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PubMed2004

An AFLP-based interspecific linkage map of sympatric, hybridizing Colias butterflies.

Colias eurytheme and C. philodice are sister species with broad sympatry in North America. They hybridize frequently and likely share a significant portion of their genomes through introgression. Both taxa have been ecologically well characterized and exploited to address a broad spectrum of evolutionary issues. Using AFLP markers, we constructed the first linkage map of Colias butterflies. The map is composed of 452 markers spanning 2541.7 cM distributed over 51 linkage groups (40 major groups and 11 small groups with 2-4 markers). Statistical tests indicate that these AFLP markers tend to cluster over the map, with the coefficient of variation of interval sizes being 1.236 (95% C.I. is 1.234-1.240). This nonrandom marker distribution can account for the nonequivalence between the number of linkage groups and the actual haploid chromosome number (N = 31). This study presents the initial step for further marker-assisted research on Colias butterflies, including QTL and introgression analyses. Further investigation of the genomes will help us understand better the roles of introgression and natural selection in the evolution of hybridizing species and devise more appropriate strategies to control these pests.

Animals↗

PubMed2005

Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species.

In geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridization occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z chromosome, suggesting an important role for genes on the Z chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyzed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.

Animals↗

PubMed2006

Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.

A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.

Alleles↗

PubMed2006

Genetically engineered underdominance for manipulation of pest populations: a deterministic model.

We theoretically investigate the potential for introgressing a desired engineered gene into a pest population by linking the desired gene to DNA constructs that exhibit underdominance properties. Our deterministic model includes two independently segregating engineered constructs that both carry a lethal gene, but suppress each other. Only genotypes containing both or neither construct are viable. Both constructs also carry the desired gene with an independent regulatory mechanism. We examine the minimal number of individuals of an engineered strain that must be released into a natural population to successfully introgress the desired gene. We compare results for strains carrying single and multiple insertions of the constructs. When there are no fitness costs associated with the inserted constructs (when the lethal sequences are not expressed), the number of individuals that must be released decreases as the number of insertions in the genome of the released strain increases. As fitness costs increase, the number of individuals that must be released increases at a greater rate for release strains with more insertions. Under specific conditions this results in the strain with only a single insertion of each construct being the most efficient for introgressing the desired gene. We discuss practical implications of our findings.

Animals↗

PubMed2006

Increased germination of diverse crop-wild hybrid sunflower seeds.

Gene flow from crop fields to wild populations produces hybrids that often differ from their wild counterparts in growth form, phenology, and life history characteristics. Germination and dormancy dynamics have a strong influence on population persistence, competitive dynamics, and ultimately, plant fitness. They may also play a role in modifying crop gene introgression, which has been of primary interest since the release of transgenic crops. We investigated how seed germination and dormancy were affected by sunflower crop wild hybridization in both laboratory and field experiments. Hybridization increased seed germination and decreased dormancy. Of the nine wild populations we assayed, most of their hybrids had higher germination than the wilds of the same population. However, absolute germination levels varied by population and testing environment. Hybrids produced by three different crop lines differed in germination, and their germination rankings shifted across populations. Increased germination in hybrids could accelerate crop gene introgression, provided that hybrids germinate in an appropriate period. Differences in relative germination of wild and hybrid seed indicated that the effect of germination on introgression will likely vary by population due, in part, to initial levels of dormancy in the population. Therefore, the implications of gene flow from crops with novel characteristics or from transgenic crops will also vary by population.

Crops, Agricultural↗

PubMed2002

Enhancement of Seedling Emergence in Sweet Corn by Marker-Assisted Backcrossing of Beneficial QTL.

Seedling emergence is an important trait that can limit commercialization of sweet corn hybrids. This study was designed to test what effect beneficial QTL alleles that enhance seedling emergence exert when introgressed, using marker-assisted backcrossing, into sweet corn commercial germplasm. Three RFLP marker alleles linked to QTL that enhanced seedling emergence were identified in an F(2:3) sweet corn mapping population. A recombinant inbred line (RIL, F(8)) derived from this population was used as a donor parent to backcross the marker-QTL alleles into three elite commercial sweet corn inbreds. Plants in the three segregating BC(2) populations were crossed to the non-recurrent commercial inbreds to produce three BC(2)F(1) populations with families either segregating or lacking the marker donor allele(s). These three populations were evaluated for seedling emergence under field conditions in two successive years. Across the three populations, BC(2)F(1) families segregating for the donor QTL allele linked to the marker umc139 (on chromosome 2), bnl9.08 (on chromosome 8), or php200689 (on chromosome 1) displayed 40.8, 30.2, and 28.2% increases in seedling emergence, respectively, over the unmodified F(1)s. The introgressed QTL alleles were observed to enhance seedling emergence in the BC(2)F(1) generation as was observed in the original F(2:3) mapping population. Marker-QTL associated effects were reproducible across generations and populations indicating that QTL identified in one population can exert similar effects in different genetic backgrounds. Results suggest that using DNA marker technology can help to identify and introgress beneficial QTL alleles, shortening the time and resources required to develop improved germplasm.

Journal Article↗

PubMed2025

A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum.

Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.

Hordeum↗

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↗

PubMed2025

Substantial non-homologous recombination and structural variation results from Brassica AABC and CCAB hybrid meiosis.

Meiotic crossovers contribute to genetic diversity and play a crucial role in homologous chromosome segregation. Non-homologous crossovers in Brassica, involving the exchange of genetic material between genomes, can be valuable for transferring novel traits or characteristics between Brassica species. However, there are a limited number of studies that specifically investigate crossover frequencies in populations of interspecific hybrids. We investigated the distribution and frequency of homologous crossover events, as well as non-homologous recombination and structural variation, in hybrids between B. juncea (AABB) × B. napus (AACC) (resulting in AABC hybrids; 5 genotypes) and B. napus (AACC) × B. carinata (BBCC) (resulting in CCAB hybrids; 4 genotypes). The analysis was performed on individuals derived from microspore culture of both unreduced and reduced gametes produced by the AABC and CCAB hybrids. All AABC and almost all CCAB unreduced gamete-derived individuals and most AABC and CCAB reduced gamete-derived individuals showed copy number variation indicative of non-homologous (A-C) recombination. Additionally, a higher frequency of homologous crossovers, also in centromeric and pericentromic regions, was observed in the diploid genomes of the AABC and CCAB hybrids. Overall, these hybrid types show high frequencies of A-C introgressions, which may be useful in B. juncea or B. carinata introgression breeding, and this increased recombination frequency may help break up existing linkage disequilibrium blocks in the Brassica A and C genomes.

Meiosis↗

PubMed2002

Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae).

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing species. Twelve Spartina species have been sequenced for two nuclear DNA regions (ITS of ribosomal DNA, and part of the Waxy gene) and one chloroplast DNA spacer (trnT-trnL). Separate and conditional combined phylogenetic analyses using Cynodon dactylon as the outgroup have been conducted. Spartina is composed of two lineages. The first clade includes all hexaploid species: the Euro-African S. maritima (2n = 60), the East-American S. alterniflora (2n = 62) and the West-American S. foliosa (2n = 60). Spartina alterniflora appears as a closely related sister species to S. foliosa. Although belonging to the same lineage, Spartina maritima appears consistently more genetically differentiated from S. alterniflora than S. foliosa. The tetraploid species S. argentinensis (2n = 40) is placed at the base of this first clade according to the Waxy data, but its position is not well resolved by the other sequences. The second well-supported main lineage within genus Spartina includes the other tetraploid American species. Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora, suggesting a possible reticulate evolution for this species. The results agree with hybridization patterns occurring in Spartina: introgression involving closely related species (S. alterniflora and S. foliosa) on one hand, and alloploid speciation involving more differentiated species (S. alterniflora and S. maritima) on the other hand.

Cell Nucleus↗

PubMed1992

Isolation of DNA markers linked to a beet cyst nematode resistance locus in Beta patellaris and Beta procumbens.

In cultivated beet no useful level of resistance of the beet cyst nematode (BCN) Heterodera schachtii Schm. has been found, unlike the situation in wild species of the section Procumbentes. Stable introgression of resistance genes from the wild species into Beta vulgaris has not been achieved, but resistant monosomic additions (2n = 18 + 1), diploids of B. vulgaris with an extra alien chromosome carrying the resistance locus, have been obtained. Here we describe a new series of resistant monosomic fragment addition material of B. patellaris chromosome 1 (pat-1). We further describe the cloning of a single-copy DNA marker that specifically hybridizes with a monosomic addition fragment of approximately 8 Mb (AN5-90) carrying the BCN resistance locus. This marker and another fragment-specific, single-copy DNA marker probably flank the BCN locus on the addition fragment present in the AN5-203 material, which is approximately 19 Mb in size. Furthermore, several specific repetitive DNA markers have been isolated, one of which hybridizes to AN5-90 and also to DNA from a smaller DNA segment of Beta procumbens, present in line B883, carrying a BCN resistance locus introgressed into the B. vulgaris genome. This suggests that the specific repetitive marker is closely linked to the BCN locus.

Animals↗

PubMed1976

Schistosomiasis at Loum, Cameroun; Schistosoma haematobium, S. intercalatum and their natural hybrid.

A survey of 500 schoolchildren in Loum in 1968 revealed an overall infection rate of 54.2% with Schistosoma intercalatum and this was the only species of schistosome encountered. In 1972 a number of children were found to be passing schistosome eggs in their urine and these eggs ranged in shape and size from the forms characteristic for S. haematobium to those of S. intercalatum. Preliminary laboratory studies demonstrated that hybridisation between the two species was occurring. Subsequent field surveys showed that the snail hosts for the two parasites (B. rohlfsi for S. haematobium and B. forskali for S. intercalatum) were both present in the river Mbette and its tributaries in Loum and the distribution of the two snail species coincided closely with the distribution of the schistosomes in the human population. Detailed study of a small group of children passing hybrid eggs in their urine revealed that few of them were passing eggs in their faeces and that those eggs which were found in faeces were not viable. Analysis of schistosome egg-shape by plotting cumulative size-frequency data on probability paper demonstrated that the graph obtained from a natural hybrid series was different from that given by a known mixture of the two separate species. The hybrid series included a number of exceptionally large eggs resembling those of S. bovis but isolation of these eggs and subsequent laboratory passage of the parasites showed that they were part of the series and were not evidence of the presence of a third species. Hybridisation experiments in the laboratory showed that the cross S. haematobium male X S. intercalatum femal is fully viable but that the reverse mating is not successful, thus accounting for the failure of the faecal eggs recovered from children with hybrid infections. Histological results from laboratory passaged hybrids suggest that the Ziehl-positive staining reaction of the egg-shells of S. intercalatum may be a recessive character. The observations reported here indicate that S. haematobium has only recently become established in Loum and that it is, through introgressive hybridisation, replacing the indigenous S. intercalatum. A suggested explanation for the change in the parasite fauna is offered and this depends upon ecological changes resulting from forest clearance and agricultural development providing improved conditions for the spread of B. rohlfsi, the snail host for S. haematobium. It is suggested that, in contrast to recent reports on the spread of S. intercalatum, this species is in fact retreating and being replaced by S. haematobium in areas where forest clearance is taking place. In conclusion it is suggested that introgressive hybridisation of this kind may have been responsible for the evolution of certain characteristic local strains of African schistosomes.

Bulinus↗

PubMed1992

Allozyme and mitochondrial DNA analysis of a hybrid zone between white-tailed deer and mule deer (Odocoileus) in west Texas.

Thirty allozyme loci and 35 mitochondrial DNA (mtDNA) restriction sites were examined in 24 white-tailed deer and 46 mule deer from a hybrid zone in West Texas. A common mtDNA genotype is shared by all of the mule deer with 67% of the white-tailed deer. At the albumin locus, 13% of the white-tailed deer and 24% of the mule deer are heterozygous, sharing alleles that are otherwise species-specific in allopatric populations; 7% of the mule deer are homozygous for the allele that is characteristic of allopatric white-tailed deer. Gene flow appears to have been bidirectional, with greater genetic introgression into mule deer. The mtDNA data suggest that matings between white-tailed and mule deer have occurred in the past. Despite evidence of genetic introgression, analysis of multilocus genotypes indicates that none of the deer examined is an F1 hybrid. Production of such hybrids appears to be generally uncommon in North American deer; management plans that assume otherwise should be reconsidered.

Alleles↗

PubMed2006

Atlantic sturgeons (Acipenser sturio, Acipenser oxyrinchus): American females successful in Europe.

Recent molecular data on the maternally inherited mitochondrial (mt) DNA have challenged the traditional view that the now extinct Baltic sturgeon population belonged to the European sturgeon Acipenser sturio. Instead, there is evidence that American sea sturgeon Acipenser oxyrinchus historically immigrated into the Baltic Sea. In this study, we test the hypothesis that A. oxyrinchus introgressed into, rather than replaced, the A. sturio population in the Baltic. We established four single nucleotide polymorphisms (SNPs) in the nuclear MHC II antigen gene with a species-specific SNP pattern. Using an ancient DNA approach and two independent lines of molecular evidence (sequencing of allele-specific clones, SNaPshot), we detected both A. sturio and A. oxyrinchus alleles in the available museum material of the now extinct Baltic sturgeon population. The hybrid nature of the Baltic population was further confirmed by very high levels of heterozygosity. It had been previously postulated that the immigration of the cold-adapted A. oxyrinchus into the Baltic occurred during the Medieval Little Ice Age, when temperature likely dropped below the degree inducing spawning in A. sturio. Under this scenario, our new findings suggest that the genetic mosaic pattern in the Baltic sturgeon population (oxyrinchus mtDNA, sturio and oxyrinchus MHC alleles) is possibly caused by sex-biased introgression where spawning was largely restricted to immigrating American females, while fertilization was predominantly achieved by abundant local European males. The hybrid nature of the former Baltic sturgeon population should be taken into account in the current reintroduction measures.

Animals↗

PubMed2002

Improvement of hybrid yield by advanced backcross QTL analysis in elite maize.

We applied an advanced backcross breeding strategy to identify quantitative trait loci (QTLs) of agronomic importance in a cross between two elite inbreds of maize, RD6502 (Mo17-type recurrent parent) and RD3013 (Iodent donor parent). Two hundred and four BC(2) families were scored at 106 SSR, 15 AFLP, and 38 Heartbreaker (MITE) loci. BC(2) testcrosses (TC) with B73 were phenotyped at six locations in the Midwest and N.Y. We detected four grain yield, six grain moisture, and three plant height QTLs at which the RD3013 allele had a favorable effect ( p < 0.05). All four yield QTLs were selected as target introgressions in the development of BC(3)TC families. As predicted by BC(2)TC analysis, BC(3)TC entries containing introgressions at yld3.1 and yld10.1 significantly outperformed non-carrier entries by 11.1% (15.6 bu/A at one location) and 6.7% (7.1 bu/A averaged across two locations), respectively, in replicated Midwestern trials ( p < 0.05). Detection of yld10.1 effects in the BC(2)TC by spatial analysis (i.e., incomplete block, response surface, autoregressive, moving average or autoregressive moving average), but not by conventional single point analysis or interval mapping, indicated the utility of local environmental control for QTL mapping in unreplicated maize progeny. This work demonstrated that the advanced backcross QTL method can be applied to identify and manipulate useful QTLs in heterotic inbreds of elite maize. Genetic gains by this approach can be coupled with the maintenance and selection of favorable epistatic gene complexes by traditional hybrid breeding for maize improvement.

Journal Article↗

PubMed2002

Ancestors of white clover ( Trifolium repens L.), as revealed by isozyme polymorphisms.

Isozymes were used to study the putative ancestors of white clover ( Trifolium repens L.). Ten enzymes were examined, and 18 loci were resolved via starch-gel electrophoresis for accessions representing T. repens, Trifolium isthmocarpum, Trifolium nigrescens, Trifolium occidentale and Trifolium uniflorum, in addition to two more distantly related species, Trifolium alpinum and Trifolium purseglovei. Nei's genetic identities indicate that T. uniflorum and T. nigrescens are the closest relatives of T. repens. The isozyme data thus support a hypothesis that the two genomes of the tetraploid T. repens could have been derived from hybridization between T. nigrescens and T. uniflorum. This conclusion is further supported by shared alleles between T. repens, T. nigrescens and T. uniflorum. However, the origin of T. repens is somewhat obscured by the presence of shared alleles between T. repens and both T. occidentale and T. isthmocarpum, suggesting that introgression of genes from the latter two species into T. repens may also have taken place. High values of genetic identity are shared between T. occidentale with T. nigrescens and T. uniflorum, also indicative of introgression. Alternatively the presence of shared alleles among the five species may reflect their recent common ancestry.

Evolution, Molecular↗

PubMed2002

QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat.

QTL interval mapping for grain protein content (GPC) in bread wheat was conducted for the first time, using a framework map based on a mapping population, which was available in the form of 100 recombinant inbred lines (RILs). The data on GPC for QTL mapping was recorded by growing the RILs in five different environments representing three wheat growing locations from Northern India; one of these locations was repeated for 3 years. Distribution of GPC values followed normal distributions in all the environments, which could be explained by significant g x e interactions observed through analyses of variances, which also gave significant effects due to genotypes and environments. Thirteen (13) QTLs were identified in individual environments following three methods (single-marker analysis or SMA, simple interval mapping or SIM and composite interval mapping or CIM) and using LOD scores that ranged from 2.5 to 6.5. Threshold LOD scores (ranging from 3.05 to 3.57), worked out and used in each case, however, detected only seven of the above 13 QTLs. Only four (QGpc.ccsu-2B.1; QGpc.ccsu-2D.1; QGpc.ccsu-3D.1 and QGpc.ccsu-7A.1) of these QTLs were identified either in more than one location or following one more method other than CIM; another QTL (QGpc.ccsu-3D.2), which was identified using means for all the environments, was also considered to be important. These five QTLs have been recommended for marker-assisted selection (MAS). The QTLs identified as above were also validated using ten NILs derived from three crosses. Five of the ten NILs possessed 38 introgressed segments from 16 chromosomes and carried 42 of the 173 markers that were mapped. All the seven QTLs were associated with one or more of the markers carried by the above introgressed segments, thus validating the corresponding markers. More markers associated with many more QTLs to be identified should become available in the future by effective MAS for GPC improvement.

Analysis of Variance↗

PubMed2002

Detection of QTL linked to Fusarium head blight resistance in Sumai 3-derived North Dakota bread wheat lines.

During the past decade Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe has resulted in severe grain yield and quality losses of wheat (Triticum aestivum L.) in the Northern Great Plains of the U.S. Given the complexity of breeding for FHB resistance, molecular markers associated with this trait will be valuable in accelerating efforts to breed resistant cultivars. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) for FHB resistance in wheat using a set of lines obtained by several cycles of crossing to North Dakota adapted genotypes, which derived their resistance from cv. Sumai 3. Microsatellite markers spanning the wheat genome were used to screen parents and derived lines. Polymorphisms for parental alleles were compared to disease scores for Type II resistance. The probability of linkage between markers and introgressed resistance genes was calculated using a binomial probability formula based on the assumption that a molecular marker at a specific distance from the introgressed gene, in a near-isogenic line (NIL), will carry the donor-parent allele as a function of the distance between marker and gene and the number of backcrosses/selfs performed in deriving the NIL. Microsatellite loci Xgwm533 and Xgwm274 were significantly associated with QTL for FHB resistance.

Data Interpretation, Statistical↗