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PubMed1993

Genetic structure and epidemiology of Ascaris populations: patterns of host affiliation in Guatemala.

In Guatemalan villages people commonly rear pigs, and both hosts may be infected with Ascaris. This study was designed to ask whether both humans and pigs are potential hosts in a single parasite transmission cycle in such villages, or alternatively, if there are two separate transmission cycles, one involving pigs and one involving human hosts. Parasites were collected from both host species from locations in the north and south of Guatemala. Allelic variation in the nuclear genome of Ascaris was measured using enzyme electrophoresis, while mitochondrial DNA (mtDNA) sequence variation was quantified using restriction mapping. Low levels of enzyme polymorphism were found in Ascaris, but allele frequencies at two loci, mannose phosphate isomerase and esterase, suggest that there is little gene exchange between parasite populations from humans and pigs. MtDNA haplotypes fall into two distinct clusters which differ in sequence by 3-4%; the two clusters broadly correspond to worms collected from humans and those collected from pigs. However, some parasites collected from humans have mtDNA characteristic of the 'pig Ascaris' haplotype cluster, while some parasites collected from pigs have mtDNA characteristic of the 'human Ascaris' haplotype cluster. These shared haplotypes are unlikely to represent contemporary cross-infection events. Patterns of phylogenetic similarity and geographical distribution of these haplotypes suggest, instead, that they are the result of two historical introgressions of mtDNA between the two host-associated Ascaris populations. The results clearly demonstrate that Ascaris from humans and pigs are involved in separate transmission cycles in Guatemala.

Alleles↗

PubMed2001

Oxygen radical absorbance capacity (ORAC) and phenolic and anthocyanin concentrations in fruit and leaf tissues of highbush blueberry.

Antioxidant capacity, as measured by oxygen radical absorbance capacity (ORAC), and total phenolic and total anthocyanin contents were evaluated in fruit tissues of 87 highbush blueberry (Vacciniumcorymbosum L.) and species-introgressed highbush blueberry cultivars. ORAC and phenolic levels were evaluated in leaf tissues of the same materials. Average values for ORAC, phenolics, and anthocyanins in fruit were 15.9 ORAC units, 1.79 mg/g (gallic acid equivalents), and 0.95 mg/g (cyanidin-3-glucoside equivalents), respectively. Cv. Rubel had the highest ORAC per gram of fresh weight values, at 31.1 units, and cv. Elliott had the highest values on the basis of ORAC per square centimeter of surface area. In leaf tissue, values for both ORAC and phenolics were significantly higher than in fruit tissue, with mean values of 490 ORAC units and 44.80 mg/g (gallic acid equivalents), respectively. Leaf ORAC had a low, but significant, correlation with fruit phenolics and anthocyanins, but not with fruit ORAC. An analysis of ORAC values versus calculated midparent values in 11 plants from the 87-cultivar group in which all parents were tested suggested that, across cultivars, ORAC inheritance is additive. An investigation of ORAC values in a family of 44 cv. Rubel x Duke seedlings showed negative epistasis for ORAC values, suggesting Rubel may have gene combinations contributing to ORAC that are broken up during hybridization.

Anthocyanins↗

PubMed2004

Fluorometric sucrose evaluation for sugar beet.

Sucrose is the economic product from sugar beet. Disease resistance is often available in low-sucrose genotypes and, prior to the deployment of such novel genes as available into the cultivated spectrum, selection for increased sucrose content is required during introgression. The objective of this work was to evaluate a relatively rapid and inexpensive enzymatic-fluorometric microtiter plate assay for sucrose quantification in sugar beet root dry matter, both for progeny testing in the greenhouse and for evaluation of field-grown mother roots. As determined using HPLC, sucrose content in diverse populations of sugar and table beet assayed over various developmental stages ranged from 0.213 to 2.416 mmol g(-1) of dry matter, and these values were used as references for both refractometry and enzymatic-fluorometric assay. As expected, refractometric analysis generally overestimated sucrose content. Enzymatic-fluorometric analyses were reasonably well correlated with HPLC results for young greenhouse-grown root tissues (R2 = 0.976), and less so with older field-grown roots (R2 = 0.605), for unknown reasons. Enzymatic-fluorometric assays may be best deployed for progeny testing of young seedlings.

Beta vulgaris↗

PubMed1998

Maternal effect of a hybrid inviability gene in Tribolium castaneum.

The Tribolium castaneum hybrid inviability gene, H, was selectively introgressed into a genetic background lacking H through serial paternal backcrosses. This revealed a poor viability phenotype (partial paralysis and poor control of the limbs, referred to as tremor) not present in the parent strains. Tremor cosegregated with H, but was expressed only when transmitted paternally and only when H was not also present maternally. The inferred maternal, self-suppressive effect of H may explain nonreciprocal incompatibilty previously observed between H and H-incompatible strains.

Journal Article↗

PubMed1999

Molecular analysis of a null mutant for pea (Pisum sativum L.) seed lipoxygenase-2.

A mutant line of Pisum fulvum was identified that lacked seed lipoxygenase-2 (LOX-2). The mutant phenotype was introgressed into a standard Pisum sativum cv. Birte to provide near-isogenic lines with or without seed LOX-2. Genetic analyses showed the mutation to behave as a single, recessive Mendelian gene. Northern and dot-blot analyses showed a large reduction in LOX-2 mRNA from developing seeds of the LOX-2-null mutant. A restriction fragment length polymorphism associated with the 5' end of the LOX-2 gene(s) co-segregated with the null phenotype, indicating that the reduction of LOX-2 mRNA was neither a consequence of deletion of the LOX genes nor a consequence of the action of a genetically distant regulatory gene. Analysis of the 5'-flanking sequences of LOX-2 genes from Birte and the near-isogenic LOX-2-null mutant revealed a number of insertions, deletions and substitutions within the promoter from the LOX-2-null mutant that could be responsible for the null phenotype. Incubation of crude seed LOX preparations from Birte and the LOX-2-null mutant showed that the latter generated relatively less 13-hydroperoxides and also produced relatively more hydroxy- and ketoacid compounds that have implications for the fresh-frozen pea industry.

Base Sequence↗

PubMed1999

Structure and expression of the gene family encoding putrescine N-methyltransferase in Nicotiana tabacum: new clues to the evolutionary origin of cultivated tobacco.

The structure and nuclear genomic organization of the gene family encoding putrescine N-methyltransferase (PMT), the key enzyme in diverting polyamine metabolism towards the biosynthesis of nicotine and related alkaloids, was examined in Nicotiana tabacum. Five genes encoding PMT are present in the N. tabacum genome and all are expressed. The complete coding region and immediate 5'- and 3'- flanking regions were characterized for four members of the gene family and the Exon 1 region of the fifth member of the family was determined. Comparison of the nucleotide and deduced amino acid sequences of the N. tabacum PMT genes with those of presumed progenitor species, N. sylvestris, N. tomentosiformis and N. otophora, revealed that three members of the N. tabacum PMT gene family were most similar to the three genes present in N. sylvestris, whereas the two remaining PMT genes were similar to PMT genes present in N. tomentosiformis and N. otophora genomes, respectively. These data are consistent with an evolutionary origin of N. tabacum resulting from a cross involving N. sylvestris and an introgressed hybrid between N. tomentosiformis and N. otophora. The five PMT genes present in N. tabacum are expressed in the roots of wild-type plants, but not in other organs. The steady-state level of all five PMT transcripts is transiently increased in roots following topping (removal of the floral meristem), although the maximum level of induction for the individual transcripts varies considerably. In contrast to wild-type plants, no increase in PMT transcript levels was observed in a low-alkaloid (nic1nic2) mutant of Burley 21. These data support a role for nic1 and nic2 in the global regulation of alkaloid formation in tobacco and provide for the first time molecular confirmation of the presumed origin of cultivated tobacco.

Amino Acid Sequence↗

PubMed2000

Molecular biology of weed control.

The vast commercial effort to utilize chemical and molecular tools to solve weed control problems has had a major impact on the basic biological sciences as well as benefits to agriculture, and the first generation of transgenic products has been successful, while somewhat crude. More sophisticated products are envisaged and expected. Biotechnologically-derived herbicide-resistant crops have been a considerable benefit, yet in some cases there is a risk that the same useful transgenes may introgress into related weeds, specifically the weeds that are hardest to control without such transgenic crops. Biotechnology can also be used to mitigate the risks. Molecular tools should be considered for weed control without the use of, or with less chemicals, whether by enhancing crop competitiveness with weeds for light, nutrients and water, or via allelochemicals. Biocontrol agents may become more effective as well as more safe when rendered hypervirulent yet non-spreading by biotechnology. There might be ways to disperse deleterious transposons throughout weed populations, obviating the need to modify the crops.

Crops, Agricultural↗

PubMed2000

Modification of wheat rDNA loci by rye B chromosomes: a chromatin organization model.

The rDNA loci, and their associated NORs, on chromosomes 1B and 6B of the hexaploid wheat cv. Lindström have been used as a chromatin marker to investigate the functional basis of the phenotype effects of introgressed supernumerary B chromosomes (Bs) of rye. The rye Bs themselves lack genes, other than those which determine their mitotic drive mechanism, and the way in which they can modulate characters determined by the A chromosome background has always been a puzzle. An isogenic line of Lindström plants carrying different numbers of Bs was used as the experimental system to see how different doses of Bs (from 0 to 6) affected the activity of the wheat NORs and the organization of their rDNA loci at interphase. Silver staining on metaphase chromosomes was used to evaluate the previous activity of the NORs, and to reveal variations in their size; and the pTa71 FISH probe from wheat was used to visualize structural modifications to the interphase rDNA loci. A single B had no measurable effect, but, as the B-number increased, there were significant changes in the physical dimensions of the metaphase NORs, reflecting reduced levels of their activity earlier in the cell cycle, and also in the condensation patterns of the interphase rDNA loci. In addition, the higher B-numbers caused a size heteromorphism between the homologous NORs. A model is discussed which interprets the phenotypic effects of Bs generically, in nucleotypic terms, based of their being 'genetically inert' but 'chromosomally active'.

Chromatin↗

PubMed2001

Use of a genetic marker to examine genetic interaction among subpopulations of pink salmon (Oncorhynchus gorbuscha).

In 1979 and 1981, a genetic marker was bred into one of the five identifiable subpopulations of pink salmon [Oncorhynchus gorbuscha (Walbaum)] in the Auke Lake drainage in Southeast Alaska. As a result of the marking effort, the frequencies of two malate dehydrogenase (MDH-B1, 2*) alleles were changed in the marked subpopulation, but not in other subpopulations that spawn at different times or places. Between 1983 and 1989, the marker allele frequencies were monitored in many of these subpopulations and in early- and late-run pink salmon spawning in nearby Waydelich Creek, located approximately 1 km away. Changes in allele frequencies at MDH-B1, 2*, used to obtain direct estimates of average migration rates (m) from the marked to the unmarked subpopulations, revealed little or no introgression into early subpopulations or into nearby Waydelich Creek. Moreover, spatially distinct late-run Auke Creek subpopulations were not immediately overrun by the more abundant marked subpopulation. These observations suggest that genetic isolation exists between temporally distinct spawning runs and that small temporal and spatial (or ecological) differences contribute to population structure. These observations should be considered in taking actions that affect conservation and harvest management or extensive culture of salmonids.

Alleles↗

PubMed2000

Unexpected low genetic differentiation among allopatric species of section Algarobia of Prosopis (leguminosae).

The Chaqueña Biogeographic Province, in South America, is the main diversity centre of Prosopis. A group of sympatric species of Section Algarobia in this region constitutes a syngameon, characterised by frequent hybridization and introgression. These processes have been postulated as responsible for the low genetic differentiation observed among species within this group. In this study genetic variability and differentiation among geographically isolated species of the same section was analysed through isoenzyme electrophoresis. Variability parameters and fixation indices were estimated to determine the genetic structure of populations. Two Argentinean, P. ruscifolia ('vinal') and P. flexuosa ('algarrobo amarillo'), and one North American species, P. glandulosa (honey mesquite) were studied. All of them showed, similarly to other species of the same section, high genetic variability and exhibit homozygote excess, probably due to population substructure and low rates of selfing. In contrast to our hypothesis, genetic similarity among species is not related to geographic distance. Genetic distances between P. glandulosa and South American species are similar to those observed among species of this subcontinent. The results obtained suggest that the high genetic similarity among the species of the section Algarobia studied is not due to hybridization.

Alleles↗

PubMed2000

High-density molecular map of chromosome region harboring stripe-rust resistance genes YrH52 and Yr15 derived from wild emmer wheat, Triticum dicoccoides.

Two stripe-rust resistance genes, YrH52 and Yr15, derived from the Israeli wild emmer wheat, Triticum dicoccoides, have been located on chromosome 1B. The main objectives of the present study were to increase marker density in the vicinity of YrH52 gene by means of AFLP, RAPD and microsatellite markers, to improve the map of another T dicoccoides-derived stripe-rust resistance gene Yr15 using microsatellite markers, and to preliminarily discriminate these two genes. Additional 26 marker loci comprising 20 AFLPs, three RAPDs, and three microsatellites were found to be linked to YrH52 gene. An updated genetic map consisting of 45 marker loci, in the region of YrH52 gene, was constructed with a total map length of 107.7 cm. The mean interval length was 0.96 cm in the region Xgwm359b-P55M53b carrying YrH52 gene. YrH52 was bracketed by Xgwm413 (Nor1 and UBC212a) and Xgwm273a (Xgwm273d) with map distance of 1.3 and 2.7 cm from either side, respectively. Eight additional microsatellite markers were found to be linked with Yr15, and the linkage map of Yr15 gene was thus obviously improved. In the YrH52-mapping population, no crossover was detected in the interval UBC212a (Xgwm413)-Yr15-Nor1, and YrH52 was located distally outside this interval. It may suggest that YrH52 is different from Yr15 even though both of them are derived from T. dicoccoides and are mapped on chromosome 1BS. The large number of molecular makers revealed in the present study would be helpful for the marker-assisted introgression of the T. dicoccoides-derived YrH52 and Yr15 stripe-rust resistance genes into elite cultivars of wheat, and the high-density map would accelerate the map-based cloning of the two genes.

Basidiomycota↗

PubMed1999

Analysis of background-dependent genetic interactions without inbred strains.

Experimental analysis of background dependent effects of genetic interactions can be designed using strains generated by introgression of small genetic regions containing identical genotypes at loci in question into different inbred strains. We use a novel multilocus paradigm, denoted conditional intergenic functional association (CIFA), to simulate this procedure, with the trade-off of power for convenience that is affordable when sufficiently strong effects are present. We analyze nine enzyme loci at three chromosomes in groups of D. melanogaster with different developmental rates that showed similar allelic frequencies at individual loci. Results obtained suggest the presence of adaptive interaction between particular alleles at two loci when genetic variation at seven background loci is eliminated. Biochemical considerations show that, in the resulting developmental context, strong interaction between these genes may emerge from shifted control of the pentose phosphate pathway, with cascading effects on the glycolysis, TCA cycle, and biosynthetic pathways: one gene may assume control of the irreversible rate-limiting step in the pentose phosphate pathway, whereas the other gene may assume control of the NADP+ level that regulates the same rate-limiting step as an electron acceptor. The newly developing functional genomics research and the absence of inbreeding make CIFA directly applicable to complex human traits in large samples.

Animals↗

PubMed2004

A reanalysis of protein polymorphism in Drosophila melanogaster, D. simulans, D. sechellia and D. mauritiana: effects of population size and selection.

Comparison of synonymous and nonsynonymous variation/substitution within and between species at individual genes has become a widely used general approach to detect the effect of selection versus drift. The sibling species group comprised of two cosmopolitan (Drosophila melanogaster and Drosophila simulans) and two island (Drosophila mauritiana and Drosophila sechellia) species has become a model system for such studies. In the present study we reanalyzed the pattern of protein variation in these species, and the results were compared against the patterns of nucleotide variation obtained from the literature, mostly available for melanogaster and simulans. We have mainly focused on the contrasting patterns of variation between the cosmopolitan pair. The results can be summarized as follows: (1) As expected the island species D. mauritiana and D. sechellia showed much less variation than the cosmopolitan species D. melanogaster and D. simulans. (2) The chromosome 2 showed significantly less variation than chromosome 3 and X in all four species which may indicate effects of past selective sweeps. (3) In contrast to its overall low variation, D. mauritiana showed highest variation for X-linked loci which may indicate introgression from its sibling, D. simulans. (4) An average population of D. simulans was as heterozygous as that of D. melanogaster (14.4% v.s. 13.9%) but the difference was large and significant when considering only polymorphic loci (37.2% v.s. 26.1%). (5) The species-wise pooled populations of these two species showed similar results (all loci = 18.3% v.s. 20.0%, polymorphic loci = 47.2% v.s. 37.6%). (6) An average population of D. simulans had more low-frequency alleles than D. melanogaster, and the D. simulans alleles were found widely distributed in all populations whereas the D. melanogaster alleles were limited to local populations. As a results of this, pooled populations of D. melanogaster showed more polymorphic loci than those of D. simulans (48.0% v.s. 32.0%) but the difference was reduced when the comparison was made on the basis of an average population (29.1% v.s. 21.4%). (7) While the allele frequency distributions within populations were nonsignificant in both D. melanogaster and D. simulans, melanogaster had fewer than simulans, but more than expected from the neutral theory, low frequency alleles. (8) Diallelic loci with the second allele with a frequency less than 20% had similar frequencies in all four species but those with the second allele with a frequency higher than 20% were limited to only melanogaster the latter group of loci have clinal (latitudinal) patterns of variation indicative of balancing selection. (9) The comparison of D. simulans/D. melanogaster protein variation gave a ratio of 1.04 for all loci and 1.42 for polymorphic loci, against a ratio of approximately 2-fold difference for silent nucleotide sites. This suggests that the species ratios of protein and silent nucleotide polymorphism are too close to call for selective difference between silent and allozyme variation in D. simulans. In conclusion, the contrasting levels of allozyme polymorphism, distribution of rare alleles, number of diallelic loci and the patterns of geographic differentiation between the two species suggest the role of natural selection in D. melanogaster, and of possibly ancient population structure and recent worldwide migration in D. simulans. Population size differences alone are insufficient as an explanation for the patterns of variation between these two species.

Alleles↗

PubMed2004

First report on RAPDs patterns able to differentiate some Argentinean species of section Algarobia (Prosopis, Leguminosae).

Prosopis species constitute a very important resource in arid and semiarid regions. Some species of section Algarobia hybridise and introgress naturally in areas of sympatry. According to previous isoenzymatic studies these species have high variability within populations. However, the genetic differentiation among species was very low, and these markers failed to provide diagnostic loci for species recognition. Here we analysed by the RAPD technique natural populations of Prosopis alba, P. ruscifolia, P. nigra, P. flexuosa, and P. vinalillo with the purpose of obtaining markers for species and hybrid identification, by analysing the distribution of genetic diversity within and among species. Genetic variability (H = 0.12-0.26) was similar in all populations. Genetic differentiation among populations (FST = 0.39) was highly significant. Hierarchical analysis of genetic structure performed by Wright (1978) method and analysis of molecular variance (AMOVA) indicated that the diversity among populations within species is low (4-13%) and most genetic diversity (54-61%) occurs within populations. The differentiation among species is intermediate (26-42%) between the previous components but highly significant. Five bands provided a tool for identifying any of the species studied, with the exception of P. vinalillo. The difficulty in diagnosing this species is discussed in reference to the hypothesis of its hybrid origin.

Argentina↗

PubMed2001

Improving plant breeding with exotic genetic libraries.

Naturally occurring variation among wild relatives of cultivated crops is an under-exploited resource in plant breeding. Here, I argue that exotic libraries, which consist of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide plant breeders with an important opportunity to improve the agricultural performance of modern crop varieties. These libraries can also act as reagents for the discovery and characterization of genes that underlie traits of agricultural value.

Breeding↗

PubMed1998

The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids.

Mi-1, a Lycopersicon peruvianum gene conferring resistance to the agricultural pests, root-knot nematodes, and introgressed into tomato, has been cloned using a selective restriction fragment amplification based strategy. Complementation analysis of a susceptible tomato line with a 100 kb cosmid array yielded a single cosmid clone capable of conferring resistance both to the root-knot nematode Meloidogyne incognita and to an unrelated pathogen, the potato aphid Macrosiphum euphorbiae. This resistance was stable. The Mi-1 gene encodes a protein sharing structural features with the nucleotide-binding site leucine-rich repeat-containing type of plant resistance genes.

Amino Acid Sequence↗

PubMed1989

Variations of a Y chromosome repeated sequence across subspecies of Mus musculus.

The complex species Mus musculus is widespread in Eurasia and consists of four parapatric genetical entities (subspecies) that have recently radiated. Two of them (M. m. domesticus and M. m. musculus) are known to interact through a narrow zone of hybridisation across which autosomal and mitochondrial exchanges are very limited and Y chromosome exchange is absent. We extend here the study of this group by the genetical analysis of 22 Asian strains of various origins (China, Korea, Japan, Taiwan, Philippines and Indonesia). A survey of protein variation at ten polymorphic loci confirmed that these animals belong to either the subspecies M. m. musculus (northern type in Asia, ranging westwards to Eastern Europe) or to M. m. castaneus (southern Asian type) and revealed a certain degree of intergradation between the two taxa. Y chromosome variations were assessed in these strains using a Y specific DNA probe representing part of a small multigene family and also in four M. m. domesticus (the Western European house mouse) strains of various origins and one M. m. bactrianus (from Pakistan). Musculus and castaneus were identically monomorphic for one type of organisation of this Y repeated family, while domesticus and bactrianus were very similar to each other, showing slightly different types of organisation. Introgression of a bactrianus Y chromosome into the territory of castaneus was found in Indonesia. The present distribution of the Y types among the four subspecies is not phylogenetically concordant with the known distributions of autosomal and mitochondrial variants.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed1993

Allozyme variability in the Italian wolf (Canis lupus) population.

Multilocus protein electrophoresis was used to estimate genetic variability in a sample of 38 Italian wolves (Canis lupus). Percentage of polymorphic loci was p = 10.0 per cent (four polymorphic loci out of 40 examined), and average observed heterozygosity was Ho = 0.028. Genotypes were in Hardy-Weinberg equilibrium. Electrophoretic analysis does not indicate a significant reduction of genetic variability at nuclear gene loci following at least one century of isolation from other European populations and demographic fluctuations suggested by recent range contraction and expansion. These findings are compared with published allozyme and mitochondrial DNA data for dogs, Canadian wolves, and introgressed wolf x coyote populations from Minnesota and Isle Royale (U.S.A.).

Animals↗