Microsatellite markers isolated from a polyploid saltbush, Atriplex nummularia Lindl. (Chenopodiaceae)

Atriplex nummularia is a polyploid Australian saltbush which has been identified as a suitable species for use in the rehabilitation of agricultural land affected by salinity. We isolated 12 polymorphic loci for a preliminary assessment of genetic variability and structure within the species as a basis for a breeding programme. Preliminary screening of loci in 40 individuals from two populations revealed multibanded genotypes consisting of up to seven alleles in a single individual, with up to 29 alleles observed at a single locus. The multibanded patterns are consistent with the polyploid status of this species.     

ALLOZYME VARIATION AMONG POPULATIONS OF BULINUS FORSKALII (EHRENBERG, 1831) (GASTROPODA: PLANORBIDAE) IN CAMEROON

Allozyme electrophoresis was used to study genetic diversityamong populations of the freshwater, hermaphroditic snail Bulinusforskalii in Cameroon. Three of 15 loci studied in 13 enzymesystems were polymorphic. Intrapopulation variation occurredin 8 of 32 populations sampled and heterozygotes were presentin 2 of these. Neither of these populations were in Hardy-Weinbergequilibrium. These findings are in agreement with reports thathave demonstrated a low genetic diversity in this very widelydistributed, eurytopic species and that have indicated thisspecies reproduces principally by self-fertilization. The restricteddistributions of rarer alleles in three loci may be due to anarrower habitat range for those phenotypes. For isocitratedehydrogenase and phosphoglucoisomerase, the faster alleleswere found throughout the range of B. forskalii extending fromthe Sahelian regions of the north to rain forest of the south.The slower, rarer alleles for these loci were restricted tothe equatorial rain forest regions. For hydroxybutyrate dehydrogenase,the opposite was true for the rarer allele, which was restrictedto a small region in the arid, tropical climate. (Received 27 April 1989; accepted 5 September 1989)     

Genetic variation within and between populations of hermaphroditic <Emphasis Type="Italic">Bulinus truncatus</Emphasis> tetraploid freshwater snails of the Albertine Rift,East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.     

Sequence characterization of microsatellites in diploid and polyploid Ipomoea

 The objectives of the present study were to evaluate the inheritance and nucleotide sequence profiles of microsatellite genetic markers in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] and its putative tetraploid and diploid ancestors, and to test possible microsatellite mutation mechanisms in polyploids by direct sequencing of alleles. Sixty three microsatellite loci were isolated from genomic libraries of I. batatas and sequenced. PCR primers were designed and used to characterize microsatellite loci in two hexaploid I. batatas populations, a tetraploid Ipomoea trifida population, and a diploid I. trifida population. Nine out of the sixty three primer pairs tested yielded a clearly discernible, heritable banding pattern; five showed Mendelian segregation. All other primer pairs produced either smeared banding patterns, which could not be scored, or no bands at all in I. batatas. All of the primers which produced discernible banding patterns from I. batatas also amplified products of similar size in tetraploid and diploid I. trifida accessions. The sequence analysis of several alleles in the three species showed differences due to mutations in the repeat regions consistent with small differences in the repeat number. However, in some cases insertions/deletions and base substitutions in the microsatellite flanking regions were responsible for polymorphisms in both polyploid and diploid species. These results provide strong empirical evidence that complex genetic mechanisms are responsible for SSR allelic variation in Ipomoea. Four I. batatas microsatellite loci showed polysomic segregation fitting tetraploid segregation ratios. To our knowledge this is the first report of segregation ratios for microsatellites markers in polyploids. Received: 4 January 1999 / Accepted: 4 January 1999     

ALLOZYME COMPARISONS AND PLOIDY LEVELS AMONG SPECIES OF THE BULINUS TRUNCATUS/TROPICUS COMPLEX (GASTROPODA: PLANORBIDAE) IN CAMEROON

Allozyme electrophoresis, ploidy level, and, to a lesser extent,anatomy and shell morphology were used to characterize snailsof the Bulinus truncatus/tropicus complex in Cameroon. Starchgel electrophoresis revealed no intrapopulation variation within20 populations examined for 14 allozyme loci in 12 enzyme systems.Interpopulation differences in allozyme patterns were used todivide the populations studied into five groups. Each groupis distinguished by a unique combination of zymograms for hydroxybutyratedehydrogenase and isocitrate dehydrogenase. Four of these groupsare tetraploids and are identified as B. truncatus. Populationsof the most commonly found B. truncatus group are generallyaphallic, are frequently associated with transmission of S.haematobium, and generally occur at altitudes below 800 m abovesea-level. Populations of B. truncatus belonging to the otherthree groups are usually euphallic, not associated with S. haematobiumtransmision, and generally occur at altitudes above 1000 m.These four groups may represent distinct biotypes of B. truncatus.Populations belonging to the fifth group are diploid, euphallic,not associated with S. haematobium transmission, and occur inhabitats above 1000 m. This is the first confirmed report ofdiploid B. truncatus/tropicus-complex snails from this regionof Africa. They are tentatively identified as B. natalensis,a species previously thought to be limited to East and SouthernAfrica. (Received 31 October 1988; accepted 20 February 1989)     

Predicting parental genotypes and gene segregation for tetrasomic inheritance

Recent genome mapping projects in tetraploid plant species require a method for analysing the segregation patterns of molecular marker loci in these species. The present study presents a theoretical model and a statistical analysis for predicting the genotypes of a pair of tetraploid parents at a codominant (for example, RFLPs, microsatellites) or dominant (for example, AFLPs, RAPDs) molecular marker locus based on their and their progeny’s phenotypes scored at that locus (gel-band patterns). The theory allows for null alleles and for any degree of double-reduction to be modelled. A simulation study was performed to investigate the properties of the theoretical model. This showed that in many circumstances both the parental genotypes can be correctly identified with a probability of nearly 1, even when the molecular data were complicated by null alleles or double-reduction. Configurations where the parental genotype cannot be identified are discussed. The power to detect double-reduction varies considerably, depending on the proportion of identical alleles carried and shared by the parents, and the number of null alleles. Incorrect deductions of the occurrence of double-reduction were rare. The method was applied to data on a microsatellite locus segregating in the parents and 74 offspring of a tetraploid potato cross. Twentyfour parental configurations were consistent with the parental gel pattern, but only one of these was compatible with all the phenotypic data on the offspring. The feasibility for extending the present model to predict segregation of several linked loci, and particularly the linkage phase, is briefly discussed. Received: 7 June 1999 / Accepted: 28 September 1999     

Genetic load in sexual and asexual diploids: segregation, dominance and genetic drift

In diploid organisms, sexual reproduction rearranges allelic combinations between loci (recombination) as well as within loci (segregation). Several studies have analyzed the effect of segregation on the genetic load due to recurrent deleterious mutations, but considered infinite populations, thus neglecting the effects of genetic drift. Here, we use single-locus models to explore the combined effects of segregation, selection, and drift. We find that, for partly recessive deleterious alleles, segregation affects both the deterministic component of the change in allele frequencies and the stochastic component due to drift. As a result, we find that the mutation load may be far greater in asexuals than in sexuals in finite and/or subdivided populations. In finite populations, this effect arises primarily because, in the absence of segregation, heterozygotes may reach high frequencies due to drift, while homozygotes are still efficiently selected against; this is not possible with segregation, as matings between heterozygotes constantly produce new homozygotes. If deleterious alleles are partly, but not fully recessive, this causes an excess load in asexuals at intermediate population sizes. In subdivided populations without extinction, drift mostly occurs locally, which reduces the efficiency of selection in both sexuals and asexuals, but does not lead to global fixation. Yet, local drift is stronger in asexuals than in sexuals, leading to a higher mutation load in asexuals. In metapopulations with turnover, global drift becomes again important, leading to similar results as in finite, unstructured populations. Overall, the mutation load that arises through the absence of segregation in asexuals may greatly exceed previous predictions that ignored genetic drift.     

Isolation and characterization of microsatellite markers in the tetraploid birch,Betula pubescens ssp. tortuosa

The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the tree limit in northern Fennoscandia. We identified nine polymorphic microsatellite loci in order to characterize the genetic structure of populations at different elevations close to the treeline. The microsatellite loci were highly polymorphic, with 14–42 alleles per locus and an average expected heterozygosity of 0.73 ± 0.25 under random chromosome segregation and 0.68 ± 0.23 under random chromatid segregation.     

Genetic interpretation of enzyme variation in sexual and agamospermous taxa of Taraxacum sections Vulgaria and Mongolica

The inheritance of 15 enzymes, comprising at least 22 genetic loci, was investigated in crosses between sexual diploid individuals of Taraxacum sections Vulgaria and Mongolica. Patterns were consistent with simple Mendelian segregation. From the inheritance information isozyme phenotypes in agamospermous plants from natural populations were inferred. In some crosses part or all of the progeny originated from self-fertilization, sofar a very rare phenomenon in the sections Vulgaria and Mongolica. It is possible that the probability of self-fertilization increases after pollination by triploid pollen, affecting the cohabitation dynamics of the various ploidy components in mixed natural stands.     

ALLOZYME VARIATION AMONG POPULATIONS OF BIOMPHALARIA PFEIFFERI (KRAUSS, 1848) (GASTROPODA: PLANORBIDAE) IN CAMEROON

Allozyme electrophoresis was used to study genetic diversityamong the freshwater, hermaphroditic snail Biomphalaria pfeifferiin Cameroon. Four of 19 loci studied were polymorphic. The allozymesfor two loci, aspartate aminotransferase-1 (AAT-1) and isocitratedehydrogenase (IDH), showed distribution patterns related toclimatic zones. AAT-1¹⁰⁰ and IDH¹⁰⁰ occurred predominantly inthe Tropical Climatic Zone, located in the northern half ofthe country. AAT-1¹⁴⁰ and IDH⁹⁰ were common in the EquatorialZone. Intrapopulation variations occurred in 5 of 19 populationsampled. Only one population, polymorphic for AAT-1 locus, waspanmictic. The other 4 populations were not in Hardy-Weinbergequilibrium. The deficiency of heterozygotes in those populationsis unusual for a member of the genus Biomphalaria and may bedue to a predominance of self-fertilization. Other explanationsinclude ecological factors or the presence of segregated sub-populationsthat do not outcross. This latter hypothesis is supported bythe total absence of heterozygotes for PGM alleles. (Received 24 August 1989; accepted 14 September 1989)     

Inheritance and dominance of self-incompatibility alleles in polyploid Arabidopsis lyrata

Natural populations of diploid Arabidopsis lyrata exhibit the sporophytic type of self-incompatibility system characteristic of Brassicaceae, in which complicated dominance interactions among alleles in the diploid parent determine self-recognition phenotypes of both pollen and stigma. The purpose of this study was to investigate how polyploidy affects this already complex system. One tetraploid population (Arabidopsis lyrata ssp kawasakiana from Japan) showed complete self-compatibility and produced viable selfed progeny for at least three generations subsequent to field collection. In contrast, individuals from a second tetraploid population (A. lyrata ssp petraea from Austria) were strongly self-incompatible (SI). Segregation of SI genotypes in this population followed Mendelian patterns based on a tetrasomic model of inheritance, with two to four alleles per individual, independent segregation of alleles, and little evidence of dosage effects of alleles found in multiple copies. Similar to results from diploids, anomalous compatibility patterns involving particular combinations of individuals occurred at a low frequency in the tetraploids, suggesting altered dominance in certain genetic backgrounds that could be due to the influence of a modifier locus. Overall, dominance relationships among S-alleles in self-incompatible tetraploid families were remarkably similar to those in related diploids, suggesting that this very important and complicated locus has not undergone extensive modification subsequent to polyploidization.     

Evolution of Multilocus Genetic Structure in Avena Hirtula and Avena Barbata

Avena barbata, an autotetraploid grass, is much more widely adapted than Avena hirtula, its diploid ancestor. We have determined the 14-locus genotype of 754 diploid and 4751 tetraploid plants from 10 and 50 Spanish sites, respectively. Allelic diversity is much greater in the tetraploid (52 alleles) than in the diploid (38 alleles): the extra alleles of the tetraploid were present in nonsegregating heteroallelic quadriplexes. Seven loci were monomorphic for the same allele (genotypically 11) in all populations of the diploid: five of these loci were also monomorphic for the same allele (genotypically 1111) in all populations of the tetraploid whereas two loci each formed a heteroallelic quadriplex (1122) that was monomorphic or predominant in the tetraploid. Seven of the 14 loci formed one or more highly successful homoallelic and/or heteroallelic quadriplexes in the tetraploid. We attribute much of the greater heterosis and wider adaptedness of the tetraploid to favorable within-locus interactions and interlocus (epistatic) interactions among alleles of the loci that form heteroallelic quadriplexes. It is difficult to account for the observed patterns in which genotypes are distributed ecogeographically except in terms of natural selection favoring particular alleles and genotypes in specific habitats. We conclude that natural selection was the predominant integrating force in shaping the specific genetic structure of different local populations as well as the adaptive landscape of both the diploid and tetraploid.     

Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa

Cultivated alfalfa (Medicago sativa) is an autotetraploid. However, all three existing alfalfa genetic maps resulted from crosses of diploid alfalfa. The current study was undertaken to evaluate the use of Simple Sequence Repeat (SSR) DNA markers for mapping in diploid and tetraploid alfalfa. Ten SSR markers were incorporated into an existing F₂ diploid alfalfa RFLP map and also mapped in an F₂ tetraploid population. The tetraploid population had two to four alleles in each of the loci examined. The segregation of these alleles in the tetraploid mapping population generally was clear and easy to interpret. Because of the complexity of tetrasomic linkage analysis and a lack of computer software to accommodate it, linkage relationships at the tetraploid level were determined using a single-dose allele (SDA) analysis, where the presence or absence of each allele was scored independently of the other alleles at the same locus. The SDA diploid map was also constructed to compare mapping using SDA to the standard co-dominant method. Linkage groups were generally conserved among the tetraploid and the two diploid linkage maps, except for segments where severe segregation distortion was present. Segregation distortion, which was present in both tetraploid and diploid populations, probably resulted from inbreeding depression. The ease of analysis together with the abundance of SSR loci in the alfalfa genome indicated that SSR markers should be a useful tool for mapping tetraploid alfalfa. Received: 10 September 1999 / Accepted: 11 November 1999     

Allozyme evidence for genetic autopolyploidy and high genetic diversity in tetraploid cranberry, Vaccinium oxycoccos (Ericaceae)

Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation. No evidence for fixed heterozygosity was found in tetraploid V. oxycoccos. In contrast, all polymorphic loci exhibited both balanced and unbalanced heterozygotes, with some individuals exhibiting a pattern consistent with the presence of three alleles. These results support an autopolyploid origin for tetraploid V. oxycoccos. However, tetraploid V. oxycoccos possessed a suite of alleles not found in diploid V. oxycoccos; half of these alleles were shared with V. macrocarpon. This suggests that autotetraploid V. oxycoccos may have undergone hybridization with V. macrocarpon or that the autotetraploid retained the genetic variation present in an ancestral diploid species. Following theoretical expectations, proportion of polymorphic loci, mean number of alleles, and observed heterozygosity were significantly higher for the autotetraploid than for the diploid. Mean inbreeding (F(IS)) was similar for diploid and tetraploid V. oxycoccos. The latter exhibited population differentiation (F(ST)) exceeding both diploid species.     

Isolation and characterization of 13 microsatellite loci for Neochamaelea pulverulenta (Cneoraceae)

We report 13 polymorphic nuclear microsatellite loci for Neochamaelea pulverulenta (Cneoraceae) using an enriched-library approach. Although this plant species is tetraploid, expected patterns for tetrasomic segregation were completely absent, and all loci analysed showed a diploid pattern of inheritance. We detected a total of 102 alleles in 57 individuals genotyped (mean number of alleles per locus was 7.85). The values of observed and expected heterozygosities ranged from 0.193 to 0.737 and 0.425 to 0.812 respectively. Disomic segregation, levels of polymorphism and the exclusionary power of the developed markers render them readily applicable for parentage assignment of dispersed seeds, and for analyses of spatial genetic structure and population connectivity.     

ALLOZYME VARIATION IN SOME POPULATIONS OF THE FRESHWATER SNAILS LYMNAEA PEREGRA, L. AURICULARIA AND L. STAGNALIS (GASTROPODA: PULMONATA)

Three species of the genus Lymnaea (Gastropoda, Pulmonata, Basommatophora)were examined for genetic variation at 11 enzymatic loci insamples collected in Brittany (North-Western France). Variabilitywas greatest in L. percgra, but the limited area of samplingdid not allow specific inferences. The UPGMA clustering of unbiasedgenetic distances (Nei, 1978) isolated first L. auriculariasamples, and secondly the single L. stagnalis sample from theL. peregra set. This scheme of relationships was opposed tothe identification of alleles shared by the three species atthe studied loci Analysis of L. peregra population structure by F-statistics(Weir & Cockerham, 1984) suggested high inbreeding and raisedthe possible role of self-fertilization. The contradiction betweenhigh variability and high homozygosity is discussed. Furthermore,population differentiation was rather weak (although statisticallysignificant), despite some remarkable differences among loci.Nm estimates using Wright's (1951) and Slatkin's (1985) methodsrevealed a gene flow unable to prevent the effect of geneticdrift among populations. The relative homogeneity of populationswith weak genetic exchange is discussed (Received 24 May 1993; accepted 21 March 1994)     

Genetic variation in Minuartia (Caryophyllaceae) in Svalbard

Based on a survey of eight enzyme systems, genetic variation in three Minuartia species was analysed and the diversity in 15 populations in Svalbard (78°N) compared to seven populations in Norway, Iceland, and Greenland. In the two sexual diploids, M. biflora and M. rubella , genetic diversity was as high in populations from Svalbard as in populations from more southerly latitudes. In M. biflora , eight out of 15 loci were polymorphic (P=53.3 %); in M. rubella eight out of 18 (P=44.4 %). The mean number of alleles per locus (A) and the number of multilocus genotypes (MG) were also higher in M. biflora than in M. rubella , A=1.60 and MG=21 vs. A=1.44 and MG=9. The proportion of genetic diversity due to variation among populations was much lower in M. biflora than in M. rubella , FST=0.249 vs. FST=0.895, and the estimated gene flow much higher, Nm=0.745 vs. Nm=0.029, indicating that M. biflora is a mixed mater and M. rubella a selfer. In the vegetatively reproducing tetraploid, M. rossii , 13 (65 %) out of 20 putative loci showed fixed heterozygosity, the mean number of alleles per 'locus' was A=1.70, and two multilocus phenotypes were observed, proving that at least two clones occur in Svalbard. No allele was shared by all three species and Nei's genetic identity for biflora-rubella was extremely low, I=0.07. The results suggest that the three species, which are currently placed in separate sections, represent lineages that diverged a long time ago.     

Genetic basis of tristyly in tetraploid Oxalis alpina (Oxalidaceae)

The inheritance of style‐morphs was investigated in tetraploid populations of tristylous Oxalis alpina (Oxalidaceae) to determine if alleles controlling style‐morphs are expressed at duplicated loci. In tetraploid populations, a dominant S allele leads to expression of the short‐styled phenotype at the short/non‐short locus and is epistatic to the M allele at the mid/long locus. The M allele results in expression of the mid‐styled phenotype but only if the S allele is absent. Long‐styled morphs are homozygous recessive at the short and mid loci. Test crosses of many tetraploid short‐styled individuals resulted in segregations of short‐, mid‐ and long‐styled individuals which, because of linkage between the short and mid loci, can only occur with polyploidy and expression of alleles at duplicated loci. Segregation patterns from three crosses suggest the possibility of disomic inheritance via preferential pairing of chromosomes in tetraploid populations of O. alpina. Segregation patterns in the progeny of mid‐styled individuals indicated that only a few individuals had more than one copy of the M allele, despite the potential for accumulation of M alleles via self‐fertilization of partially self‐compatible mid‐styled morphs in some populations. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 308–318.     

Loss of duplicate gene expression in tetraploid Chenopodium

Genetic analyses indicate that single-banded leucine aminopeptidase (LAP) phenotypes in tetraploid Chenopodium reflect homozygosity for null alleles at either locus of a polyduplicated pair. Other duplicated isozyme loci show simplification to the diploid phenotype. Loss of duplicate gene expression in the LAP system has occurred independently in putatively specialized taxa occupying the distributional periphery of a New World tetraploid complex. The geographic/taxonomic pattern of genetic variation suggests that fixation of null alleles is mediated by stochastic genetic phenomena associated with migration. Plants homozygous for null alleles at both LAP loci show no detetable activity in assays involving several exopeptidase substrates, although growth and fertility of double-null plants are not markedly reduced. Our data confirm that loss of duplicate gene expression can occur in isozyme systems of polyploid plant taxa. Thus, lack of electrophoretically detectable duplicate gene expression is not a certain indication of diploidy. However, loss of duplicate gene expression in population systems known to be of allopolyploid origin is a clear indication of phyletic derivation.