Genetic variability of Siberian fir <Emphasis Type="Italic">Abies sibirica</Emphasis> Ledeb. inferred from AFLP markers

Genetic variability of AFLP markers was studied in 20 populations of Siberian fir (Abies sibirica, Pinaceae) and in two populations of Far-Eastern species Manchurian fir A. nephrolepis and Sakhalin fir A. sachalinensis each. Four pairs of selective primers were used. In total, 168 samples from three fir species were genotyped for 117 polymorphic loci. According to the AMOVA results, the variability proportion characterizing the differences among three Abies species was several times higher (F _CT = 0.53) than that acounting for population differences within the species (F _SC = 0.125). Differentiation of the A. sibirica populations based on AFLP markers exceeded 14% (F _ST = 0.141). Significant correlation between the genetic distances calculated from the AFLP data and the geographic distances between populations was found. The results of AFLP variability analysis supported and supplemented the conclusions inferred previously from allozyme and cpSSR data: several genetically similar geographic groups of Siberian fir were identified. These groups differ both in allele frequencies and in the levels of genetic variation.     

The diversity of chloroplast microsatellite loci in Siberian fir (Abies sibirica Ledeb.) and two Far East fir species A. nephrolepis (Trautv.) Maxim. and A. sachalinensis Fr. Schmidt

The genetic variability in 29 populations of Abies sibirica, three of A. nephrolepis, and seven of A. sachalinensis was studied using SSR markers of chloroplast DNA. Stable amplification and polymorphic products were obtained using primer pairs Pt71936 and Pt30204 (with nine and forteen alleles, respectively) of 10 pairs. Totally, 70 haplotypes were found, 43 in A. sibirica, 49 in A. sachalinensis, and 31 in A. nephrolepis. The highest values of genetic diversity parameters were observed in A. sachalinensis, and the lowest in A. nephrolepis. The Siberian fir differs from Far East species by the uneven multimodal frequency distributions of allele length in both cpSSR loci, which is explained by the presence of few separated from each other dominating haplotypes. This fact indicates that A. sibirica and the Far East species have different demographic histories. In A. sibirica, the proportion of diversity between populations in the total genetic diversity, calculated taking into account the differences between haplotypes (R(ST)) was 8.34% and 4.42% without accounting for haplotypes differences (R(ST) > G(ST), P= 0.01). The pairwise G(ST) correlate significantly with geographic distances between the populations A. sibirica and with genetic distances D calculated from allozyme data. No such correlations were found with the R(ST) parameter. The results of cpSSR variability analysis strongly support the conclusions inferred from allozyme data: several geographic groups of comparatively genetically close populations are identified, which may be explained by the invasion of colonization of the present-day Siberian fir range.     

Genetic variation and population differentiation in Siberian fir Abies sibirica lebed. Inferred from allozyme markers

Genetic variation in 24 populations of Siberian fir Abies sibirica Lebed. from the Urals, West Siberia, East Siberia, South Siberia, and the Baikal region were examined using allozyme markers. Three out of fifteen allozyme loci proved to be polymorphic. Heterozygosity He was 6.6-9.6%, which is substantially lower than that in other widely spread boreal conifers. Our results suggest that the Siberian fir populations are subdivided into four geographic groups: (1) the Baikal Lake group, (2) the Sayan and the Altai group, (3) the Middle and Southern Urals group, and (4) Subpolar and Northern Urals group. This pattern of geographic differentiation may be explained by the preservation of the Siberian fir during the last glacial maximum (18 000-22000 years B.P.) in isolated refugia with subsequent recolonization of the present area. FST in the populations examined was 10.16%, which is comparable to the estimate for Larix sibirica (7.9%), a conifer species having a similar range and pattern of geographic population differentiation.     

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow.     

Population genetic structure of wild-growing ginseng (Planax ginseng C. A. Meyer) assessed using AFLP markers

Genetic variability in ten populations of wild-growing ginseng was assessed using AFLP markers with the application of fragment analysis on a genetic analyzer. The variation indices were high in the populations (P = 55.68%; H(S) = 0.1891) and for the species (P = 99.65%; H(S) = 0.2857). Considerable and statistically significant population differentiation was demonstrated (theta = 0.363; Bayesian approach, "full model"; F(ST) = 0.36, AMOVA). The results of AMOVA and Bayesian analysis indicate that 64.46% of variability is found within the populations. Mantel test showed no correlation between the genetic and geographic distances among the populations (r = -0.174; P = 0.817). Hierarchical AMOVA and analysis of genetic relationships based on Euclidean distances (NJ, PCoA, and MST) identified two divergent population groups of ginseng. Low gene flow between these groups (N(m) = 0.4) suggests their demographic independence. In accordance to the concept of evolutionary significant units (ESU), these population groups, in terms of the strategy and tactics for conservation and management of natural resources, should be treated as management units (MUs). The MS tree topology suggests recolonization of southern Sikhote-Alin by ginseng along two directions, from south and west.     

Genetic variation and population structure of oriental migratory locust, Locusta migratoria manilensis, in China by allozyme, SSRP-PCR, and AFLP markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5-98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6-66.7%). The genetic distances between the populations were relatively low. Shannon's index and Nei's gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Increased genetic divergence between two closely related fir species in areas of range overlap

Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence.     

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

The diversity of chloroplast microsatellite loci in Siberian fir (Abies sibirica Ledeb.) and two Far East fir species A. nephrolepis (Trautv.) Maxim. and A. sachalinensis Fr. Schmidt

The genetic variability in 29 populations of Abies sibirica, three of A. nephrolepis, and seven of A. sachalinensis was studied using SSR markers of chloroplast DNA. Among ten primer pairs examined, pairs Pt71936 and Pt30204 gave stable amplification and polymorphic products (with nine and fourteen alleles, respectively). Totally, 70 haplotypes were found, 43 in A. sibirica, 49 in A. sachalinensis, and 31 in A. nephrolepis. The highest values of genetic diversity parameters were observed in A. sachalinensis, and the lowest in A. sibirica. The Siberian fir differs from Far East species by the uneven multimodal frequency distributions of allele length in both cpSSR loci, which is explained by the presence of few separated from each other dominating haplotypes. This fact indicates that A. sibirica and the Far East species have different demographic histories. In A. sibirica, the proportion of diversity between populations in the total genetic diversity, calculated taking into account the differences between haplotypes (R _ST) was 8.34 and 4.42% without accounting for haplotypes differences (R _ST > G _ST, P = 0.01). The pairwise G _ST correlate significantly with geographic distances between the populations A. sibirica and with genetic distances D calculated from allozyme data. No such correlations were found with the R _ST parameter. The results of cpSSR variability analysis strongly support the conclusions inferred from allozyme data: several geographic groups of comparatively genetically close populations are identified, which may be explained by the history of colonization of the present-day Siberian fir range. Original Russian Text ? S.A. Semerikova, V.L. Semerikov, 2007, published in Genetika, 2007, Vol. 43, No. 12, pp. 1637–1646.     

Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

Jacaranda decurrens (Bignoniaceae) is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2%) polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA) using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA) and Pearson''s correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006) between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Genetic diversity, population structure, and differentiation of Siberian larch, Gmelin larch, and Cajander larch on SSR-marker data

The genetic diversity of SSR markers was studied in six populations of Siberian larch, two popu-lations of Gmelin larch, and four populations of Cajander larch. Seven pairs of nuclear microsatellite loci were used for this analysis. 103 allelic variants were detected in 365 individuals of three species of larch. According to the AMOVA results, the variability proportion that characterizes the differences between three Larix species was twice as higher (15%) than the proportion that accounts for among-population differences within the species (6%). The differentiation of the populations of three species of larch based on SSR markers exceeded 12% (F _ST = 0.121). A significant correlation of the genetic distances with the geographic distances between populations was found (r = 0.835, P = 0.01).     

Genetic enrichment of the arctic clonal plant Saxifraga cernua at its southern periphery via the alpine sexual Saxifraga sibirica

Isolation of populations at the margins of a species range may lead to decreasing genetic diversity via genetic drift and inbreeding. Hybridization between peripheral populations of two species can, however, counteract genetic impoverishment. The mainly clonal, polyploid plant Saxifraga cernua has a wide arctic distribution but also extends southwards into alpine sites. In the Ural Mountains, its peripheral distribution overlaps with that of its sexually reproducing, diploid relative Saxifraga sibirica, and fertile polyploids of more or less intermediate appearance are found in this overlap zone. We used amplified fragment length polymorphism (AFLP) analysis to address the potential impact of interspecific gene flow on genetic diversity in the peripheral populations. A total of 149 plants from 17 populations along a 1650 km south-north gradient were analysed for 253 markers. The results suggest that three Middle Ural populations containing fertile and morphologically more or less intermediate plants have been affected by hybridization. All of these plants formed a strongly supported (100%) group with S. cernua in a neighbour-joining tree, but their AFLP phenotypes assigned either to S. cernua or to artificial (simulated) F(1) hybrids between S. cernua and S. sibirica in multilocus assignment tests. The three populations were highly diverse with virtually every plant representing a distinct AFLP phenotype, providing additional evidence for formation of later-generation hybrids and/or backcrossing to S. cernua. In contrast, other peripheral populations of S. cernua were typically monoclonal, suggesting that hybridization with S. sibirica can increase genetic diversity in S. cernua at its southern periphery.     

Genetic Diversity and Population Structure of Yellow Camellia (Camellia nitidissima) in China as Revealed by RAPD and AFLP Markers

Camellia nitidissima, a rare plant but a useful genetic resource for commercial cultivation of ornamental camellias, is distributed in a narrow region of South China and North Vietnam. In this study, RAPD and AFLP markers were used to assess the genetic diversity and population structure of six natural populations of C. nitidissima from Guangxi in South China. Twenty RAPD primers amplified 183 bands, of which 143 bands were polymorphic, and 8 AFLP primer pairs produced 502 bands, of which 364 were polymorphic. Independent as well as combined analyses of the cluster analyses of the RAPD and AFLP fragments showed that the six populations could be classified into two major genetic groups corresponding to the Nanning and Fangcheng areas. The Mantel test revealed significant correlation between the genetic and geographic distances of C. nitidissima populations (r = 0.953, p = 0.036). AMOVA analysis allowed the partitioning of the genetic variation between groups (36.09%), among populations within groups (25.78%), and within populations (38.14%). An understanding of both the genetic diversity and the population structure of C. nitidissima in China can also provide insight into the conservation and management of this endangered species.     

AFLP markers demonstrate local genetic differentiation between two indigenous oak species [ Quercus robur L. and Quercus petraea (Matt.) Liebl.] in Flemish populations

The nuclear genetic variation within and between four sessile ( Q. petraea) and six pedunculate ( Q. robur) autochthonous Flemish oak populations was investigated with AFLP markers. One sessile and one pedunculate oak population were additionally screened for detailed leaf characteristics using an image analysis system. Principal coordinate analysis on the AFLP data classified the oaks in two main groups, according to their taxonomic status. No species-specific AFLP markers were found using four primer combinations, but marker frequency differences up to 71% were recorded between both species. Analysis of the genetic structure showed that the divergence between species, as observed by ordination, was significant. Both species revealed similar diversity levels. A smaller though significant differentiation was also revealed for both species among populations within species. Molecular and morphology based approaches showed a high degree of consistency. Screening of 60 AFLP primer combinations using a bulking strategy did not allow identifying species-specific markers, which supports the conclusions reached in previous studies. The distribution of genetic variability at the species and at the population level is discussed.     

Genetic variation and differentiation of Abies alba Mill. populations from Ukrainian Carpathians

Using electrophoretic analysis of 11 enzyme systems, we studied the genetic structure and differentiation of eight natural populations of silver fir Abies alba Mill. in the Ukrainian Carpathians. Of 24 isozyme loci identified, 66.8% proved to be polymorphic. The mean numbers of alleles and genotypes per locus in the populations were respectively 3.1 and 4.5. Each A. alba tree was on average heterozygous at 15.9% of genes. In six populations, the genotypic distribution for all of the loci examined corresponded to Hardy-Weinberg proportions. The populations studied had low levels of subdivision (F(ST) = 0.018; GST = 0.019) and differentiation. Nei's genetic distances between the A. alba populations in the region ranged from 0.002 to 0.009, being on average 0.006.     

Population genetic structure of wild-growing ginseng (<Emphasis Type="Italic">Planax ginseng</Emphasis> C.A. Meyer) assessed using AFLP markers

Genetic variability in ten populations of wild-growing ginseng was assessed using AFLP markers with the application of fragment analysis on a genetic analyzer. The variation indices were high in the populations (P = 55.68%, H _S = 0.1891) and for the species (P = 99.65%; H _S = 0.2857). Considerable and statistically significant population differentiation was demonstrated (θ_B = 0.363; Bayesian approach, “full model”; F _ST = 0.36, AMOVA). The results of AMOVA and Bayesian analysis indicate that 64.46% of variability is found within the populations. Mantel test showed no correlation between the genetic and geographic distances among the populations (r = −0.174; p = 0.817). Hierarchical AMOVA and analysis of genetic relationships based on Euclidean distances (NJ, PCoA, and MST) identified two divergent population groups of ginseng. Low gene flow between these groups (N _m = 0.4) suggests their demographic independence. In accordance to the concept of evolutionary significant units (ESU), these population groups, in terms of the strategy and tactics for conservation and management of natural resources, should be treated as management units (MUs). The MS tree topology suggests recolonization of southern Sikhote-Alin by ginseng along two directions, from south and west.     

Swiss Mattenklee landraces,a distinct and diverse genetic resource of red clover (<Emphasis Type="Italic">Trifolium pratense</Emphasis> L.)

Genetic variability within and among 19 landraces and cultivars of red clover ( Trifolium pratense L.) was investigated by means of amplified fragment length polymorphism (AFLP) analysis in order to assess the potential value of Swiss Mattenklee landraces as genetic resources for plant breeding and the preservation of biodiversity. Populations were classified into three groups according to their origin and agronomic features: Mattenklee landraces (8), Mattenklee cultivars (8) and field clover cultivars (3). Analysis of molecular variance based on 276 polymorphic AFLP markers revealed 80% of total variability to be due to variability within populations while 12% were attributed to variability among groups. Stepwise discriminant analysis identified a subset of 126 AFLP markers which best separated individual plants into the three respective groups. Genetic distances between populations were considerably larger among groups than among populations within the same group, providing further evidence for the genetic distinction between Mattenklee landraces, Mattenklee cultivars and field clover cultivars. AFLP markers identified two landrace clusters, containing three and four populations respectively, which, together with one additional landrace, may sufficiently represent the genetic variability of all eight landraces investigated. The results of this study strongly suggest that Swiss Mattenklee landraces form a genetically distinct group of red clover. The data obtained provide criteria on how to efficiently manage, preserve and exploit Mattenklee germplasm.     

Species distinction in Irish populations of Quercus petraea and Q. robur: morphological versus molecular analyses

BACKGROUND AND AIMS: Populations of oak (Quercus petraea and Q. robur) were investigated using morphological and molecular (AFLP) analyses to assess species distinction. The study aimed to describe species distinction in Irish oak populations and to situate this in a European context. METHODS: Populations were sampled from across the range of the island of Ireland. Leaf morphological characters were analysed through clustering and ordination methods. Putative neutral molecular markers (AFLPs) were used to analyse the molecular variation. Cluster and ordination analyses were also performed on the AFLP markers in addition to calculations of genetic diversity and F-statisitcs. KEY RESULTS: A notable divergence was uncovered between the morphological and molecular analyses. The morphological analysis clearly differentiated individuals into their respective species, whereas the molecular analysis did not. Twenty species-specific AFLP markers were observed from 123 plants in 24 populations but none of these was species-diagnostic. Principal Coordinate Analysis of the AFLP data revealed a clustering, across the first two axes, of individuals according to population rather than according to species. High F(ST) values calculated from AFLP markers also indicated population differentiation (F(ST) = 0.271). Species differentiation accounted for only 13 % of the variation in diversity compared with population differentiation, which accounted for 27 %. CONCLUSIONS: The results show that neutral molecular variation is partitioned more strongly between populations than between species. Although this could indicate that the populations of Q. petraea and Q. robur studied may not be distinct species at a molecular level, it is proposed that the difficulty in distinguishing the species in Irish oak populations using AFLP markers is due to population differentiation masking species differences. This could result from non-random mating in small, fragmented woodland populations. Hybridization and introgression between the species could also have a significant role.     

Relationships between four measures of genetic distance and breeding behavior in spring wheat

We estimated the genetic distances among 10 spring wheat genotypes based on pedigree data, morphological traits and AFLP markers, used individually and combined with morphological traits, to find the best predictors of general- and specific-combining abilities among parental genotypes. Ten wheat parents were crossed in a diallel form, disregarding reciprocal hybrids, totaling 45 combinations. The F(1) hybrids, F(2) populations and parents were evaluated in the field in 2007. The experimental plots consisted of 20 plants for F(1) hybrids and 40 plants for parental and F(2) populations. All methods (pedigree data, AFLP markers and morphological traits, used individually and combined) were found to be useful for the assessment of genetic diversity. The significant coefficient correlations ranged from low (0.45) to moderate (0.67) between the distance measures and hybrid performance. There was significant agreement between the distance measures based on AFLP markers vs morphological traits + AFLP markers (r = 0.47) and between pedigree data vs morphological traits + AFLP markers (r = 0.43). The pedigree distance was positively associated with traits 100-kernel weight and grain yield per plant in F(1) (correlations of 0.67 and 0.62, respectively) and F(2) (correlations of 0.62 and 0.59, respectively) generations. These correlation values indicate that the genetic distance, based on pedigree data, could replace diallel crosses for the selection of parents with higher combining ability and with moderate reliability.