exchange of genetic information between refugia by range-wide paternal introgression is possible in wind-pollinated plant species.

Abies↗
PubMed2002

[Natural hybridization between 2 sympatric species of mice, Mus musculus domesticus L. and Mus spretus Lataste].

Using protein loci and DNA markers, we show by a multilocus genetic analysis that certain populations of the two sympatric mouse species Mus musculus domesticus and Mus spretus show clear signs of partial introgression. Given the sterility of F1 males and the known partial genetic incompatibilities between the genomes of the two species, our finding does not invalidate the biological species complex, but allows to think that very limited genetic exchanges remain possible even long after the divergence of taxa. This may have some consequences on the dynamics of certain kinds of invasive or advantageous DNAs like transposable elements or pathogen resistance genes.

Africa, Northern↗
PubMed2026

The curious case of sporadic nematode susceptibility in "Tifguard" peanut (Arachis hypogaea): seed mixture or genetic instability?

The Runner-type peanut (Arachis hypogaea L.) cultivar "Tifguard" carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of "Tifguard" plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1% to 5%); suggesting that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant "Tifguard" but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

Arachis↗