Level Of Genetic Similarity Research Articles

Genetic variation and spatial structure in sugar maple (Acer saccharum Marsh.) and implications for predicted global‐scale environmental change

SummaryCurrent ecosystem model predictions concerning the effects of global temperature increase on forest responses do not account for factors influencing long‐term evolutionary dynamics of natural populations. Population structure and genetic variability may represent important factors in a species' ability to adapt to global‐scale environmental change without experiencing major alterations in current range limits. Genetic variation and structure in sugar maple (Acer saccharum Marsh.) were examined across three regions, between two stands within regions, and among four to five open‐pollinated families within stands (total N = 547 genotypes) using 58 randomly amplified polymorphic DNA (RAPD) markers. Differences within open‐pollinated families account for the largest portion of the total variation (29%), while differences among regions represent less than 2% of the total variation. Genetic diversity, as indicated by estimates of percent polymorphic loci, expected heterozygosity, fixation coefficients, and genetic distance, is greatest in the southern region, which consists of populations with the maximum potential risk due to climate change effects. The high level of genetic similarity (greater than 90%) among some genotypes suggests that gene flow is occurring among regions, stands, and families. High levels of genetic variation among families indicate that vegetational models designed to predict species' response to global‐scale environmental change may need to consider the degree and hierarchical structure of genetic variation when making large‐scale inferences.

Genetic diversity of Alternaria alternata isolated from tomato in California assessed using RAPDs

Black mould lesions were caused by Alternaria alternata in 76% of 228 tomato fruit with characteristic sunken black lesions collected from fields of processing tomatoes in California. Analysis of 29 RAPD primers revealed a high level of genetic diversity among the 69 isolates tested. Two major phenetic groups (Group 1 with 55 isolates and Group 2 with 14) were identified independently by PCA and by UPGMA of Jaccard similarity coefficients. Only 34 of 137 RAPD markers were monomorphic for all isolates and the genetic similarity between the two groups was 50%. Co-infection of black mould lesions by genetically distinct strains of A. alternata occurred in two of 10 isolates tested. There was no evidence for geographic clustering of isolates with high levels of genetic similarity, suggesting that isolates are widely dispersed across California. Only one isolate was identified which also caused stem canker disease on a susceptible tomato cv., suggesting that these strains play a minor role in causing black mould on processing tomatoes in California. This isolate and two other known stem canker isolates were clustered together with 11 other isolates in Group 2. Group 2-specific bands were also identified in a survey of seven additional isolates known to produce host-specific toxins.

Effectiveness of different classes of molecular marker for classifying and revealing variation in rice (Oryza sativa) germplasm

We have examined the effectiveness of similar numbers of markers from four molecular marker systems (AFLP, isozymes, ISSR and RAPD) for revealing genetic diversity and discriminating between infraspecific groups of Oryza sativa germplasm. Each marker system classifies the germplasm into three major groups (most effectively with isozymes and AFLPs), but with differences (primarily with ISSR) between the precise classifications generated. However, at the highest levels of genetic similarity there was only partial agreement as to relationships between individual accessions when different markers were used. When variance was partitioned among and within the three subspecific groups, although the differences were not significant, greater variation was found among than within groups using AFLP and isozymes, with the reverse for RAPD and ISSR. Measurement of polymorphism using average heterozygosity and effective number of alleles gave similar results for each marker system. These results are discussed in relation to various genetic resources conservation activities, and the advisability of extrapolating to other sets of germplasm particularly of other crop species.

Genetic variation within and between southern Ontario populations of Sclerotinia homoeocarpa

Restriction fragment length polymorphisms (RFLP) of the intergenic spacer region (IGS) of rDNA and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability among 181 isolates of Sclerotinia homoeocarpa from Ontario and 10 isolates from Japan. RAPD and IGS‐RFLP analyses revealed polymorphisms within and between populations of S. homoeocarpa, distinguishing 151 genotypes. Both types of markers gave similar results in phenetic analysis of genetic distances between populations. Cluster analysis showed that Japanese isolates of S. homoeocarpa were genetically distinct from Ontario isolates, demonstrating significant intraspecific differentiation. An average genetic similarity of 0.66 was found between Japanese isolates. Among Ontario isolates, average genetic similarity was 0.86, and genotypic diversity analysis showed that 49.3% of the total genetic variation observed within Ontario populations occurred among individuals within populations compared to 50.7% between populations. Gametic linkage disequilibrium analysis within Ontario populations revealed an average 15.6% significant nonrandom associations between putative RAPD loci, and that half of the populations showed signs of significant linkage disequilibrium. These results suggest that both clonal propagation and recombination events occurred in local populations of S. homoeocarpa. The high level of genetic similarity between populations and the low levels of intraspecific genetic variation may reflect a small founding population for southern Ontario isolates of S. homoeocarpa.

Diversity of selected hop cultivars detected by fluorescent AFLPs

The amplified fragment length polymorphism (AFLP) technique was used to assay eight hop cultivars. The application of fluorescent-labelled primers proved to be a valuable tool and substituted radiolabelling. Digestion with the enzymes EcoRI/ MseI and amplification with primers having three selective bases at the 3’end resulted in distinct banding patterns for imaging with a fluorescent scanner. A total of 523 AFLP fragments derived from eight primer combinations were analysed. On average, 18 polymorphisms per combination were displayed. The Saazer “noble” hop cultivars ‘Saazer’, ‘Tettnanger’ and ‘Spalter’ could not be discriminated. The lowest genetic similarity (GS) between lines was computed for the bitter hops ‘Hallertauer Magnum’ and ‘Wye Target’: GS value of 0.89. The high level of genetic similarity of the analysed hop cultivars is discussed.

Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai).

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.

Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour

Subpopulation genetic structure was studied in a population of the short‐lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep‐sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub‐populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.

Study of the genetic variability and similarity among and within Arachis villosulicarpa, A. pietrarellii and A. hypogaea through isoenzyme analysis

Arachis villosulicarpa is a perennial species cultivated for its soft and tasty seeds by indigenous inhabitants of the Mato Grosso State, Brazil. Besides A. hypogaea, this species is considered as the only species of Arachis which represents a valuable food source for human consumption. Due to the lack of knowledge concerning the genetic diversity of A. villosulicarpa, this study was conducted to evaluate the genetic variability of the accessions from the Germplasm Collection of CENARGEN/EMBRAPA (Brasilia, DF, Brazil) and Instituto Agrono^mico (IAC, Campinas, SP, Brazil). In addition, the genetic similarity between A. villosulicarpa, the related wild species A. pietrarellii, and the cultivated peanut A. hypogaea cv. Tatu was evaluated. From the entire sample analyzed of A. villosulicarpa, the accession from Instituto Agrono^mico showed the highest indices of diversity for both enzymatic systems analyzed, pointing this accession as a promising source of genetic variabil ity that must be preserved in the Germplasm Bank. A high level of genetic similarity was observed between A. pietrarellii and A. villosulicarpa, supporting previous suggestions that A. pietrarellii could be the ancestral progenitor species of A. villosulicarpa or that both species originated from a common ancestor.

Genetic Variation in a Population of Black Bears as Revealed by DNA Fingerprinting

Analyses of DNA-fingerprint data of black bears ( Ursus americanus ), using an alkaline-phosphatase labeled, multilocus probe, revealed moderate to high levels of genetic similarity of individuals within a population in the Chapleau Crown Game Preserve in northern Ontario. Band-sharing coefficients were calculated between pairs of adult males (0.55 ± 0.02, n = 30), adult females (0.60 ± 0.04, n = 30), adult males and females (0.56 ± 0.04, n = 30), and known first-order relationships (0.82 ± 0.02, n = 12). A preliminary examination of band-sharing coefficients of bears from across Ontario revealed lower similarity levels (0.26 ± 0.04, n = 75). These values were similar to background band-sharing coefficients in natural avian and other mammalian populations.

DNA Marker-based Study of Genetic Relatedness in United States Sweetpotato Cultivars

The polymerase chain reaction (PCR)-based DNA amplification fingerprinting (DAF) approach was used to investigate genetic relationships among 30 U.S. sweetpotato (Ipomoea batatas L. Lam.) genotypes including heirloom cultivars and recent releases. Phenogram, pairwise similarity matrix, and principal coordinate plots were developed based on Jaccard's coefficients using band-sharing data generated by seven octamer primers. All cultivars showed unique fingerprint patterns indicating the utility of DAF in cultivar identification. Many heirloom cultivars such as `Creole' and `Porto Rico' were readily differentiated from recently developed cultivars. Modern cultivars such as `Jewel', `Carver', `Nugget', and `Scarlet' exhibited a high degree of similarity reflecting ancestral relatedness. `Regal' and `Excel', recently developed using a population-based breeding approach, showed greater divergence from all other cultivars. Those cultivars, developed as a result of somatic mutations, exhibited high levels of genetic similarity to their normal-type parents and yet had distinct fingerprint profiles. With few exceptions, genetic relationships derived from DAF data appear to be consistent with available pedigree information.

Genetic Similarity among Central and South American Populations of Leishmania (viannia) braziliensis

Four populations of Leishmania (Viannia) braziliensis from Central America, Colombia, Peru and Brazil were analyzed and compared for up to 20 enzyme loci. Each of the 180 isolates could be identified as L. braziliensis using combined data from glucose phosphate isomerase and mannose phosphate isomerase. When the most common enzyme band was present at a frequency of < or = 0.95, the populations were polymorphic (more than a single allomorph for an enzyme) for more than 50% of the loci. Included were diagrammatic representations of the enzyme polymorphisms. Comparisons of levels of enzyme polymorphism and of genetic similarity among other Leishmania populations, L. tropica, L. major, L. mexicana, and L. donovani sensu lato, were discussed. The mean +/- SD level of genetic similarity among the four populations was 0.924 +/- 0.036 (range 0.878-0.966), which indicates that L. braziliensis is probably one reproductive population from Mexico in the north to Brazil and Peru in the south.

Genetic Analysis of Laboratory and Wild Strains of the Melon Fly (Diptera: Tephritidae) Using Random Amplified Polymorphic DNA–Polymerase Chain Reaction

The technique of random amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR) has been to used identify genetic markers in a collection of strains of the melon fly, Bactrocera cucurbitae (Coquillet), having known histories. These strains originated from 2 different geographic localities (Hawaii and Okinawa) and have been in laboratory culture anywhere from zero (wild caught) up to several hundred generations. Levels of genetic variability have been documented and quantified using RAPD–PCR and a similarity index to compare individuals within and between strains. In general, strains subjected to laboratory culture for many generations have higher levels of within-strain similarity because of a loss of genetic variability, as might be expected from selection, inbreeding, or drift effects. One longterm laboratory strain of Hawaiian origin had more than twice the level of genetic similarity than a wild caught sample of similar origin. Levels of genetic similarity between strains also are effected by differential fixation of markers, again even for strains of similar geographic origin.

Isozyme Variation in Lychee (Litchi chinensis Sonn.)

A genetic diversity analysis involving 49 Iychee (Litchi chinensis Sonn.) accessions using eight enzyme systems encoding 12 loci (Idh-1, Idh-2, Mdh-2, Per-1, Pgi-2, Pgm-1, Pgm-2, Skdh, Tpi-1, Tpi-2, Ugpp-1, and Ugpp-2) revealed moderate to high levels of genetic variability. Cluster analysis of the isozyme data from 40 genetically different accessions of the total 49 identified three groups at the 50% level of genetic similarity, the largest of which contained 32 of the 40 accessions distributed in three sub-groups. The groups including the three subgroups differed in frequency and composition of alleles at different loci. Polymorphism was observed in 77% of the loci, with an overall mean of 2.2 alleles per locus and an observed heterozygosity of 0.387. The unbiased genetic identities (I) between groups ranged from 0.809 to 0.937. Summing over all 11 polymorphic loci, 16% of gene diversity was due to differentiation between groups and 84% within groups. Comparison of isozyme fingerprints revealed that some accessions with identical names, particularly of `No mai tsz', `Kwai mi', and `Hak ip', possessed different isozyme genotypes, while other accessions with different names displayed identical isozyme genotypes. Isozyme fingerprinting will be useful in revealing and resolving questions of clonal identity, which are common in Iychee germplasm collections.

Isozyme variation in lychee ( Litchi chinensis Sonn.)

A genetic diversity analysis involving 49 lychee ( Litchi chinensis Sonn.) accessions using eight enzyme systems encoding 12 loci ( Idh-1, Idh-2, Mdh-2, Per-1, Pgi-2, Pgm-1, Pgm-2, Skdh, Tpi-1, Tpi-2, Ugpp-1, and Ugpp-2) revealed moderate to high levels of genetic variability. Cluster analysis of the isozyme data from 40 genetically different accessions of the total 49 identified three groups at the 50% level of genetic similarity, the largest of which contained 32 of the 40 accessions distributed in three sub-groups. The groups including the three sub-groups differed markedly both in frequency and composition of alleles at different loci. On average, 77% of the loci were polymorphic with an overall mean of 2.2 alleles per locus and an observed heterozygosity of 0.387. The unbiased genetic identities ( I) between groups ranged from 0.809 between Groups 1b and 2 to 0.937 between Groups 1b and 1c. Group 2 has diverged from the other groups with an average genetic identity of 0.821. Summing over all 11 polymorphic loci, 16% of gene diversity was due to differentiation between groups and 84% to that within groups. Comparison of isozyme fingerprints revealed that some accessions identically named, such as ‘No mai tsz’, ‘Kwai mi’, and ‘Hak ip’, possessed different isozyme genotypes, whereas some others with different names displayed identical isozyme genotypes.

Acidiphilium multivorum sp. nov., an acidophilic chemoorganotrophic bacterium from pyritic acid mine drainage.

Six strains of acidophilic chemoorganotrophic bacteria from acid mine drainage were studied in their taxonomic aspects. They were gram negative, aerobic, mesophilic, oxidase negative, catalase positive, urease positive, nonsporeforming, and rod-shaped. Carotenoid and bacteriochlorophyll a were formed. Two strains had a polar flagellum and other two strains fimbriae. They used a wide variety of organic compounds for growth, but did not use ferrous iron, elemental sulfur, and thiosulfate as the sole energy source. Acetate was inhibitory to growth. Growth was enhanced by adding high concentrations of glucose or complex organic compounds such as trypticase soy (BBL) and yeast extract. Methanol was utilized as the sole source of carbon and energy. The major ubiquinone was Q-10. The major cellular fatty acid was straight-chain unsaturated C18:1 acid. The hydroxy acid was 3-OH C14:0 acid. The DNA base composition was 66.2 to 68.1mol% guanine plus cytosine. The isolates showed relatively low levels of genetic similarity to Acidiphilium cryptum and Acidiphilium organovorum. On the basis of the phenotypic, chemotaxonomic, and genotypic characters, we conclude the isolates as a new species, for which we propose Acidiphilium multivorum sp. nov. The type strain is AIU 301 (JCM 8867).

Isozyme variation in oaks of the Apostle Islands in Wisconsin: genetic structure and levels of inbreeding inQuercus rubraandQ. ellipsoidalis(Fagaceae)

Isozyme variability was examined in populations representing the red oak complex (Quercussubg.Erythrobalanus) on an island archipelago and adjoining peninsula in Lake Superior, near Bayfield, Wisconsin. A concomitant study of morphometric variation described in the companion manuscript, revealed a continuum in leaf morphology extending from an interior mainland site to the outermost island. The existence of this clinal variation presented an ideal opportunity to examine the genetic structure of a hybrid population along with the putative progenitor species. Dormant leaf bud samples were collected from specimens ofQuercus rubraL.,Q. ellipsoidalisHill, and their putative hybrids from three islands and two locations on the peninsula. Acorns were collected from some of these same trees from one peninsula location and two islands. Twelve putative enzyme loci from six enzyme systems were analyzed. Allele frequency data indicated little differentiation between populations. Mean FSTvalues for the adult trees and acorns were 0.042 and 0.020. Genetic identities according to Nei ranged from 0.958 to 0.999. Despite these high levels of genetic similarity, the populations appeared to be highly inbred as indicated by positive mean FSTvalues of 0.183 and 0.373 for the adult trees and acorns. Estimates of migration rate per generation (Nm) for the adult trees was 5.70, a value that is low when compared to estimates for other plant species with similar life history characteristics.

Genetic similarity using DNA fingerprinting in cattle to determine relationship coefficient.

The relation between relationship coefficient and genetic similarity was evaluated using DNA fingerprinting in Japanese Black cattle. We proposed a new method for evaluating heterozygous and homozygous minisatellite loci. Genetic similarity by DNA fingerprinting was estimated by two methods--band sharing (BS) and a new evaluation called genetic similarity (GS). Linear regressions of the relationship coefficient (y) on levels of BS (x1) and GS (x2) yielded the equations y = 0.049 + 0.684x1 and y = -0.206 + 1.149x2, with highly significant correlation coefficients of .631 and .813, respectively. It was suggested that DNA fingerprinting could be applied to estimate the relationship coefficient not only in cattle but also in other species.

Allozyme Variation among Breeding Populations of Red-Winged Blackbirds: The California Conundrum

ABS?RC?.--We examined allozyme variation in 10 breeding populations of Red-winged Blackbirds (Agelaius phoeniceus) across the United States, which represented samples from 9 of 14 putative subspecies in North America. Variation at 13 of 28 resolvable loci revealed a high level of genetic similarity for all seven populations from Florida and New York through the Great Plains to Oregon and northeastern California (pairwise Nei's distances, all _<0.004). Differences in allozyme frequencies we found suggest that fewer subspecies exist in the continental United States than are currently recognized. The most interesting result was that the genetic distance between the populations sampled at Sacramento and San Francisco Bay national wildlife refuges, which are only 214 km apart, had a Nei's distance approximately 10 times as great as the genetic distance between Florida and Oregon populations. Salton Sea, California, the remaining population sampled, was also highly differentiated. Strong site fidelity, the nonmigratory behavior of populations at Salton Sea and San Francisco, or both probably explain their relative allozyme distinctness, but the possibility that the brackish environment in which these birds live enforces a selective regime that reduces successful immigration or emigration to other habitats is intriguing. Received 20 August 1990, accepted 10 January 1991.

Genetic Analysis of Leishmania Mexicana Populations from Texas, Latin America, and the Caribbean

A genetic analysis using enzyme data of 72 Leishmania mexicana isolated from hosts in Texas, Latin America, and the Caribbean is presented. All isolates from each country were combined and considered as local populations. Allomorph (allele determined by electrophoresis) frequencies for 20 enzyme (loci) were calculated and 7 populations (Texas, Mexico, Belize, Guatemala, Ecuador [EC], Venezuela, and the Dominican Republic [DR]) were compared pairwise in the statistic of genetic identity (I) (level of genetic similarity). All populations were found to be genetically similar with a mean I value for all comparisons of 0.890 +/- 0.067. When DR was included as one of the pair compared, I = 0.811 +/- 0.034. Among comparisons that include EC (excluding EC vs. DR), I = 0.875 +/- 0.026. The mean I for the other comparisons was less than 0.9. The data indicate that the DR population is divergent enough from the others that it can be considered at the subspecies/incipient species level of evolutionary divergence; the EC population is, to a lesser extent, distinct from the others, and the other 5 represent geographic populations of 1 widely distributed species. A diagrammatic representation of the allomorphs among the 72 isolates is included. There were some allomorph/geographical (or local) population relationships noted.

Biochemical identities and differences among Leishmania species and subspecies.

An analysis was presented for identification of 20 species and subspecies of Leishmania by cellulose acetate electrophoresis data from the enzymes glucose phosphate isomerase, mannose phosphate isomerase, and phosphogluconate dehydrogenase. Most Leishmania could be identified from data of these three enzymes. The CAE data for 20 enzymes from over 300 New and Old World isolates were combined, and an analysis of the data which included calculations of genetic identities and genetic distances was reported. High levels of genetic similarity and low levels of genetic distance were noted among comparisons of local populations of the same Leishmania, and lower levels of similarity and higher levels of distance were noted among intracomplex pairings. The biochemical data suggested that similarities and differences among Leishmania could be quantified as they have been in other organisms. For the most part the data presented were consistent with the taxonomic rankings which were based on morphology, behavior, ecology, and other biochemical data.