Cecilia Bessega

Consistency between marker- and genealogy-based heritability estimates in an experimental stand of Prosopis alba (Leguminosae)

Prosopis represents a valuable forest resource in arid and semiarid regions. Management of promising species requires information about genetic parameters, mainly the heritability (h(2)) of quantitative profitable traits. This parameter is traditionally estimated from progeny tests or half-sib analysis conducted in experimental stands. Such an approach estimates h(2) from the ratio of between-family/total phenotypic variance. These analyses are difficult to apply to natural populations of species with a long life cycle, overlapping generations, and a mixed mating system, without genealogical information. A promising alternative is the use of molecular marker information to infer relatedness between individuals and to estimate h(2) from the regression of phenotypic similarity on inferred relatedness. In the current study we compared h(2) of 13 quantitative traits estimated by these two methods in an experimental stand of P. alba, where genealogical information was available. We inferred pairwise relatedness by Ritlands method using six microsatellite loci. Relatedness and heritability estimates from molecular information were highly correlated to the values obtained from genealogical data. Although Ritlands method yields lower h(2) estimates and tends to overestimate genetic correlations between traits, this approach is useful to predict the expected relative gain of different quantitative traits under selection without genealogical information.

Consistency of population genetics parameters estimated from isozyme and RAPDs dataset in species of genus Prosopis (Leguminosae, Mimosoideae)

Genetic variability, population structure and differentiation among 17 populations of 5 species and 2 natural interspecific hybrids of section Algarobia of genus Prosopis were analyzed from data of 23 isozyme and 28 RAPD loci. Both markers indicated that the studied populations are highly variable. P. alba populations in average showed lower values of genetic variability estimates from isozyme data, but this trend was not observed for RAPD markers. The hierarchical analyses of the distribution of genetic variability showed that the highest proportion of variation occurred within populations, the differentiation among species was intermediate and the lowest component was observed among populations within species. The consistency between results from both dataset implies that they are not biased and reflect the actual genetic structure of the populations analyzed. The matrices of Euclidean distances obtained from the two sets of markers were highly correlated according to Mantel test. In both cases the corresponding phenogram and MDS plot tended to cluster conspecific populations while hybrid populations were not intermediate between putative parents. Some disagreements between isozyme and RAPD phenograms were observed mainly in the affinities of hybrid populations. Such inconsistencies might result from reticular rather than dichotomic evolutionary relationships. The phenetic associations retrieved gave no support to the division of the section Algarobia into series.

Isozyme and RAPD studies in Prosopis glandulosa and P. Velutina (Leguminosae, Mimosoideae)

Abstract Allozyme and random amplified polymorphic DNA (RAPD) techniques have been compared for their usefulness for genetic and taxo-nomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of geneticvariability. Genetic structure and differentiation were analyzed through non-hierarchical Wright’s F DT . For all populations considered, bothmarkers produced low gene flow (Nm 1), in agreement with that expected for conspecific populations. However, in RAPD data the expectedreduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test) forall populations was significant (P = 0.02) when based on isozymes, but not so (P = 0.33) when based on RAPDs. No significantassociations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX) enabled usto distinguish between P. glandulosa and P. velutina , but no diagnostic band for recognition of populations or species studied here weredetected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P.glandulosa and a lower coefficient of variation than those obtained from isozymes.

Unexpected low genetic differentiation among Allopatric species of section Algarobia of Prosopis (Leguminosae)

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

New microsatellite loci for Prosopis alba and P. chilensis (Fabaceae)

Premise of the study: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. Methods and Results: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. Conclusions: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.

Landscape genetic structure of natural populations of Acacia caven in Argentina

Acacia caven is a South American species which shows remarkable climate tolerance and ecological adaptability; as such, this species is suitable for colonizing anthropogenically degraded sites. This species is widely distributed, and six varieties have been described based on both morphological traits and molecular markers. Moreover, Aronson (1992) suggests that, for this species, geographical separation could be associated with ecological differentiation. In this study, amplified fragment length polymorphisms were used to study genetic variation within and among 15 populations of A. caven from five eco-regions of Argentina and to investigate (1) whether the varieties are genetically coherent, (2) whether the varieties correspond consistently to a single eco-region, (3) the proportion of the species diversity explained within and among varieties and eco-regions. Eight of the 225 bands appear to be under positive selection. The remaining 217 neutral loci showed a high percentage of polymorphism (99.1%). The estimates of genetic diversity Hj were generally high. The FST (0.315) was highly significant, providing evidence for genetic structure among populations. Hierarchical analysis of molecular variance indicated that variation among eco-regions was 8.2% and highly significant. The higher component of variance was found within populations (67.5%). STRUCTURE analysis suggested that the optimal number of K = 11. The results showed that, in most cases, geographic separation is associated with ecological differentiation. Since differentiation of A. caven populations studied here in eco-regions was highly significant, sampling should include a large number of trees within populations as well as covering the wide ecological diversity of the species.

Accuracy of dominant markers for estimation of relatedness and heritability in an experimental stand of Prosopis alba (Leguminosae)

The estimation of genetic components of phenotypic variance is based on the resemblance between relatives. In natural populations of most forest tree species without genealogical information, a possible alternative approach is the use of relatedness estimates obtained indirectly from molecular marker data. Heritability (h2) is then estimated from the covariance of estimated relatedness and phenotypic resemblance. In a stand of Prosopis alba planted in 1991 in Argentina, relatedness was estimated for all individual pairs of trees by means of the information proceeding from 128 dominant markers (57 AFLPs and 71 ISSRs) and compared with estimates obtained from six microsatellite loci previously studied. We empirically compared the accuracy of different relatedness estimators based on dominant markers proposed by Lynch and Milligan (Mol Ecol 3:91–99, 1994), Hardy (Mol Ecol 12:1577–1588, 2003), Wang (Mol Ecol 13:3169–3178, 2004), and Ritland (Mol Ecol 14:3157–3165, 2005). Heritabilities of 13 quantitative traits were then estimated from the regression of pairwise phenotypic distances on pairwise relatedness according to Ritland (Genet Res 67:175–185, 1996a). Relatedness inferred from molecular markers was in all cases significantly correlated with actual relatedness, although Ritlands estimator showed the highest bias but the lowest variance. Dominant marker-based h2 estimates were evidently downwards biased and showed poor correlation with those based on family records. In conclusion, the use of dominant molecular markers evidently produces much greater underestimates of h2 than from using co-dominant ones, attributable to the lower accuracy in the indirect estimation of relatedness coefficient. Many traits with enough genetic variability as to respond readily to selection would remain undetected; only those with very high heritability would show significant h2 estimates.

Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae)

Abstract Signals of selection on quantitative traits can be detected by the comparison between the genetic differentiation of molecular (neutral) markers and quantitative traits, by multivariate extensions of the same model and by the observation of the additive covariance among relatives. We studied, by three different tests, signals of occurrence of selection in Prosopis alba populations over 15 quantitative traits: three economically important life history traits: height, basal diameter and biomass, 11 leaf morphology traits that may be related with heat-tolerance and physiological responses and spine length that is very important from silvicultural purposes. We analyzed 172 G1-generation trees growing in a common garden belonging to 32 open pollinated families from eight sampling sites in Argentina. The multivariate phenotypes differ significantly among origins, and the highest differentiation corresponded to foliar traits. Molecular genetic markers (SSR) exhibited significant differentiation and allowed us to provide convincing evidence that natural selection is responsible for the patterns of morphological differentiation. The heterogeneous selection over phenotypic traits observed suggested different optima in each population and has important implications for gene resource management. The results suggest that the adaptive significance of traits should be considered together with population provenance in breeding program as a crucial point prior to any selecting program, especially in Prosopis where the first steps are under development.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

Evidence of heterogeneous selection on quantitative traits of Prosopis flexuosa (Leguminosae) from multivariate QST–FST test

Prosopis flexuosa is an arboreal Leguminosae that grows in arid and semiarid temperate zones of Argentina, in the Monte eco-region. It is a promising native forest species for recovering arid and semiarid regions because it plays an important role in erosion control as well as in soil fertility. Furthermore, it provides diverse economical resources. The main challenge to the forestry sector is finding a balance between production and forest protection. For this purpose, it is necessary to gather information about genetic parameters. In this study, we measured the distribution of the variation of 14 quantitative traits in an experimental half-sib stand, where families are representative of hierarchically structured populations. We applied a multivariate extension of the classical QST–FST neutrality test to determine the relative importance of drift versus selection in the distribution of genetic variability. We found strong evidence that different selective regimes act on different traits and that selection favors different optima in each sampling site. The selection to different optima is much stronger among than within provenances. This result helps explain the possible causes for the regional variation observed in P. flexuosa and to define the management units and the evolutionarily significant units for this species.