Numerical analysis of allozyme variation inCucurbita pepo

Cucurbita pepo, represented by cultivated forms of squash, pumpkins, and ornamental gourds, is a morphologically diverse species. Although several classifications of the cultivars have been proposed, none has been fully accepted. In an attempt to clarify the systematics of theC. pepo cultivars, allozyme variation was assayed. Twelve loci representing 6 enzyme systems (GOT, IDH, MDH, PER, PGI, and PGM) were screened. Seven of the loci were polymorphic. Electrophoretic data were collected for 50 accessions representing 14 commercial cultivars and a landrace from Mexico. Statistical analyses of the allozyme data revealed a biochemical basis for characterizing cultivars that agrees with morphology. Principal component analysis and cluster analysis revealed a major subdivision within the species above the level of cultivars. Genetic identities among groups of cultivars were much lower than those usually found among conspecific populations for outcrossing plants, possibly reflecting the influences of populational subdivision, drift, and selection particular toC. pepo.     

Genetic diversity of nine faba bean (Vicia faba L.) populations revealed by isozyme markers

Seven isozyme systems (Sod, 6-Pgd, Me, Est, Skdh, Fdh and Gdh) representing nine loci were used to study the genetic diversity of nine faba bean populations. Seven loci revealed polymorphic bands and showed the same quaternary structure as that found in several species. They revealed a high number of phenotypes. Indeed, from 3 to 9 phenotypes per locus were investigated in this study. The percentage of polymorphic loci (P = 59.3 %) was higher than that mentioned in the autogamous species (P = 20.3 %) and less than the optimum (P=96 %) indicated for allogamous plants. Total genetic diversity (H _T) and within population genetic diversity (H _S) were estimated with the isozyme markers. The contribution of among population genetic diversity (D _ST) to total genetic diversity was 22%. Enzyme markers pointed out an average inbreeding level for whole population (F _IT) and within population (F _IS). Within population genetic diversity represents 78% of total diversity. Intra-population genetic diversity (H _S = 0.206) was ranged with the respect of allogamous species and was clearly higher than that of among population genetic diversity (D _ST = 0.057) indicating an out-crossing predominance in the studied populations. The expected heterozygosity was higher than that observed heterozygosity at the allogamous species was confirmed in this study. Although, the mean estimated gene flow was less than 1(Nm=0.814), the dendrogram based on Nei’s genetic distance of the 9 populations using UPGMA method showed some genetic drift between populations.     

A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni

Systematic characterization of ẖybrid incompatibility (HI) between related species remains the key to understanding speciation. The genetic basis of HI has been intensively studied in Drosophila species, but remains largely unknown in other species, including nematodes, which is mainly due to the lack of a sister species with which C. elegans can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However, the paucity of dominant and visible marker prevents the efficient mapping of HI loci between the two species. To elucidate the genetic basis of speciation in nematode species, we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome and mapped them into the defined locations by PCR and Next-Generation Sequencing (NGS). Aided by the marker, we backcrossed the GFP-associated C. briggsae genomic fragments into C. nigoni for at least 15 generations and produced 111 independent introgressions. The introgression fragments cover most of the C. briggsae genome. We finally dissected the patterns of HI by scoring the embryonic lethality, larval arrest, sex ratio and male sterility for each introgression line, through which we identified pervasive HI loci and produced a genome-wide landscape of HI between the two nematode species, the first of its type for any non-Drosophila species. The HI data not only provided insights into the genetic basis of speciation, but also established a framework for the possible cloning of HI loci between the two nematode species. Furthermore, the data on hybrids confirmed Haldane’s rule and suggested the presence of a large X effect in terms of fertility between the two species. Importantly, this work opens a new avenue for studying speciation genetics between nematode species and allows parallel comparison of the HI with that in Drosophila and other species.     

Isozyme analysis of genetic variability and population structure of Lactuca L. germplasm

Isozymes were used to investigate the genetic variability, population structure, and relationships of Lactuca germplasm. The isozyme systems revealed 16 putative loci of a total of 31 alleles. Out of these 16 loci, 11 were polymorphic. The average values of expected heterozygosity (H_e), observed heterozygosity (H_o), mean number of alleles per locus (A) and effective number of alleles per locus (A_e) were 0.2227, 0.266, 1.3005 and 1.369, respectively. The average fixation indices were lower than zero for most of the accessions studied, indicating an excess of heterozygotes. Genetic differentiation among accessions (F_ST) exhibited that 51.3% of the isozyme variation was recorded among accessions, and 48.7% of the genetic variation resided within accessions. The average values of total heterozygosity (H_T) and intra-accessional genetic diversity (H_S) were 0.352 and 0.171, respectively. Moreover, the inter-accessional genetic diversity (D_ST) ranged from 0 to 0.424 with an average of 0.18. Cluster analysis revealed that L. sativa cultivars were distributed throughout different Lactuca species. Thereby, isozymes results confirms the hypothesis of the polyphyletic origin of L. sativa. This high level of genetic variation proved that isozymes are efficient for polymorphism analysis of Lactuca germplasm.     

Genetic variation in populations of the arctic perennial Pedicularis dasyantha (Scrophulariaceae), on Svalbard,Norway

Isozyme variability was examined in 13 geographically isolated populations of the endemic arctic hairy lousewort (Pedicularis dasyantha) in the Svalbard Archipelago, 80° N latitude, Norway. Of the 23 enzyme systems screened on five buffer systems 18 were interpretable. Of the 31 reliable loci, only 6-phosphogluconate dehydrogenase (6-Pgd), was polymorphic. However, no heterozygotes were detected. Frequencies for allele 1 among the populations varied from 1.00 in the north to 0.00 in the south and 0.53 in the central “overlap” region. At the species level the mean number of alleles per locus (A) was 1.03. Percentage of polymorphic loci (P) was 3%. Expected heterozygosity (H_e) was 0.016. At the population level the mean number of alleles per locus was 1.01, and 1.1% of the loci were polymorphic. H_e was 0.004. These values are low compared to endemic, widespread, selling, and outcrossed species. Flower color morphs were distinct. They varied within and among the 13 populations. The frequency of color morphs coincided with allele frequencies of 6-PGD: allele 1 was found in dark purple morphs, and allele 2 was found in light morphs. This species shows more isozyme genetic variability than the five other species reported in the genus but generally less variation than other species with limited regional distributions. Low-level genetic variation in this diploid species may be a result of colonization events coupled with genetic drift, founder effects, and strong natural selection. Additional factors include the self-compatible reproductive system and the long-lived perennial habit.     

Signatures of adaptation and genetic structure among the mainland populations of Pinus radiata (D. Don) inferred from SNP loci

Insights into the relative contributions of locus specific and genome-wide effects on population genetic diversity can be gained through separation of their resulting genetic signals. Here we explore patterns of adaptive and neutral genetic diversity in the disjunct natural populations of Pinus radiata (D. Don) from mainland California. A first-generation common garden of 447 individuals revealed significant differentiation of wood phenotypes among populations (P _ST), possibly reflecting local adaptation in response to environment. We subsequently screened all trees for genetic diversity at 149 candidate gene single nucleotide polymorphism (SNP) loci for signatures of adaptation. Ten loci were identified as being possible targets of diversifying selection following F _ST outlier tests. Multivariate canonical correlation performed on a data set of 444 individuals identified significant covariance between environment, adaptive phenotypes and outlier SNP diversity, lending support to the case for local adaptation suggested from F _ST and P _ST tests. Covariation among discrete sets of outlier SNPs and adaptive phenotypes (inferred from multivariate loadings) with environment are supported by existing studies of candidate gene function and genotype–phenotype association. Canonical analyses failed to detect significant correlations between environment and 139 non-outlier SNP loci, which were applied to estimate neutral patterns of genetic differentiation among populations (F _ST 4.3 %). Using this data set, significant hierarchical structure was detected, indicating three populations on the mainland. The hierarchical relationships based on neutral SNP markers (and SSR) were in contrast with those inferred from putatively adaptive loci, potentially highlighting the independent action of selection and demography in shaping genetic structure in this species.     

Allozyme variation and phylogeny in annual species ofCicer (Leguminosae)

Allozymic variation at 30 isozyme loci was examined electrophoretically in nine annual and one perennial species ofCicer. While most of the accessions examined were monomorphic, species can be differentiated on the basis of their enzyme phenotypes. Several groups of species were identified based upon genetic distance values. For example,C. arietinum, C. reticulatum, andC. echinospermum shared the same alleles for most of the loci exmained. PerennialC. anatolicum is also closely related to this group. Similarly,C. judaicum, C. bijugum, andC. pinnatifidum formed another group. Two annual species,C. chorassanicum andC. yamashitae clustered together, whereasC. cuneatum was the most distantly related species. Correlations were found between genetic distances and geographic distribution. Results from enzyme electrophoresis tend to support the previously reported taxonomic treatments based upon crossability and morphological similarity. However,C. yamashitae, which has been classified in the second crossability group, is quite distinct genetically and morphologically from the remaining species of the group. An isozyme gene duplication observed in the genus suggested the monophyletic origin of the species examined in the present study.     

Murine Adipose Tissue-Derived Stromal Cell Apoptosis and Susceptibility to Oxidative Stress In Vitro Are Regulated by Genetic Background

Adipose tissue-derived stromal cells (ADSCs) are of interest for regenerative medicine as they are isolated easily and can differentiate into multiple cell lineages. Studies of their in vitro proliferation, survival, and differentiation are common; however, genetic effects on these phenotypes remain unknown. To test if these phenotypes are genetically regulated, ADSCs were isolated from three genetically diverse inbred mouse strains- C57BL/6J (B6), BALB/cByJ (BALB), and DBA/2J (D2)- in which genetic regulation of hematopoietic stem function is well known. ADSCs from all three strains differentiated into osteogenic and chondrogenic lineages in vitro. ADSCs from BALB grew least well in vitro, probably due to apoptotic cell death after several days in culture. BALB ADSCs were also the most susceptible to the free radical inducers menadione and H₂O₂. ADSCs from the three possible F1 hybrids were employed to further define genetic regulation of ADSC phenotypes. D2, but not B6, alleles stimulated ADSC expansion in BALB cells. In contrast, B6, but not D2, alleles rescued BALB H₂O₂ resistance. We conclude that low oxidative stress resistance does not limit BALB ADSC growth in vitro, as these phenotypes are genetically regulated independently. In addition, ADSCs from these strains are an appropriate model system to investigate genetic regulation of ADSC apoptosis and stress resistance in future studies. Such investigations are essential to optimize cell expansion and differentiation and thus, potential for regenerative medicine.     

Genetic diversity of populations of a rare species of Dictamnus gymnostylis Stev. in Bashkir Cis-Urals

We examined genetic diversity in populations of Dictamnus gymnostylis Stev., a rare species growing in the Bashkir Cis-Urals, based on the analysis of 8 gene-enzyme systems and detected a fairly high level of intraspecific genetic diversity and population differentiation. We determined the average number of alleles per locus (A) as 1.57; the portion of polymorphic loci (P ₉₅) as 0.508; the observed heterozygosity (H _o) as 0.139; and the expected heterozygosity (H _e) as 0.169. Of the total genetic diversity, 88.3% stems from variability within populations, and 11.7% is due to variation among populations. The average value for the Nei’s genetic distance (D) constituted 0.028.     

Genetic variation and hybridization in SwedishSchoenus (Cyperaceae)

Schoenus ferrugineus andS. nigricans have restricted distributions in Sweden and are almost exclusively confined to calcareous fen habitats. AtS. nigricans sites,S. ferrugineus is usually also present, and hybrids are frequently found. In this report, I used allozymes to estimate the amount of gene flow between the two species, and to compare the partitioning of genetic diversity in each of them. Thirteen loci were analysed at eight different enzyme systems. Seven loci were variable between or within the species. The two species had completely different alleles at two of the seven variable loci, whereas there was overlap at five loci. In all, 22 different alleles were found. Six of these alleles were confined toS. nigricans, and five alleles were confined toS. ferrugineus. Nei's genetic identity was 0.55.—InS. ferrugineus, three loci (23%) were polymorphic, and the average number of alleles per polymorphic locus was 2.0 (each polymorphic locus had two alleles). InS. nigricans, three loci (23%) were polymorphic, and the average number of alleles per polymorphic locus was 2.3.—The proportion of genetic diversity due to variation among sites (G _ST) was fairly similar in the two species, mean over loci = 0.12 inS. ferrugineus and 0.15 inS. nigricans. However, the proportion of genetic diversity due to variation among individuals within sites (G _IS) differed markedly between the two species, mean over loci = 0.54 inS. ferrugineus and 0.17 inS. nigricans. Accordingly, there was a much higher individual heterozygosity inS. nigricans than inS. ferrugineus. — Most hybrids were interpreted as F₁ hybrids. However, a small proportion, 0.5–1.6 %, were F_n hybrids or back-crosses.—On the Swedish mainland, all former occurrences ofS. nigricans are extinct, but viable hybrids are still present at a few sites in southernmost Sweden.     

Development of microsatellite markers for the red tide‐forming harmful species Chattonella antiqua,C. marina,and C. ovata (Raphidophyceae)

We have developed 11 microsatellite markers that are specific to Chattonella antiqua, C. marina, and C. ovata, the red tide‐forming harmful phytoplanktons. The 11 loci were amplified in the three species. The number of alleles per locus ranged from 5 to 16. The three species shared most microsatellite regions, although the genetic differences in specific loci were detected among them. These markers of the Chattonella species will be beneficial for biogeographical, detailed taxonomic, studies.     

Patterns of allozyme variation and clonal diversity in Carex lasiocarpa and C. pellita (Cyperaceae)

We compared genetic variability and clonal diversity in the closely related sedges Carex lasiocarpa and C. pellita using allozyme markers at 12 loci. Both species produce spreading rhizomes, occur in open habitats, and can form large clones; C. lasiocarpa primarily along lakeshores, or in bogs, fens, or marshes, and C. pellita more commonly along riverbanks and ditches or in wet meadows. Polymorphism was high in both species, similar to that of other rhizomatous Carex and to other species with comparable growth forms and life histories. Total gene diversity was higher for C. lasiocarpa (H_T = 0.266) than for C. pellita (H_T = 0.248), but the coefficient of differentiation among populations was lower. Rare alleles usually occurred as heterozygotes rather than homozygotes, and significant deviations from Hardy-Weinberg equilibrium were found at few loci, suggesting that both species are predominantly outcrossing. Mean clone size, diversity, and evenness were not significantly different between the two species, although populations varied from monoclonal to those where nearly every sampled shoot belonged to a different clone. No significant differences in genetic variation or clone size of C. pellita were found when comparisons were made between groups based on climate (warmer vs. cooler) or successional stage (pioneer vs. established). However, within C. lasiocarpa, genetic variability decreased and clone size increased in cooler climates and at established sites.     

High Polymorphism and Autotetraploid Origin of the Rare Endemic SpeciesOxytropis chankaensisJurtz. (Fabaceae) Inferred from Allozyme Data

Using starch electrophoresis, we examined 19 enzyme systems presumably controlled by 35 loci in the rare endemic tetraploid speciesOxytropis chankaensisJurtz. (Fabaceae). Electrophoretic patterns and their genetic interpretation are presented. The isozyme data suggest tetrasomic inheritance in O. chankaensis. Three or four alleles at a particular locus were found in a number of individual plants, which indicate the autotetraploid origin of this species. Seventeen loci were shown to be polymorphic. As reliable gene markers for population systems, we recommend highly active polymorphic systems showing good allozyme separation (Ce-2, Gpi-2, Gpt-2, Idh-2, Lap, Mdh-2, and Mdh-3). Parameters of allozyme variability proved to be very high for a rare species with a restricted range: P = 48.6%, A = 2, A _p = 3.06, H _ob = 0.173.     

Development and characterization of new microsatellite markers for ginseng (<Emphasis Type="Italic">Panax ginseng</Emphasis> C. A. Meyer)

Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. Its roots are highly prized for several medicinal properties. The present study describes development and characterization of twenty-two polymorphic microsatellite markers for this species. A total of 99 alleles were detected with an average of 4.5 alleles per locus across 20 accessions. Values for observed (H _O ) and expected (H _E ) heterozygosities ranged from 0.05 to 1.00 and from 0.18 to 0.73, respectively. Eleven loci deviated from Hardy–Weinberg equilibrium (P < 0.001). Significant (P < 0.05) heterozygote deficiency was observed at 13 loci. Exact test for linkage disequilibrium showed significant values (P < 0.05) between 12 pairs of loci. These microsatellite markers provide powerful tools for understanding population and conservation genetics of this species and also for genetic differentiation and authentication of different Panax species being used in commercial ginseng products.     

Genetic control of leucine aminopeptidase and esterase isozymes in the interspecific cross Cucurbita ecuadorensis x C. maxima

Starch gel electrophoretic analyses of crude seed extracts of Cucurbita ecuadorensis, C. maxima, their F₁ and F₂, and three of the four possible interspecific backcrosses reveal that the genus is polymorphic for alpha-naphthyl acetate esterases (Est) and leucine aminopeptidase (LAP). The two electrophoretic forms of both Est and LAP are controlled by codominant alleles. The two loci do not exhibit linkage. Neither the LAP nor the Est phenotypes exhibit a significant deviation from the expected 1:1 ratio in interspecific backcrosses when the donor parent alleles are transmitted through female gametes, but there is a significant deviation for Est when transmission is through male gametes. Differential gametic selection involving the Est-1 locus suggests structural differences between the genomes of the parental species for the chromosomal region in which this locus occurs. No structural differences are indicated between the parental genomes for the chromosome region bearing the Lap-1 locus.     

Genetic architecture of a feeding adaptation: garter snake (Thamnophis) resistance to tetrodotoxin bearing prey

Detailing the genetic basis of adaptive variation in natural populations is a first step towards understanding the process of adaptive evolution, yet few ecologically relevant traits have been characterized at the genetic level in wild populations. Traits that mediate coevolutionary interactions between species are ideal for studying adaptation because of the intensity of selection and the well-characterized ecological context. We have previously described the ecological context, evolutionary history and partial genetic basis of tetrodotoxin (TTX) resistance in garter snakes (Thamnophis). Derived mutations in a voltage-gated sodium channel gene (Na_v1.4) in three garter snake species are associated with resistance to TTX, the lethal neurotoxin found in their newt prey (Taricha). Here we evaluate the contribution of Na_v1.4 alleles to TTX resistance in two of those species from central coastal California. We measured the phenotypes (TTX resistance) and genotypes (Na_v1.4 and microsatellites) in a local sample of Thamnophis atratus and Thamnophis sirtalis. Allelic variation in Na_v1.4 explains 23 per cent of the variation in TTX resistance in T. atratus while variation in a haphazard sample of the genome (neutral microsatellite markers) shows no association with the phenotype. Similarly, allelic variation in Na_v1.4 correlates almost perfectly with TTX resistance in T. sirtalis, but neutral variation does not. These strong correlations suggest that Na_v1.4 is a major effect locus. The simple genetic architecture of TTX resistance in garter snakes may significantly impact the dynamics of phenotypic coevolution. Fixation of a few alleles of major effect in some garter snake populations may have led to the evolution of extreme phenotypes and an ‘escape’ from the arms race with newts.     

ELECTROPHORETIC ANALYSIS OF GENETIC VARIATION IN THE CHAROPHYTA. I. GENE DUPLICATION VIA POLYPLOIDY1

Electrophoretic analysis of 12 species of Chara indicates that functional gene duplication via polyploidy has commonly occurred in the genus. Duplication has been followed by differentiation of the loci encoding phosphoglucose isomerase (PGI). This has led directly to generation of substantial levels of genie variation both within and between taxa. A simple genetic model is proposed to account for the large array of PGI phenotypes encountered in natural populations. Constraints imposed by the reproductive biology of members of the genus, such as selfing, appear to have resulted in selective premiums on intrinsic mechanisms of generating genetic variation. Levels of variation in PGI were higher than would be predicted on the basis of charophyte reproductive characteristics; haploid loci segregate approximately two alleles within each species.     

Phosphoglucose isomerase and esterase phenotypes in Crassostrea angulata and C. gigas

The phenotype distributions and the allele frequencies of the phosphoglucose isomerase and esterase loci examined in the samples of Crassostrea angulata (Essex, England) and C. gigas (Brittany) do not differ significantly and the two populations as such are indistinguishable. The validity of the species C. angulata is questioned and it is postulated that the two samples may be geographic isolates of the same species, i.e. C. gigas. The hatchery reared population of C. gigas from Conway is distinguishable from the other samples of Crassostrea examined. The lack of phenotype diversity is attributed to founder effects of the small parental stock imported in 1965. The distributions of all phenotypes are in agreement with Hardy-Weinberg expectations. Phosphoglucose isomerase (E.C. 5.3.1.9.) is a dimer governed by at least four alleles in C. angulata and five alleles in C. gigas. The slower (Es-S) zone of the esterase electrophoretogram would appear, in both species to be governed by four alleles at a single locus. There was no esterase banding which was specific to either species of Crassostrea.     

Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function

Although two related species may have extremely similar phenotypes, the genetic networks underpinning this conserved biology may have diverged substantially since they last shared a common ancestor. This is termed Developmental System Drift (DSD) and reflects the plasticity of genetic networks. One consequence of DSD is that some orthologous genes will have evolved different in vivo functions in two such phenotypically similar, related species and will therefore have different loss of function phenotypes. Here we report an RNAi screen in C. elegans and C. briggsae to identify such cases. We screened 1333 genes in both species and identified 91 orthologues that have different RNAi phenotypes. Intriguingly, we find that recently evolved genes of unknown function have the fastest evolving in vivo functions and, in several cases, we identify the molecular events driving these changes. We thus find that DSD has a major impact on the evolution of gene function and we anticipate that the C. briggsae RNAi library reported here will drive future studies on comparative functional genomics screens in these nematodes.     

Genetic diversity and differentiation of the Critically Endangered Hispaniolan palm Coccothrinax jimenezii M.M. Mejía & R.G. García based on novel SSR markers

Coccothrinax jimenezii M.M. Mejía & R.G. García is a Critically Endangered palm species restricted to Haiti (one population near the city of Gonaïves with 43 individuals) and the Dominican Republic (one population on the shores of Lago Enriquillo with 18 individuals). The species faces two major conservation challenges: (1) water level rise in the hypersaline Lago Enriquillo and (2) overexploitation of leaves for making brooms in Haiti. Six SSR microsatellite loci were used to access levels of genetic variation and the genetic structure of these two populations. Only the Gonaïves site had loci that deviated from Hardy–Weinberg Equilibrium (2 loci). Both populations exhibited a relatively large number of private alleles (13 in Lago Enriquillo and 14 in Gonaïves) and did not show evidence of genetic bottlenecks. Inbreeding coefficients were much larger in Gonaïves (F_is = 0.232) than in Lago Enriquillo (F_is = 0.093). We detected high genetic differentiation among these sites (F_st = 0.497) suggesting that additional taxonomic studies are needed to determine if individuals from these two sites should be recognized as belonging to two different taxa. Because of taxonomic uncertainties we recommend not to translocate individuals between sites in future conservation activities involving this species.