Daniel Verhaegen

Quantitative trait dissection analysis in Eucalyptus using RAPD markers : 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages

Abstract The objective of this study was to use random amplified polymorphic DNA (RAPD) to determine the genetic location and effects of genomic regions controlling wood density, stem growth and stem form in two species of Eucalyptus. Two hundred F1 trees generated from an interspecific cross E. urophylla×E. grandis between two elite trees were used. Genetic maps were constructed for each parent with markers segregating in the 1:1 ratio in FS progeny. A total of 86 and 92 markers distributed among 11 linkage groups covered 1295 cM and 1312 cM for the E. urophylla and E. grandis parent, respectively. Traits were measured three times up to selection age (38 months). The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters. Several regions controlling part of the variation for the studied traits were identified by interval mapping. Some regions of the genome exerted effects on more than one trait, providing a genetic explanation for at least some of the correlation between the traits. On the basis of an age-by-age analysis, a partial stability of QTL expression was observed with 68% of the QTL being expressed at two ages and 32% being age-specific. No QTL were significant for all three ages. Taking advantage of repeated measurements on the same material across different ages, we investigated with a maximum statistical power, the effect of marker genotype on traits, with age and QTL×age interaction effects being removed. A two-way analysis of variance made it possible to detect significant marker-trait associations over the period studied. Most of them had already been detected in the annual analysis. This result is very encouraging for the application of marker information to the early selection of hybrid trees to be vegetatively propagated for the production of clonal varieties.

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Maré to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautés, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci–population combinations (per population FIS = 0–0.03 on Grande‐Terre and Ile des Pins, and 0–0.67 on Loyautés). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyauté and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.

Diversity and genetic structure of teak (Tectona grandis L.f) in its natural range using DNA microsatellite markers

Teak (Tectona grandis L.f.) is considered to be an extraordinarily durable building timber with a worldwide reputation. Its widespread use has entailed the over-exploitation of natural forests and a large reduction in natural diversity. Fifteen microsatellite markers were used to study the genetic variability and structure of 166 teak trees distributed over the whole natural area of teak. Analysis showed that in the teak natural area there were four main centers of genetic variability. Two clusters were in India and could be considered as main centers of genetic diversity in teak. The third cluster mainly consisting of populations in Thailand and Laos was genetically very distinct from the Indian populations but presented only half as much allelic variability. A fourth cluster from Central Laos showed even less genetic variability. The use of SSR markers for conservation of teak forest diversity is discussed.

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

BackgroundEucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs.ResultsLinkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway.ConclusionsGiven the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.

Isolation and characterization of microsatellite markers for Acacia senegal (L.) Willd., a multipurpose arid and semi‐arid tree

Acacia senegal is a multipurpose African tree that improves the soil fertility of degraded areas. The species is exploited mainly for gum arabic, but it also supplies fuel wood and fodder for animals. Despite its wide distribution in Africa, no microsatellite markers have yet been characterized for this species. In this study, we characterized 11 polymorphic microsatellite loci specifically designed for A. senegal and analysed 247 individuals from three populations from Niger. On average, 10.9 alleles per locus were detected and expected heterozygosity ranged from 0.160 to 0.794, showing the ability of the markers to detect genetic diversity in this species.

Eighteen SSR-primers for tetraploid Adansonia digitata and its relatives

Co-dominant markers suitable for molecular ecological studies in the genus Adansonia are highly desirable in order to be able to address a number of interesting research questions related to the special life history traits, gene flow, and distribution dynamics of the Adansonia species. This note presents a set of 18 SSR-primers developed for Adansonia digitata, and tested for cross-amplification on all members of the Adansonia genus. All reported primers were found to amply loci with more than two alleles per locus in Adansonia digitata, reflecting its tretraploid nature. Segregation of alleles in open pollinated progenies from trees with four alleles per locus indicated polysomic inheritance for 14 of the 18 loci.

Highlighting the occurrence of tetraploidy in Acacia senegal (L.) Willd. and genetic variation patterns in its natural range revealed by DNA microsatellite markers

Acacia senegal (L.) Willd. is the main species producing the internationally traded gum arabic. Genetic studies of this species are rare and until now the chromosome number was thought to be diploid (2n = 2x = 26). Here, using chromosome number counting, we demonstrate for the first time that tetraploids (2n = 4x = 52) also occur in A. senegal. Nuclear and chloroplast microsatellite markers were used to estimate and compare genetic variation within this newly described polyploidy complex in the Sudano-Sahelian region in Africa. Genetic diversity was higher in diploids, suggesting that the formation of tetraploids is recent and that mutation–drift equilibrium has not yet been reached. The two cytotypes do not have the same genetic structure and are genetically differentiated. Among tetraploids, populations are greatly differentiated and do not share the same chlorotypes. Based on these results, we discuss recurrent formation of tetraploids from different diploid progenitors across the distribution range of A. senegal in the Sudano-Sahelian zone.

Microsatellite primer amplification by multiplexing: A first application to Eucalyptus grandis

Multiplexing was used to increase the efficiency of microsatellite analysis inEucalyptus grandis. Primers were chosen based on the range of eucalyptus SSR alleles and their hybridization temperatures. Choice of PCR conditions proved to be the most important factor; concentrations of primers must be adjusted for use in combination. Results show that 6 primers can be analyzed in 2 PCR reactions, one containing 2 and the other containing 4 primers. Multiplexing promises to be a particularly efficient tool for microsatellite diversity analysis inEucalyptus grandis.

Structure and genetic diversity of Ixora margaretae an endangered species A baseline study for conservation and restoration of natural dry forest of New Caledonia

The dry forests of New Caledonia are an exceptional ecosystem because of their numerous endemic botanical species and their highly diversified fauna of insects, mollusks, reptiles and birds. Unfortunately, the area of the dry forests has been significantly reduced, mainly by human activities. Ecological, phenological and genetic analysis of Ixora margaretae, a symbolic species of the sclerophyll forest, has revealed contrasting traits among natural stands. The division of the natural range and then the separation of forest islands has greatly reduced the existing genetic variability of this species. The genetic diversity is strongly structured in genetic clusters which correspond well to specific ecotypes according to the environmental conditions and the forest types. Furthermore, genetic analysis of the reproductive and non-reproductive trees as well the half-sib families obtained by complete protection of mother trees has revealed substantial genetic drift which has resulted in increased loss of allelic variability. The total consumption of seeds by mainly rats confirms the observed absence of natural regeneration. All these results show that measures taken to protect the stands of dry forests will not be enough to maintain sufficient genetic variability of I. margaretae populations in the long term. Assisted regeneration with control of the increase in variability will be necessary to maintain the biodiversity of the species. The results obtained for I. margaretae must be confirmed with other symbolic species in order to take the necessary measures for the effective preservation of the dry forests in New Caledonia.

Differentiation between two sub-species of Acacia senegal complex: Acacia senegal (L.) Willd. and Acacia dudgeoni Craib ex Holland using morphological traits and molecular markers

The Acacia senegal complex is formed by closely related species of Acacia senegal (L.) Willd. These species share several botanical characters, so from a morphological point of view, there is no clear discontinuity between some of them. A. dudgeoni Craib ex Holland is one species of the A. senegal complex that was formerly described as A. senegal ssp. senegalensis var. samoryana (A. Chev.) Rob. In order to differentiate Acacia senegal from A. dudgeoni, we analyzed a range of morphological traits such as tree height and diameter in natural stands, and, at the nursery stage, seedling height, number of branches, main root depth, biomass dry weight and leaf characteristics. Within addition, molecular polymorphism analyses were conducted using 11 microsatellite markers. Leaf characteristics and molecular markers appear to be the most effective tools to distinguish A. senegal from A. dudgeoni. These tools can improve our understanding of the relationship between two species belonging to the same species complex.