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PubMed2006

Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites.

In the present report, the polymorphisms from 9 microsatellites were used to assess genetic diversity and relationships in 4 Creole cattle breeds from Argentina and Bolivia, 4 European taurine breeds, and 2 American zebu populations. The Creole populations display a relatively high level of genetic variation as estimated by allelic diversity and heterozygosity, whereas the British breeds displayed reduced levels of genetic diversity. The analysis of molecular variance indicated that 7.8% of variance can be explained by differences among taurine and zebu breeds. Consistent with these results, the first principal component (PC), which comprised the 40% of the total variance, clearly distinguishes these 2 groups. In addition, all constructed phylogenetic trees cluster together Nelore and Brahman breeds with robust bootstrap values. Only 1% of variance was due to difference between American Creole and European taurine cattle. Although this secondary split was supported by the classical genetic distance and the second PC (15%), the topology of trees is not particularly robust. The presence of zebu-specific alleles in Creole cattle allowed estimating a moderate degree of zebu admixture. When these data were compared with mitochondrial and Y chromosomal studies, a clear pattern of male-mediated introgression was revealed. The results presented here contribute to the understanding of origin and history of the American Creole cattle.

Alleles↗

PubMed2002

Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences.

The nature of gene flow in plants -- including the propensity for interspecific introgression -- makes them interesting candidates for phylogeographical analysis. Plant phylogeography studies have been limited, however, by the availability of suitable intraspecific variation. In this study, DNA sequence variation from a nuclear gene [Glyceraldehyde 3-phosphate dehydrogenase; (G3pdh)] was used to examine the population history of Manihot esculenta ssp. flabellifolia and a potentially hybridizing species, M. pruinosa. These species occur in the rainforest-savanna ecotone adjoining the Amazon basin, a region believed to have undergone major habitat shifts since the Pleistocene. Geographical distributions of the G3pdh haplotypes indicate genetic isolation-by-distance across the range of M. esculenta ssp. flabellifolia. However, there is greater genetic similarity between northeastern and western populations than would be expected given the present species distribution. A nested clade analysis suggests that northeastern and western populations were connected by gene flow until relatively recently, when they became fragmented. This inferred fragmentation event is consistent with post-Pleistocene habitat shifts proposed for the Amazon basin. At the interspecific level, haplotype sharing with M. pruinosa may reflect either recent interspecific introgression or incomplete lineage sorting between these closely related species.

Brazil↗

PubMed2001

Genetic dissection of region around the Sa gene on rat chromosome 1: evidence for multiple loci affecting blood pressure.

A region with a major effect on blood pressure (BP) is located on rat chromosome 1 in the vicinity of the Sa gene, a candidate gene for BP regulation. Previously, we observed a single linkage peak for BP in this region in second filial generation rats derived from a cross of the spontaneously hypertensive rat (SHR) with the Wistar-Kyoto rat (WKY), and we have reported the isolation of the region containing the BP effect in reciprocal congenic strains (WKY.SHR-Sa) and (SHR.WKY-Sa) derived from these animals. Here, we report the further genetic dissection of this region. Two congenic substrains each were derived from WKY.SHR-Sa (WISA1 and WISA2) and SHR.WKY-Sa (SISA1 and SISA2) by backcrossing to WKY and SHR, respectively. Although there was some overlap of the introgressed regions retained in the various substrains, the segments in WISA1 and SISA1 did not overlap. Furthermore, although the Sa allele in WISA1, WISA2, and SISA2 remained donor in origin, recombination in SISA1 reverted it back to the recipient (SHR) allele. Surprisingly, all 4 substrains demonstrated a highly significant BP difference compared with that of their respective parental strain, which was of a magnitude similar to those seen in the original congenic strains. The findings strongly indicate that there are at least 2 quantitative trait loci (QTLs) affecting BP in this region of rat chromosome 1. Furthermore, the BP effect seen in SISA1 indicates that at least a proportion of the BP effect of this region of rat chromosome 1 cannot be due to the Sa gene. SISA1 contains an introgressed segment of <3 cM, and this will facilitate the physical mapping of the BP QTL(s) located within it and the identification of the susceptibility-conferring genes. Our observations serve to illustrate the complexity of QTL dissection and the care needed to interpret findings from congenic studies.

Animals↗

PubMed2006

Divergence with gene flow in Anopheles funestus from the Sudan Savanna of Burkina Faso, West Africa.

Anopheles funestus is a major vector of malaria across Africa. Understanding its complex and nonequilibrium population genetic structure is an important challenge that must be overcome before vector populations can be successfully perturbed for malaria control. Here we examine the role of chromosomal inversions in structuring genetic variation and facilitating divergence in Burkina Faso, West Africa, where two incipient species (chromosomal forms) of A. funestus, defined principally by rearrangements of chromosome 3R, have been hypothesized. Sampling across an approximately 300-km east-west transect largely contained within the Sudan-Savanna ecoclimatic zone, we analyzed chromosomal inversions, 16 microsatellite loci distributed genomewide, and 834 bp of the mtDNA ND5 gene. Both molecular markers revealed high genetic diversity, nearly all of which was accounted for by within-population differences among individuals, owing to recent population expansion. Across the study area there was no correlation between genetic and geographic distance. Significant genetic differentiation found between chromosomal forms on the basis of microsatellites was not genomewide but could be explained by chromosome 3R alone on the basis of loci inside and near inversions. These data are not compatible with complete reproductive isolation but are consistent with differential introgression and sympatric divergence between the chromosomal forms, facilitated by chromosome 3R inversions.

Africa, Western↗

PubMedDate not supplied

Four independent electrophoretic markers in spadefoot toads.

Four enzyme-encoding genes (Idh-1, Idh-2, Ldh-1, and Mdh-1), with alleles diagnostic for the spadefoot toads Scaphiopus multiplicatus and Scaphiopus bombifrons, were investigated in order to characterize their inheritance and linkage relationships. Electrophoretic phenotypes in the offspring of natural crosses exhibit Mendelian segregation, behaving as genotypes produced by alternative alleles at four independently assorting loci. These phenotypes are useful markers of genetic identity and the degree of genetic admixture in the analyses of hybrid zone dynamics for these two species. Concurrent use of a morphological index verified the diagnostic value of the markers. The morphological index is useful for the identification of parental species and many F1 hybrids, however offspring of backcrosses usually express parental species characteristics. Electrophoretic typing allows the identification of all hybrids and 87 percent of the offspring from backcrosses. It also facilitates the identification of tadpoles, which are extremely difficult to distinguish morphologically. The technique is useful for the assessment of introgression and the evaluation of reproductive interaction in these species, even though it slightly underestimates backcross offspring.

Alleles↗

PubMed1995

Variation in ribosomal DNA internal transcribed spacers 1 among eastern populations of Ixodes scapularis (Acari: Ixodidae).

The base sequence of the internal transcribed spacer 1 (ITS 1) of ribosomal DNA of the tick Ixodes scapularis Say (= I. dammini Spielman, Clifford, Piesman & Corwin) was determined to assess genetic divergence between populations along the eastern (Atlantic) seaboard of the United States. Twenty sequences were obtained from localities down the eastern margin of the species's range: 10 from the southeast (Georgia and Florida), seven from the middle east (North Carolina, Maryland), and three from the northeast (Massachusetts, New Jersey, New York). Both the neighbor-joining and parsimony methods cluster most of the southeastern sequences together and most of the middle eastern sequences together but fail to cluster those from the northeast. In addition, an F ratio test revealed significant between-region sequence variation. Thus, there appears to be genetic structuring on at least a macrogeographic scale. Only 23% (SEM = 6.4%) of the sequence variation occurs between regions, with the vast majority of variation, 77% (SEM = 6.4%), being within region. These data, plus other published data, indicate that I. scapularis constitutes a single species. However, the pattern of variation is consistent with restricted gene flow between regions or, alternatively, with recent introgression between northern and southern types in the middle-eastern part of the species's range.

Animals↗

PubMed1992

Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21.

Nearly isogenic lines (NILs) of rice (Oryza sativa) differing at a locus conferring resistance to the pathogen Xanthomonas oryzae pv. oryzae were surveyed with 123 DNA markers and 985 random primers using restriction fragment length plymorphism (RFLP) and random amplified polymorphic DNA (RAPD) analysis. One chromosome 11 marker (RG103) detected polymorphism between the NILs that cosegregated with Xa21. All other chromosome 11 DNA markers tested were monomorphic between the NILs, localizing the Xa21 introgressed region to an 8.3 cM interval on chromosome 11. Furthermore, we identified two polymerase chain reaction (PCR) products (RAPD2148 and RAPD818) that detected polymorphisms between the NILs. Genomic sequences hybridizing with RAPD818, RAPD248 and RG103 were duplicated specifically in the Xa21 NIL. All three markers cosegregated with the resistance locus, Xa21, in a F2 population of 386 progeny. Based on the frequency with which we recovered polymorphic Xa21-linked markers, we estimated the physical size of the introgressed region to be approximately 800 kb. This estimation was supported by physical mapping (using pulsed field gel electrophoresis) of the sequences hybridizing with the three Xa21-linked DNA markers. The results showed that the three Xa21-linked markers are physically close to each other, with one copy of the RAPD818 sequences located within 60 kb of RAPD248 and the other copy within 270 kb of RG103. None of the enzymes tested generated a DNA fragment that hybridized with all three of the markers indicating that the introgressed region containing the resistance locus Xa21 is probably larger than 270 kb.

Chromosome Mapping↗

PubMed1998

Mitochondrial and nuclear DNA sequence variability among populations of rainbow trout (Oncorhynchus mykiss).

Mitochondrial and nuclear DNA variability was examined to assess population genetic structure and phylogeographic relationships in rainbow trout. Single-strand conformation polymorphisms and restriction site differences within 1055 bp of the mitochondrial D-loop region and 1566 bp of nuclear DNA in six single-copy nuclear DNA regions identified 31 mitochondrial genotypes and 50 nuclear alleles. Gene trees were constructed by sequencing each variant allele or mitochondrial genotype identified. Examination of 30 populations in 10 native rainbow trout groups using analysis of molecular variance (AMOVA) indicated that 65% of mitochondrial variability and 35% of nuclear variability was explained by differences among the 10 groups. Phylogenetic patterns evident in mitochondrial and nuclear DNA were not always concordant. Differences in the evolutionary patterns detected by mitochondrial and nuclear DNA may reflect the differential impact of past introgression events on variability in the two genomes.

Alleles↗

PubMed2006

Cyto-nuclear epistasis: two-locus random genetic drift in hermaphroditic and dioecious species.

We report the findings of our theoretical investigation of the effect of random genetic drift on the covariance of identity-by-descent (ibd) of nuclear and cytoplasmic genes. The covariance in ibd measures of the degree to which cyto-nuclear gene combinations are heritable, that is, transmitted together from parents to offspring. We show how the mating system affects the covariance of ibd, a potentially important aspect of host-pathogen or host-symbiont coevolution. The magnitude of this covariance influences the degree to which the evolution of apparently neutral cytoplasmic genes, often used in molecular phylogenetics, might be influenced by selection acting on unlinked nuclear genes. To the extent that cyto-nuclear gene combinations are inherited together, genomic conflict is mitigated and intergenomic transfer it facilitated, because genes in both organelle and nuclear genomes share the same evolutionary fate. The covariance of ibd also affects the rate at which cyto-nuclear epistatic variance is converted to additive variance necessary for a response to selection. We find that conversion is biased in species with separate sexes, so that the increment of additive variance added to the nuclear genome exceeds that added to the cytoplasmic genome. As a result, the host might have an adaptive advantage in a coevolutionary arms race with vertically (maternally) transmitted pathogens. Similarly, the nuclear genome could be a source of compensatory mutations for its organellar genomes, as occurs in cytoplasmic male sterility in some plant species. We also discuss the possibility that adaptive cytoplasmic elements, such as favorable mitochondrial mutations or endosymbionts (e.g., Wolbachia), have the potential to release heritable nuclear variation as they sweep through a host population, supporting the view that cytoplasmic introgression plays an important role in adaptation and speciation.

Alleles↗

PubMed2003

Intra- and interspecific genetic complexities of two Eothenomys species in Honshu, Japan.

Differences in the nuclear ribosomal DNA (rDNA), mitochondrial DNA (mtDNA), cytochrome b (Cytb), and Y chromosomal Sry genes were used to assess intra- and interspecific relationships in two Japanese red-backed voles, Eothenomys andersoni and E. smithii, focusing on areas where the two species might come into contact. In the Kii Peninsula, southwestern Honshu, which contains an allopatric population of E. andersoni isolated from its main range, the rDNA-RFLP data provide robust evidence of past mutual interspecific gene introgression, while the Cytb and Sry sequences were specific to this population. In central Honshu, where E. andersoni and E. smithii inhabit higher and lower altitudes, respectively, with a narrow sympatric zone, the rDNA-RFLP and Sry variation was specific for each species, while introgression of the mtDNA from E. smithii to E. andersoni was seen. These complex patterns in the gene markers are consistent with our previous notions derived from sex chromosome variation. Our previous and present data strongly suggest that the evolution of these vole species, which are morphologically and cytogenetically distinct, involves complex genetic interactions and the resultant combinations of genes are sometimes peculiar, mainly due to the Cytb haplotypes. However, phylogenetic analysis using a combination of maternal, paternal, and biparental markers has proven useful for understanding the evolutionary history given the complex phylogenetic background.

Animals↗

PubMed2005

Phylogenetic relationships of the lamprologine cichlid genus Lepidiolamprologus (Teleostei: Perciformes) based on mitochondrial and nuclear sequences, suggesting introgressive hybridization.

Using sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2, 1047bp) and a segment of the non-coding mitochondrial control region, as well as nuclear sequences including two introns from the S7 ribosomal protein and the loci TmoM25, TmoM27, and UME002, we explore the phylogenetic relationships of Lepidiolamprologus, one of seven lamprologine cichlid genera in Lake Tanganyika, East Africa. Analyses consisted of direct optimization using POY, including a parsimony sensitivity analysis, and maximum likelihood and Bayesian inference for comparison. With respect to Lepidiolamprologus, the results based on the mitochondrial dataset were robust to parameter variation in POY. Lepidiolamprologus cunningtoni was resolved in a large clade sister to ossified group lamprologines, among which the remaining Lepidiolamprologus were nested. In addition to L. attenuatus, L. elongatus, L. kendalli, and L. profundicola, Neolamprologus meeli, N. hecqui, N. boulengeri, N. variostigma, and two undescribed species were resolved in a two-pore Lepidiolamprologus clade sister to Lamprologus callipterus and two species of Altolamprologus. Lepidiolamprologus nkambae, in marked conflict with morphological and nuclear DNA evidence, nested outside of the two-pore Lepidiolamprologus clade, suggesting that the mtDNA signal has been convoluted by introgressive hybridization.

Animals↗

PubMed2003

Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa).

The evolutionary history of a wild-cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty-two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.

Crops, Agricultural↗

PubMedDate not supplied

Morphological, cytogenetic, and molecular evidence for introgressive hybridization in birch.

Extensive morphological variation of tetraploid birch (Betula pubescens) in Iceland is believed to be due to gene flow from diploid dwarf birch (B. nana) by means of introgressive hybridization. A combined morphological and cytogenetic approach was used to investigate this phenomenon in two geographically separated populations of natural birch woodland in Iceland. The results not only confirmed introgressive hybridization in birch, but also revealed bidirectional gene flow between the two species via triploid interspecific hybrids. The populations showed continuous morphological variation connecting the species, but karyotypically they consisted of only three types of plants: diploids, triploids, and tetraploids. No aneuploids were found. Some of the tetraploid plants had B. pubescens morphology as expected, but most of them had intermediate characters. Most of the diploid plants were B. nana, but some were intermediates and a few had B. pubescens morphology. The triploid plants were either intermediates or they resembled one of the two species. Similar introgressive variation was observed among the diploid and triploid progeny of open-pollinated B. nana in a garden. Birch samples including field plants and artificial hybrids were further examined using a molecular method based on genomic Southern hybridization. The experiments verified introgression at the DNA level.

Betula↗

PubMed2004

A PCR-based marker for targeting small rye segments in wheat background.

We attempted to develop a PCR-based marker that detects various segments of rye chromosome incorporated into wheat. We designed three sets of PCR primers based on the nucleotide sequence data of a rye repetitive sequence previously reported. One of the primer sets amplified a clear ca. 1.4 kb fragment in a rye cultivar but not in any form of wheat, diploid, tetraploid or hexaploid. We used this critical primer set for PCR of various wild species and cultivars of rye, an array of wheat plants carrying different rye chromosomes or small segments from different regions of rye chromosome 1R, and plants carrying parts of the rye B chromosome. The PCR amplified the 1.4 kb fragment in all the plant materials examined. We believe this PCR primer set will be useful as a universal PCR-based marker for the introgression of rye chromosome segments in the wheat genome.

Chromosomes, Plant↗

PubMed2004

Mitochondrial gene introgression between spined loaches via hybridogenesis.

This report deals with an unusual mode of mitochondrial gene introgression between Cobitis hankugensis (C. sinensis) and C. longicorpus which is mediated by a unisexual hybridogenetic system of diploid-triploid C. hankugensis-longicorpus complex. Mitochondrial DNA sequences of 3329-3330bp encompassing from upstream ND6 to 12S rDNA indicated that mitochondrial genomes from the diploid hybrids, triploid hybrids, and their parental species are almost identical. Because triploid hybrids produce haploid ova with C. hankugensis chromosome set, normal diploid C. hankugensis regenerates upon insemination with C. hankugensis sperm. If the hybrid carries C. longicorpus mitochondrial genome, the regenerated C. hankugensis is a nucleo-cytoplasmic hybrid, thus accomplishing the unusual mode of mitochondrial gene introgression.

Animals↗

PubMed2000

The BLAST algorithms: practical application in molecular cloning, marker-assisted selection (MAS) and introgression of wheat.

BLAST (Basic Local Alignment Search) analyses of Hordeum chilense RAPD markers have shown DNA sequence similarities with several plant genes. Biologically significant hits were scored for: plastocianin (Hordeum vulgare), alpha-gliadin (Triticum aestivum), Grandel-6 retrotransposon (Zea diploperennis), retrofit (gag/pol) copia-like, transposon-like element (Oryza longistaminata), copia-like retrotransposon Hopscotch polyprotein (gag/pol) (Zea mays) and several retrotransposons/retroelements from other species (Arabidopsis thaliana, Oryza sativa, Pisum sativum and Zea mays). Statistically significant hits also included endochitinase (Brassica napius), ribulose-1,5-bisphosphate carboxylase (Euglena gracilis), piruvate, orthophosphate dikinase (Flaveria trinervia), and an ORF flanked by ARS sequences (Triticum aestivum). Interestingly, it was also found that the currently recommended BLAST algorithm (version 2.0.11; gapped) at did not produce any biologically significant hits, whereas the previous version (1.4.11; ungapped) did generate biologically significant results. Thus, we suggest using the new BLAST 2.0.x when strong homologies are expected in short sequence stretches between closely related species. In other instances (and particularly when searching for lower similarities, yet spanning significantly larger stretches between more distant species), the BLAST 1.4.x could yield additional results. BLAST searches are valuable tools to identify and clone DNA sequences of interest, with applications in Marker-Assisted Selection (MAS) and wheat introgression.

Algorithms↗

PubMed2006

Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley.

Hordeum vulgare subsp. spontaneum, the wild progenitor of barley, is a potential source of useful genetic variation for barley breeding programs. The objective of this study was to map quantitative trait loci (QTLs) in an advanced backcross population of barley. A total of 207 BC3 lines were developed using the 2-rowed German spring cultivar Hordeum vulgare subsp. vulgare 'Brenda' as a recurrent parent and the H. vulgare subsp. spontaneum accession HS584 as a donor parent. The lines were genotyped by 108 simple-sequence repeat (SSR) markers and evaluated in field tests for the measurement of grain yield and its components, such as ear length, spikelet number per spike, grain number per spike, spike number, and 1000-grain mass, as well as heading date and plant height. A total of 100 QTLs were detected. Ten QTLs with increasing effects were found for ear length, spikelet number, and grain number per spike. Three QTLs contributed by HS584 were found to significantly decrease days to heading across all years at 2 locations. In addition, 2 QTLs from HS584 on chromosomes 2H and 3H were associated with resistance to leaf rust. Based on genotypic data obtained from this population, 55 introgression lines carrying 1 or 2 donor segments were selected to develop a set of doubled-haploid lines, which will be used to reconfirm and investigate the effects of 100 QTLs for future genetic studies.

Chromosome Segregation↗

PubMed2004

Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers.

Japanese rice ( Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.

Analysis of Variance↗