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PubMed2025

Dissecting seed composition QTL from wild soybean: fine-mapping, candidate gene identification, and evaluation of introgression effects on agronomic performance.

Seed composition QTL from wild soybean were confirmed and validated in two genetic backgrounds across multiple environments, candidate genes were identified, and agronomic performance of backcross introgression lines was evaluated. Through selection for soybean yield, breeders have inadvertently reduced seed protein content and increased oil due to phenotypic and genetic correlations between these three traits. Therefore, identifying alleles that increase protein without adversely affecting oil and yield is of interest for breeders and the entire soybean value chain. Previously, a G. max × G. soja population was used to map a protein-associated region to ~ 4.6 Mbp on chromosome (Chr) 14. The G. soja allele significantly increased protein 6.5-7.2 g kg-1, without significantly decreasing oil. Additionally, two oil quantitative trait loci (QTL) were reported on Chrs 8 and 14. In this study, we aimed to confirm the Chr 14 protein QTL, evaluate QTL effects on seed composition and agronomic performance, and further fine-map to identify candidate genes. We validated and fine-mapped the Chr 14 protein QTL to a 0.6 Mbp region in a different genetic background, where the G. soja allele significantly increased protein by 9.3 g kg-1. Further, we confirmed the Chr 14 oil QTL linked to the protein QTL and the Chr 8 oil QTL. Chr 14 protein QTL effects on agronomic traits were evaluated in a backcross population across eight environments. The QTL significantly increased protein content, without significantly impacting oil, maturity, or plant height. While the QTL impacted yield and lodging, its effect and significance varied within environments. The candidate genes identified for these three validated seed composition QTL, along with additional molecular markers developed, offer valuable resources for improving seed composition in soybean breeding programs.

Quantitative Trait Loci↗

PubMed2002

Strain and sex differences in repeated ethanol treatment-induced motor activity in quasi-congenic mice.

The B6.C quasi-congenic Recombinant QTL Introgression (RQI) strains of the b4i5 series have similar genetic background, but differ in about 5% of their genome from the C57BL/6ByJ (B6) background strain because they carry short chromosome segments introgressed from the BALB/cJ (C) donor strain. These RQI strains were derived from mouse lines selectively bred for high activity of mesencephalic tyrosine hydroxylase (TH/MES), therefore genetic variation in dopamine system-related behaviours, such as ethanol-induced motor activity, can be expected. Males and females of 17 RQI and two progenitor strains were tested for initial motor activity for 15 min after a habituating injection of saline, which was followed by an i.p. injection of saline or ethanol (2 g/kg) and an additional test of motor activity for 30 min. This procedure was repeated during 4 subsequent days. In all strains, the first-day ethanol treatment showed an inhibitory effect. With repetition of the treatment the inhibitory effect decreased, and a stimulatory effect could be observed with significant strain- and sex-dependent variation. Females exhibited higher activity in the saline group than males, and reached an equilibrium of inhibition and stimulation sooner than males with repetition of the ethanol treatment. The highest (> 25-fold) difference in activity after repeated ethanol treatment was detected between females of the two strains B6.Cb4i5-Alpha4/Vad and B6.Cb4i5-Beta13/Vad. These results firstly suggest that females are more sensitive to repeated ethanol exposure than males, secondly they support the observations that ethanol has both inhibitory and stimulatory effects on motor activity, which are affected by sex, genotype, and repetition of treatment, and thirdly offer new quasi-congenic animal models with highly different responses to ethanol allowing one to more quickly move to gene detection.

Animals↗

PubMed2001

Cross-species amplification of the Hordeum chilense genome using barley sequence-tagged-sites (STSs).

A selection of 51 barley Sequence-Tagged Sites (STSs) were studied for their utility in Hordeum chilense. They included four primer sets from wheat origin and six primer sets from oat origin. Forty-four primer pairs amplified H. chilense products consistently. Five primer pairs were suitable for studying the introgression of H. chilense in wheat because they amplified H. chilense products of distinct size. Six of the STSs showed polymorphism between different H. chilense accessions. The results showed that barley STSs could be useful for the genetic characterization of H. chilense, tritordeums and derived introgression lines.

Avena↗

PubMed2002

Physical and genetic mapping in the grasses Lolium perenne and Festuca pratensis.

A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.

Chromosomes, Plant↗

PubMed2000

Reinforcement and divergence under assortative mating.

Traits that cause assortative mating such as the flowering time in plants and body size in animals can produce reproductive isolation between hybridizing populations. Can selection against unfit hybrids cause two populations to diverge in their mean values for these kinds of traits? Here I present a haploid analytical model of one population that receives gene flow from another. The partial pre-zygotic isolation between the two populations is caused by assortative mating for a trait that is influenced by any number of genes with additive effects. The post-zygotic isolation is caused by selection against genetic incompatibilities that can involve any form of selection on individual genes and gene combinations (epistasis). The analysis assumes that the introgression rate and selection coefficients are small. The results show that the assortment trait mean will not diverge from the immigrants unless there is direct selection on the trait favouring it to do so or there are genes of very large effect. The amount of divergence at equilibrium is determined by a balance between direct selection on the assortment trait and introgression from the other population. Additional selection against hybrid genetic incompatibilities reduces the effective migration rate and allows greater divergence. The role of assortment in speciation is discussed in the light of these results.

Animals↗

PubMed2026

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗

PubMed2003

Transposable elements reveal the impact of introgression, rather than transposition, in Pisum diversity, evolution, and domestication.

The genetic structure and evolutionary history of the genus Pisum were studied exploiting our germplasm collection to compare the contribution of different mechanisms to the generation of diversity. We used sequence-specific amplification polymorphism (SSAP) markers to assess insertion site polymorphism generated by a representative of each of the two major groups of LTR-containing retrotransposons, PDR1 (Ty1/copia-like) and Cyclops (Ty3/gypsy-like), together with Pis1, a member of the En/Spm transposon superfamily. The analysis of extended sets of the four main Pisum species, P. fulvum, P. elatius, P. abyssinicum, and P. sativum, together with the reference set, revealed a distinct pattern of the NJ (Neighbor-Joining) tree for each basic lineage, which reflects the different evolutionary history of each species. The SSAP markers showed that Pisum is exceptionally polymorphic for an inbreeding species. The patterns of phylogenetic relationships deduced from different transposable elements were in general agreement. The retrotransposon-derived markers gave a clearer separation of the main lineages than the Pis1 markers and were able to distinguish the truly wild form of P. elatius from the antecedents of P. sativum. There were more species-specific and unique PDR1 markers than Pis1 markers in P. fulvum and P. elatius, pointing to PDR1 activity during speciation and diversification, but the proportion of these markers is low. The overall genetic diversity of Pisum and the extreme polymorphism in all species, except P. abyssinicum, indicate a high contribution of recombination between multiple ancestral lineages compared to transposition within lineages. The two independently domesticated pea species, P. abyssinicum and P. sativum, arose in contrasting ways from the common processes of hybridization, introgression, and selection without associated transpositional activity.

DNA Transposable Elements↗

PubMed2001

Evidence for broadscale introgressive hybridization between two redfish (genus Sebastes) in the North-west Atlantic: a rare marine example.

The evolutionary importance of introgressive hybridization has long been recognized by plant evolutionists, and there is now a growing recognition for its potential role in animals as well. Detailed empirical investigations of this evolutionary process, however, are still lacking in many animal groups, particularly in the marine environment. Using integrated microsatellite DNA data (eight loci analysed over 803 individuals representing 17 sampling locations) and multivariate statistical procedures (principal component, factorial correspondence and admixture proportion analyses), we: (i) provide a detailed dissection of the dynamics of introgressive hybridization between Sebastes fasciatus and S. mentella, two economically important redfishes from the North-west Atlantic; and (ii) infer the factors potentially involved in the maintenance of the hybrid zone observed in the gulf of St. Lawrence and south of Newfoundland. This study provided one of the rare examples of extensive introgressive hybridization in the ocean, and highlighted the predominant role of this process in shaping the extent of genetic diversity, interspecific differences and population structuring among redfishes from the North-west Atlantic. The extensive (average rate of introgression = 15%) but geographically circumscribed and asymmetrical pattern of introgressive hybridization, the sympatric persistence of two reproductively isolated introgressed groups, the differential patterns of linkage disequilibrium among samples, and the maintenance of genetic integrity of both species outside the defined zone of introgression despite high potential for gene flow, all implicated selection in promoting and maintaining the observed pattern of introgression.

Animals↗

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↗

PubMed2003

Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations.

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.

Animals↗