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PubMed2002

[Molecular analysis of leaf-rust resistant introgression lines obtained by crossing hexaploid wheat Triticum aestivum with tetraploid wheat Triticum timopheevii].

Twenty-four Triticum eastivum x T. timopheevii hybrid lines developed on the basis of five varieties of common wheat and resistant to leaf rust were analyzed by the use of microsatellite markers specific for hexaploid common wheat T. aestivum. Investigation of intervarietal polymorphism of the markers showed that the number of alleles per locus ranged from 1 to 4, depending on the marker (2.5 on average). In T. timopheevii, amplification fragments are produced by 80, 55, and 30% of primers specific to the A, B, and D common wheat genomes, respectively. Microsatellite analysis revealed two major areas of introgression of the T. timopheevii genome: chromosomes of homoeological groups 2 and 5. Translocations were detected in the 2A and 2B chromosomes simultaneously in 11 lines of 24. The length of the translocated fragment in the 2B chromosome was virtually identical in all hybrid lines and did not depend on the parental wheat variety. In 15 lines developed on the basis of the Saratovskaya 29, Irtyshanka, and Tselinnaya 20, changes occurred in the telomeric region of the long arm of the 5A chromosome. Analysis with markers specific to the D genome suggested that introgressions of the T. timopheevii genome occurred in chromosomes of the D genome. However, the location of these markers on T. timopheevii chromosomes is unknown. Our data suggest that the genes for leaf-rust resistance transferred from T. timopheevii to T. aestivum are located chromosomes of homoeological group 2.

Chromosomes↗

PubMed1996

The estrogen receptor locus is associated with a major gene influencing litter size in pigs.

Identification of individual major genes affecting quantitative traits in livestock species has been limited to date. By using a candidate gene approach and a divergent breed cross involving the Chinese Meishan pig, we have shown that a specific allele of the estrogen receptor (ER) locus is associated with increased litter size. Female pigs from synthetic lines with a 50% Meishan background that were homozygous for this beneficial allele produced 2.3 more pigs in first parities and 1.5 more pigs averaged over all parities than females from the same synthetic lines and homozygous for the undesirable allele. This beneficial ER allele was also found in pigs with Large White breed ancestory. Analysis of females with Large White breed background showed an advantage for females homozygous for the beneficial allele as compared to females homozygous for the other allele of more than 1 total pig born. Analyses of growth performance test records detected no significant unfavorable associations of the beneficial allele with growth and developmental traits. Mapping of the ER gene demonstrated that the closest known genes or markers were 3 centimorgans from ER. To our knowledge, one of these, superoxide dismutase gene (SOD2), was mapped for the first time in the pig. Analysis of ER and these linked markers indicated that ER is the best predictor of litter size differences. Introgression of the beneficial allele into commercial pig breeding lines, in which the allele was not present, and marker-assisted selection for the beneficial allele in lines with Meishan and Large White background have begun.

Animals↗

PubMed2003

Gene flow between cassava, Manihot esculenta Crantz, and wild relatives.

Controlled and natural hybridization between cassava and wild relatives does occur. Barriers within the genus appear to be weak due to recent evolution of the group. All Manihot species examined cytogenetically have a chromosome number of 2n = 36. However, they behave meiotically as diploids. The weak interspecific barriers have led to an extremely heterozygous gene pool that may begin a sequence of hybridization followed by speciation. Introgression from cassava into a number of wild species (M. neusana, M. alutacea, M. reptans and M. anomala) has been detected by both morphological marker genes and molecular techniques. Winged fruit, setaceous bracteoles, and wide leaf sinus were dominant genes that came from cassava and appeared in the hybrids. The characteristic protein bands of cassava were recognized in the hybrid seed protein electrophoresis.

Crosses, Genetic↗

PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Journal Article↗

PubMed2006

Extensive Natural Hybridization Between Two Geckos, Gekko tawaensis and Gekko japonicus (Reptilia: Squamata), Throughout Their Broad Sympatric Area.

The status of natural hybridization between the two Japanese geckos, Gekko tawaensis and Gekko japonicus, was surveyed by use of 15 diagnostic allozyme loci. Of 438 specimens examined, 9 were identified as F(l), 1 was a first backcross with G. japonicus, and 15 were identified as more successive generations. Hybridizations were detected at 7 of the 15 localities interspersed throughout a broad sympatric area of the two species, forming a mosaic hybrid zone. A comparison of species-hybrid composition between 2-year samples from a single locality and a 5-year interval showed no evidence for progressive introgression or establishment of a hybrid swarm, despite constant emergences of F(l) hybrids. Nonprevalence of the hybrid genotypes was also indicated by the analysis using hybrid index scores for all other localities examined. These results suggest that strong selection acts against hybrid genotypes. Morphological features of hybrid individuals were also provided.

Alleles↗

PubMed2006

Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders.

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.

Animals↗

PubMed2006

Distortion of symmetrical introgression in a hybrid zone: evidence for locus-specific selection and uni-directional range expansion.

The fate of species integrity upon natural hybridization depends on the interaction between selection and dispersal. The relative significance of these processes may be studied in the initial phase of contact before selection and gene flow reach equilibrium. Here we study a hybrid zone of two salamander species, Lyciasalamandra antalyana and Lyciasalamandra billae, at the initial phase of hybridization. We quantify the degree and mode of introgression using nuclear and mtDNA markers. The hybrid zone can be characterized as an abrupt transition zone, the central hybrid zone being only c. 400 m, but introgressed genes were traced up to 3 km. Introgression was traced in both sexes but gene flow may be slightly male-biased. Indirect evidence suggests that hybrid males are less viable than females. Introgression occurred at two levels: (1) locus-specific selection led to different allelic introgression patterns independent of species, while (2) asymmetrical species-level introgression occurred predominately from L. antalyana to L. billae due to range expansion of the former. This indicates that foreign genes can be incorporated into novel genomic environments, which in turn may contribute to the great diversity of morphological variants in Lyciasalamandra.

Amphibians↗

PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Potato (Solanum tuberosum L.) is cultivated for its tubers, which serve as a major crop. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of flowering time, that functions as a tuberigen, the equivalent of a florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of the tetraploid potato cultivar, Atlantic. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129 218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Solanum tuberosum↗

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↗

PubMed2003

An autoimmune diabetes locus (Idd21) on mouse chromosome 18.

Twenty-four named Idd loci that contribute to the development of autoimmune diabetes in the nonobese diabetic (NOD) mouse have been mapped by linkage and congenic analysis. Previously, meta-analysis of genome-wide linkage scans supported the existence of a locus for susceptibility to autoimmune phenotypes on rodent Chromosome (Chr) 18, in a position orthologous to the human typc 1 diabetes susceptibility locus IDDM6 (human Chr 18q12-q23). However, an autoimmune diabetes susceptibility locus has not previously been reported on mouse Chr 18. In this study, we demonstrate linkage of the majority of mouse Chr 18 to diabetes in a (ABH x NOD)F1 x NOD backcross. Congenic analysis, introgressing at least 92% of Biozzi ABH Chr 18 onto the NOD background, confirmed the presence of a diabetes locus. The chromosome substitution strain (NOD.ABH-Chr18) had reduced diabetes incidence compared with NOD mice (P < 0.0001). We have named the Chr 18 diabetes locus Idd21.

Alleles↗

PubMed2026

Quantifying niche overlap and transgression in allopolyploid hybrids: Case study of Sorbus subgenus Aria.

BACKGROUND AND AIMS: Apomixis, the formation of seeds without recombination, facilitates adaptation and persistence under environmental change. By preserving hybrid genotypes over long time periods, apomixis may conserve adaptive trait combinations from parental niche margins. We tested whether apomictic entities occupy intermediate, marginal, or transgressive niche space relative to their parents and whether differentiation is associated with ploidy. METHODS: We studied polyploid Sorbus subgenus Aria in the Franconian Jura (Germany), comprising two progenitors Sorbus aria and S. collina, seven triploid entities, and a pool of genetically heterogenous individuals (single genotypes). Genetic structure was assessed using MIG-seq. Overall niche differentiation between parental taxa and hybrids was evaluated using Sørensen similarity of two-dimensional hypervolumes derived from principal component analysis (PCA) axes. Niche shifts were further analyzed using hypervolumes based on the three strongest PCA variables. Across 762 occurrences, observations ranged from 11 to 453 individuals per entity. KEY RESULTS: Environmental niche space was transgressive in three, significantly allocated towards the margins of parental niche space in one, while remaining intermediate in the other entities. Niche transgression occurred towards milder temperatures and drier conditions. Genetic analyses confirmed morphologically defined entities, although one morphotype was polyphyletic. Tetraploid S. collina significantly occupied warmer and wetter environments compared to other cytotypes. Triploids differed from S. aria along microtopographic gradients represented by the second PCA axis. CONCLUSIONS: Apomictic Sorbus entities show diverse strategies in niche occupation and can occupy environmental niche space at and beyond the limits of their parental taxa. Apomicts may conserve evolutionary adaptations at the edges of parental niche space that may otherwise be lost from, or fail to emerge in, the parental gene pool. Over long timescales these trait combinations may re-enter the parental gene pool through introgression, thereby reintroducing adaptations critical for survival under changing conditions.

Aria↗

PubMed1999

Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: the B genome of wheat.

Study of bread wheat (Triticum aestivum) may help to resolve several questions related to polyploid evolution. One such question regards the possibility that the component genomes of polyploids may themselves be polyphyletic, resulting from hybridization and introgression among different polyploid species sharing a single genome. We used the B genome of wheat as a model system to test hypotheses that bear on the monophyly or polyphyly of the individual constituent genomes. By using aneuploid wheat stocks, combined with PCR-based cloning strategies, we cloned and sequenced two single-copy-DNA sequences from each of the seven chromosomes of the wheat B genome and the homologous sequences from representatives of the five diploid species in section Sitopsis previously suggested as sister groups to the B genome. Phylogenetic comparisons of sequence data suggested that the B genome of wheat underwent a genetic bottleneck and has diverged from the diploid B genome donor. The extent of genetic diversity among the Sitopsis diploids and the failure of any of the Sitopsis species to group with the wheat B genome indicated that these species have also diverged from the ancestral B genome donor. Our results support monophyly of the wheat B genome.

Chromosome Mapping↗

PubMed2006

The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr.

A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specificity in the incompatibility response. The main evidence is the lack of polymorphism at the SCR locus in A. thaliana. However, the nearby SRK gene, which determines stigma specificity in self-incompatible Brassicaceae species, has extremely high sequence diversity, with 3 very divergent SRK haplotypes, 2 of them present in multiple strains. Such high diversity is extremely unusual in this species, and it suggests the possibility that multiple, different SRK haplotypes may have been preserved from A. thaliana's self-incompatible ancestor. To study the evolution of S-haplotypes in the A. thaliana lineage, we searched the 2 most closely related Arabidopsis species Arabidopsis lyrata and Arabidopsis halleri, in which most populations have retained SI, and found SRK sequences corresponding to all 3 A. thaliana haplogroup sequences. Our molecular evolutionary analyses of these 3 S-haplotypes provide an independent estimate of the timing of the breakdown of SI and again exclude an ancient transition to selfing in A. thaliana. Comparing sequences of each of the 3 haplogroups between species, we find that 2 of the 3 SRK sequences (haplogroups A and B) are similar throughout their length, suggesting that little or no recombination with other SRK alleles has occurred since these species diverged. The diversity difference between the SCR and SRK loci in A. thaliana, however, suggests crossing-over, either within SRK or between the SCR and SRK loci. If the loss of SI involved fixation of the PsiSCR1 sequence, the exchange must have occurred during its fixation. Divergence between the species is much lower at the S-locus, compared with reference loci, and we discuss two contributory possibilities. Introgression may have occurred between A. lyrata and A. halleri and between their ancestral lineage and A. thaliana, at least for some period after their split. In addition, the coalescence times of sequences of individual S-haplogroups are expected to be less than those of alleles at non-S-loci.

Arabidopsis↗

PubMedDate not supplied

Close linkage between the Cf-2/Cf-5 and Mi resistance loci in tomato.

Analysis of restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers in tomato plants segregating for resistance to the fungus Cladosporium fulvum was used to localize the resistance genes Cf-2 and Cf-5 to the same region of chromosome 6. This region, between GP79 and Aps-1, is the same as that reported for the Mi gene, which confers resistance to root-knot nematodes (meloidogyne spp.). Recombination values based on F2 populations from crosses between near-isogenic lines of L. esculentum 'Moneymaker' carrying Cf-2 or Cf-5 and Lycopersicon pennellii, indicate that this region occupies 4-5 centiMorgans (cM). However, in F2 populations from crosses between the L. esculentum stock LA1190 carrying yv and these lines, this value is 1-2 cM. The Cf-2 gene, introduced into L. esculentum from L. pimpinellifolium, is on an introgressed segment that extends from a point distal to GP79 to a point between TG232 and H2D1. The origin of Cf-5 was found to be L. esculentum var. cerasiforme rather than L. pimpinellifolium as previously reported. No RFLP markers and only one RAPD marker showed a polymorphism between Moneymaker and the near-isogenic line carrying Cf-5.

Base Sequence↗

PubMed2006

Evolutionary history of a mosquito endosymbiont revealed through mitochondrial hitchhiking.

Due to cytoplasmic inheritance, spread of maternally inherited Wolbachia symbionts can result in reduction of mitochondrial variation in populations. We examined sequence diversity of the mitochondrial NADH dehydrogenase subunit 4 (ND4) gene in Wolbachia-infected (South Africa (SA), California and Thailand) and uninfected (SA) Culex pipiens complex populations. In total, we identified 12 haplotypes (A-L). In infected populations, 99% of individuals had haplotype K. In the uninfected SA population, 11 haplotypes were present, including K. Nuclear allozyme diversity was similar between infected and uninfected SA populations. Analysis of nuclear DNA sequences suggested that haplotype K presence in uninfected SA Cx. pipiens was probably due to a shared ancestral polymorphism rather than hybrid introgression. These data indicate that Wolbachia spread has resulted in drastic reduction of mitochondrial variability in widely separated Cx. pipiens complex populations. In contrast, the uninfected SA population is probably a cryptic species where Wolbachia introgression has been prevented by reproductive isolation, maintaining ancestral levels of mitochondrial diversity. Molecular clock analyses suggest that the Wolbachia sweep occurred within the last 47000 years. The effect of Wolbachia on mitochondrial dynamics can provide insight on the potential for Wolbachia to spread transgenes into mosquito populations to control vector-borne diseases.

Animals↗

PubMed2002

[Homoeologous grouping of R. kamoji chromosomes introduced in wheat using RFLP molecular marks].

Twenty six DNA probes from seven homoeologous groups of triticeae were screened to reveal the RFLP between 45 wheat-R. kamoji derivatives and their parents R. kamoji, Chinese Spring, Yangmai 5. The result showed that the introduced R. kamoji chromosomes in 16 wheat-R. kamoji alien chromosome lines including additions, substitution or putative translocations were grouped into homoeologous group 1, 3, 5, 6 and 7. Alien chromosome pairs could be readily transmitted into the descendants. The added chromosomes in K139, K141, K214, K218, K219 and K224 disomic addition lines were grouped into homoeologous group 1, but the added chromosomes in K214 and K218 were different from K219 and K224 which originated from different genomes of R. kamoji. Ditelosomic addition line K147 might involve a R. kamoji chromosome long arm homoeologous to group 1 of wheat, and the added R. kamoji 1 L chromosomes in K139, K141 and K147 probably derived from different three genomes of R. kamoji. U chromosome of R. kamoji. showed homology to wheat homoeologous group 1. Homoeologous group 1 chromosome of R. kamoji, particularly its long arm is related to genes for scab resistance. Result also demonstrated a possible rearrangement occurred between homoeologous group 1 and group 6 of R. kamoji. Two R. kamoji chromosomes introduced in K203 were grouped to homoeologous group 1 and 6, respectively. In K166, the introgressed R. kamoji chromosome involved the short arm of group 5. Another alien chromosome line K177 was revealed as to be with introduced chromosome involving group 5L, 6S and 7SL of R. kamoji. Results also confirmed the homoeology between S, H and Y genomes of R. kamoji.

Chimera↗

PubMed2004

Reduced metaphase I associations between the short arms of homologous chromosomes in a Hordeum vulgare L. x H. bulbosum L. diploid hybrid influences the frequency of recombinant progeny.

Hordeum vulgare (cultivated barley) x H. bulbosum (bulbous barley grass) hybrids have been used to obtain disease-resistant recombinant lines (RLs). The RLs contain chromatin transferred from the wild species mostly onto the long arms of recipient barley chromosomes. To determine whether differences in meiotic metaphase I (MI) associations between the long and short arms of homologous chromosomes can account for the preponderance of introgressions on the long arms, we carried out fluorescent in situ hybridisation on MI chromosome preparations obtained from pollen mother cells of a diploid interspecific hybrid. By using various probes, we established that MI associations between the long arms occurred more frequently than between the short arms for the five chromosomes tested.

Chromosome Pairing↗

PubMed2001

Potential failsafe mechanisms against the spread and introgression of transgenic hypervirulent biocontrol fungi.

Microbial biocontrol agents are typically inefficient owing to the evolutionary necessity to be in balance with their hosts to survive. If transgenetically rendered hypervirulent, however, they could be competitive alternatives to pesticides. Potential means are delineated to prevent, contain or mitigate uncontrollable spread of hypervirulent biocontrol organisms, mutations that increase their host range, and the sexual or asexual introgression of hypervirulence genes into pathogens of other organisms. The use of asporogenic deletion mutants as a platform for generating transgenic hypervirulent biopesticides would prevent such spread. Hypervirulence genes flanked with available 'transgenetic mitigator' (TM) genes (genes that are neutral or positive to the biocontrol agent but deleterious to recombinants) would decrease virulence to non-target species.

Fungi↗