Introgression Of Genetic Material Research Articles

Population Genomics of Secondary Contact

One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from an endemic population. The simulated coalescent histories are sampled from models that describe the evolution of entire chromosomes, thereby allowing the expected length of introgressed haplotypes to be estimated. The results indicate that our ability to identify reticulate evolution from genetic data is highly variable and depends critically upon the duration of the period of allopatry, the timing of the secondary contact event, as well as the sizes of the populations at the time of contact. One particularly interesting result arises when secondary contact occurs close to the time of a severe founder event, in this case, genetic introgression can be substantially more difficult to detect. However, if secondary contact occurs after such a founding event, when the range of the colonizing population increases, introgression is more readily detectable across the genome. This result may have important implications for our ability to detect introgression between ancestrally bottlenecked modern human populations and archaic hominin species, such as Neanderthals.

Genetic Evidence of Introgressive Invasion of the Globally Imperiled Scirpus longii by the Weedy Scirpus cyperinus (Cyperaceae) in Nova Scotia

Random Amplified Polymorphic DNA (RAPD) markers were used to determine whether populations of the global rarity Scirpus longii (Long's bulrush) are vulnerable to loss by introgression of genetic material from the weedy S. cyperinus (woolgrass). Shoots from 104 Scirpus plants were obtained from 10 sites in the watershed of the lower Medway River in Nova Scotia, Canada. A putative site of introgression (a seasonally flooded bog) was divided into five subsites: one large stand of vegetative plants and four patches of annually flowering plants clustered at one end of the site. Thirty-five dominant DNA markers were found among individuals from all sites and eight species-specific markers were identified for each of the two species. Nineteen different combinations of species-specific markers were present in the 39 individuals from the site of introgression, and, as expected for introgression, there was strong correlation (r = −0.80, p < 0.0001) between the numbers of the two types of markers. The vegetative and flowering subsites had distinctive hybrid indices: 0.76 and 0.27 of S. longii genome, respectively. The former indicates that S. cyperinus contributed about one-quarter of the genetic material of the plants from the subsite that accounts for more than 99% of the Scirpus at the site of introgression. Hybrid indices also show evidence of introgression in two of the 12 plants obtained at one of the presumed S. longii sites. Our results indicate that gene flow has occurred between S. cyperinus and S. longii at two S. longii populations, hybrid plants are capable of sexual reproduction, and Long's bulrush in Nova Scotia is vulnerable to loss by introgression. Conservation at the landscape level is needed to suppress anthropogenic disturbances that might allow S. cyperinus to threaten the genetic integrity of S. longii.

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193) is about four times lower than the genomic background (K = 0.0743). We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the species stopped forming fertile hybrids, thereby complementing the average portrait of divergence between species provided by genomic data.

Origin of resistance to plum pox virus in Apricot: what new AFLP and targeted SSR data analyses tell

Amplified fragment length polymorphisms (AFLP) and targeted simple sequence repeats (SSR) were employed to assess genetic similarity of North American apricots having natural resistance to plum pox virus (PPV) within diversified germplasm including six nondomesticated apricot species. On a dendrogram constructed from 231 AFLP loci, the position of the North American cultivars reflects relatedness to the European apricots and introgression of non-European germplasm as well. The occurrence of diagnostic AFLP markers supports an introgression of Chinese germplasm into the North American PPV resistant assortment and supports a different breeding history for ‘Stark Early Orange’ (SEO) and Goldrich-Harlayne lineages. Five SSR loci linked to the PPV resistance region on G1 provided evidence that the investigated lineages (SEO and ‘Harlayne’–‘Goldrich’) have the same or related source of resistance introduced presumably from Northern China. Possible introgression of genetic material from nondomesticated apricots P. mandshurica sp, P. sibirica var. davidiana and P. mume sp. was detected and discussed.

Mapping of a gene (Vir) for a non-glaucous, viridescent phenotype in bread wheat derived from Triticum dicoccoides, and its association with yield variation

The introgression of desirable genes or alleles from the wild relatives of hexaploid wheat can be a valuable source of genetic variation for wheat breeders to enhance modern varieties. The UK Group 1 bread making variety Shamrock is an example where the introgression of genetic material from wild emmer (Triticum dicoccoides) has been used to develop a modern cultivar. A striking character of Shamrock is its unique viridescent colour compared to other UK wheats, a trait that coincides with a non-glaucous phenotype. A doubled haploid population segregating for the trait (Shamrock × Shango) was examined to map the location of Vir, and analyse any associated pleiotropic effects. The viridescence gene located to the distal end of the short arm of chromosome 2B. QTL analysis of productivity traits shows an association between Vir and a significant delay in senescence, resulting in an extension of the grain filling period. A stable yield QTL, accounting for up to a quarter of the variation in one case, was also identified at or near Vir, indicating significant yield benefits either by linkage or pleiotropy.

Environmental biosafety and transgenic potato in a centre of diversity for this crop

The Nuffield Council on Bioethics suggests that introgression of genetic material into related species in centres of crop biodiversity is an insufficient justification to bar the use of genetically modified crops in the developing world. They consider that a precautionary approach to forgo the possible benefits invokes the fallacy of thinking that doing nothing is itself without risk to the poor. Here we report findings relevant to this and other aspects of environmental biosafety for genetically modified potato in its main centre of biodiversity, the central Andes. We studied genetically modified potato clones that provide resistance to nematodes, principal pests of Andean potato crops. We show that there is no harm to many non-target organisms, but gene flow occurs to wild relatives growing near potato crops. If stable introgression were to result, the fitness of these wild species could be altered. We therefore transformed the male sterile cultivar Revolucion to provide a genetically modified nematode-resistant potato to evaluate the benefits that this provides until the possibility of stable introgression to wild relatives is determined. Thus, scientific progress is possible without compromise to the precautionary principle.

Gene introgression into Coffea arabica by way of triploid hybrids (C. arabica x C. canephora).

Interspecific triploid hybrid plants between the tetraploid species Coffea arabica L. and the diploid species C. canephora P. were backcrossed to C. arabica. Although characterised by a low production and an important fruit dropping, all attempted crosses (ie, 6) generated BC(1) progenies. Flow cytometric analysis of the nuclear DNA content revealed that most of the BC1 individuals were nearly tetraploid. Among the male gametes produced by the interspecific triploid hybrids, those presenting a high number of chromosomes appeared strongly favoured. Only pollen mother cells having nearly 22 chromosomes were effective, the others leading to deficient endosperm and fruit dropping. Molecular markers (ie, microsatellite and AFLP) combined with evaluations of morphological characteristics and resistance to leaf rust were applied to verify the occurrence of gene transfer from C. canephora into C. arabica, and to estimate the amount of introgression present in BC(1) individuals. The results reveal a strong deficiency in the C. canephroa alleles indicating a severe counter-selection against the introgression of genetic material from C. canephora into C. arabica by way of triploid hybrids. However, introgressants displaying desirable traits such as a high resistance to leaf rust were obtained. The low level of introgression could be an advantage by facilitating the recovery of the recurrent parent and possibly reducing the number of required backcrosses. On the other hand, this could be a limitation when attempting the transfer of a complex trait or several simply inherited traits.

Evaluation of phylogenetic relationships between five polyploid Aegilops L. species of the U-genome cluster by means of chromosomal analysis

Four tetraploid (Aegilops ovata, Ae. biuncialis, Ae. columnaris, and Ae. triaristata) and one hexaploid (Ae. recta) species of the U-genome cluster were studied using C-banding technique. All species displayed broad C-banding polymorphism and high frequency of chromosomal rearrangements. Chromosomal rearrangements were represented by paracentric inversions and intragenomic and intergenomic translocations. We found that the processes of intraspecific divergence of Ae. ovata, Ae. biuncialis, and Ae. columnaris were probably associated with introgression of genetic material from other species. The results obtained confirmed that tetraploid species Ae. ovata and Ae. biuncialis occurred as a result of hybridization of a diploid Ae. umbellulata with Ae. comosa and Ae. heldreichii, respectively. The dissimilarity of the C-banding patterns of several chromosomes of these tetraploid species and their ancestral diploid forms indicated that chromosomal aberrations might have taken place during their speciation. Significant differences of karyotype structure, total amount and distribution of C-heterochromatin found between Ae. columnaris and Ae. triaristata, on the one hand, and Ae. ovata and Ae. biuncialis, on the other, evidenced in favor of different origin of these groups of species. In turn, similarity of the C-banding patterns of Ae. columnaris and Ae. triaristata chromosomes suggested that they were derived from a common ancestor. A diploid species Ae. umbellulata was the U-genome donor of Ae. columnaris and Ae. triaristata; however, the donor of the second genome of these species was not determined. We assumed that these tetraploid species occurred as a result of introgressive hybridization. Similarity of the C-banding patterns of chromosomes of Ae. recta and its parental species Ae. triaristata and Ae. uniaristata indicated that the formation of the hexaploid form was not associated with large modifications of the parental genomes.

Characterisation of wheat-rye recombinants with RFLP and PCR probes

The introgression of genetic material from alien species into wheat has become an important tool in modern wheat breeding. Ideally, only the trait of interest and no flanking material should be transferred. Random recombination between the genetic material is therefore of paramount importance. In a model system, we examined 17 recombinants putatively between chromosome 1D of wheat and 1R of rye with 60 random RFLP and three PCR markers. The recombinants had been generated by removing the normal effect of the Ph1 gene in the wheat background. Amongst the nine short-arm recombinants, three breakpoints were identified but no differentiation could be made between the five proximal recombinants. For the eight long-arm recombinants analysed only two breakpoints were identified with 36 markers. However, only a single RFLP marker was able to differentiate between the recombinants. Indeed the long-arm results are consistent with the possibility that only the rye telomeric region had been transferred. These results indicate either a strong clustering of the RFLP markers near the centromere or else imply that recombination induced between wheat and rye in the absence of the normal effect of the Ph1 gene occurs at only restricted sites. The results allow new primary recombinants to be selected for intercrossing to generate secondary recombinants which are expected to have a smaller interstitial rye segment than that present in DR-A1.

Isolation and characterization of wheat-rye recombinants involving chromosome arm 1DS of wheat

The introgression of genetic material from alien species is assuming increased importance in wheat breeding programs. One example is the translocation of the short arm of rye chromosome 1 (1RS) onto homoeologous wheat chromosomes, which confers disease resistance and increased yield on wheat. However, this translocation is also associated with dough quality defects. To break the linkage between the desirable agronomic traits and poor dough quality, recombination has been induced between 1RS and the homoeologous wheat arm IDS. Seven new recombinants were isolated, with five being similar to those reported earlier and two havina new type of structure. All available recombinantsw ere characterized with DNA probes for the loci Nor-R1, 5SDna-R1, and Tel-R1. Also, the amount of rye chromatin present was quantified with a dispersed rye-specific repetitive DNA sequence in quantitative dot blots. Furthermore, the wheat-rye recombinants were used as a mapping tool to assign two RFLP markers to specific regions on chromosome arms 1DS and 1RS of wheat and rye, respectively.

Breeding experiments to distinguish two sibling species of Halicarcinus (Crustacea, Brachyura)

Hybridization experiments and various salinities were used in investigating the status of two Halicarcinus lacustris‐like, forms, one of which has no free larval stages (direct‐development) and the other of which has normal larval stages (indirect‐development).Hybrids were produced, at least from indirect‐development female x direct‐development male crosses, but introgression of genetic material was limited to F2 hybrids from the female parental form. There were no intergrades between the two modes of development in F1 and F2 hybrids or as a response to salinity.These forms are established as sibling species. The name lacustris applies to the direct‐development form and the other is a new species, H. paralacustris, which is described. Hybridization in the field is unlikely due to geographical and reproductive isolating mechanisms. Contrary to a previous view, it seems that H. lacustris had a recent origin in Australia and transport by water birds is suggested as the mode of dispersal through south‐east Australasia.