[Show abstract][Hide abstract] ABSTRACT: The desert locust (Schistocerca gregaria) has been feared agricultural pest since early civilization, with plagues documented in ancient texts. Population genetic studies of the desert locust are needed to determine genetic variation and movement pattern for efficient control of the pest. In this study, we complemented the limited available microsatellite collection for the desert locust with 34 new polymorphic and multiplexed microsatellite loci. To this aim, we screened an expressed sequence tags library and constructed a partial genomic library enriched for dinucleotide repeats to develop high‐throughput and high‐quality genotyping assays. We then paid particular attention to quality control and carefully validated 26 of these novel microsatellites and six previously described loci for the absence of null alleles in Western African field populations. This large panel of high‐quality microsatellite markers provides new opportunity to infer dispersal rates between populations of the desert locust and help prioritize early monitoring and control. Furthermore, high potential for cross‐taxa utility of markers was observed within Schistocerca genus, which includes other locust pest species, with reliable amplification achieved for at least ten of loci per species. Microsatellite markers developed from transcriptome resources were largely devoid of null alleles and were conserved across species compared with those derived from traditional genomic libraries. Accordingly, the number of highly reliable microsatellite markers was greatly improved compared with that of previous studies on Orthopteran species, and this strategy might be broadly applied in other insect species prone to null alleles.
[Show abstract][Hide abstract] ABSTRACT: Ecuador's economic history has been closely linked to Theobroma cacao L cultivation, and specifically to the native fine flavour Nacional cocoa variety. The original Nacional cocoa trees are presently in danger of extinction due to foreign germplasm introductions. In a previous work, a few non-introgressed Nacional types were identified as potential founders of the modern Ecuadorian cocoa population, but so far their origin could not be formally identified. In order to determine the putative centre of origin of Nacional and trace its domestication history, we used 80 simple sequence repeat (SSR) markers to analyse the relationships between these potential Nacional founders and 169 wild and cultivated cocoa accessions from South and Central America. The highest genetic similarity was observed between the Nacional pool and some wild genotypes from the southern Amazonian region of Ecuador, sampled along the Yacuambi, Nangaritza and Zamora rivers in Zamora Chinchipe province. This result was confirmed by a parentage analysis. Based on our results and on data about pre-Columbian civilization and Spanish colonization history of Ecuador, we determined, for the first time, the possible centre of origin and migration events of the Nacional variety from the Amazonian area until its arrival in the coastal provinces. As large unexplored forest areas still exist in the southern part of the Ecuadorian Amazonian region, our findings could provide clues as to where precious new genetic resources could be collected, and subsequently used to improve the flavour and disease resistance of modern Ecuadorian cocoa varieties.
PLoS ONE 11/2012; 7(11):e48438. DOI:10.1371/journal.pone.0048438 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: There is a serious lack of information on the genetic diversity and population dynamics of the 110 tropical Vanilla species, although these are keys elements to adjust conservation strategies. Nineteen polymorphic microsatellite markers were developed from two African leafless Vanilla species V. roscheri and V. humblotii to use in population genetic studies. A transferability analysis of these markers on seven Vanilla species from various geographical origins was conducted. Nine microsatellites were polymorphic in a population of 22 individuals of V. humblotii from Mayotte (Comoros Archipelago). These markers had two to eight alleles per locus and observed heterozygosity ranged from 0.23 to 0.64. Amplification parameters were calibrated to facilitate multiplexing and rapid multi-loci genotyping.
[Show abstract][Hide abstract] ABSTRACT: A (GA)n and (GT)n microsatellite-enriched library was constructed and 25 nuclear simple sequence repeat (SSR) loci were characterized in the Lesser Antillean Iguana (Iguana delicatissima). All SSR loci were found to be polymorphic after screening for diversity in different cultivars, and a cross-taxa amplification tests showed the potential transferability of most SSR markers in Iguana iguana. First to be published for I. delicatissima, this new SSR resource will be a powerful tool for intraspecific genetic studies and for investigation of hybridization events with Iguana iguana.
[Show abstract][Hide abstract] ABSTRACT: The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships.
Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed.
We determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika-Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.
Annals of Botany 02/2012; 109(5):937-51. DOI:10.1093/aob/mcs010 · 3.65 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Sideroxylon majus (Sapotaceae) is an endangered endemic tree of La Réunion Island that has suffered from human actions. It is present in small
and isolated populations that encounter severe difficulties to regenerate. To have powerful tools for population genetic studies,
we have isolated and characterized 14 polymorphic microsatellite markers from S. majus. The 14 loci were tested on 57 individuals from 6 populations. The number of alleles per locus varied from 2 to 20, with
an average of 11.8. The observed and expected heterozygosity levels ranged from 0.053 to 1.000, and 0.116 to 0.917, respectively.
Six of the 14 loci deviated from Hardy–Weinberg equilibrium. These polymorphic microsatellite markers constitute new tools
to study the genetic diversity and spatial genetic structure of S. majus. The cross-species amplifications indicate that most of these loci can be used to investigate population genetic structure
in S. grandiflorum, S. boutonianum and S. sessiliflorum. These studies will provide useful results for the elaboration of effective conservation strategies.
KeywordsConservation genetics–Endangered species–
[Show abstract][Hide abstract] ABSTRACT: Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable
disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density
genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined
to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function.
A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function.
Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage
groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3cM was found, with approximately
one SSR every 2cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage
of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%,
and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5′UTR and 3′UTR regions.
This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful
for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out
association mapping studies.
–EST-SSR–Genetic map–Candidate genes
[Show abstract][Hide abstract] ABSTRACT: Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. Twelve microsatellite loci were identified
using the method of microsatellite-enriched libraries. Polymorphism was assessed in samples (N=62) from four geographically
distinct populations in Thailand. Number of alleles per locus ranged from 9 to 15 (average 11.6). Observed and expected heterozygosities
varied from 0.28 to 1.0 and from 0.44 to 0.91, respectively. There was no evidence for linkage disequilibrium, however, four
loci showed evidence of departure from Hardy–Weinberg equilibrium in one population. Presence of null alleles was not detected
in all the 12 loci. These first microsatellites primers developed for L. neilli will provide information on the fine-scale genetic structure of this threatened species and will help in the development
of future conservation policies.
–Murine rodent–Microsatellite–Multiplex–Genetic structure–Southeast Asia
[Show abstract][Hide abstract] ABSTRACT: We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
[Show abstract][Hide abstract] ABSTRACT: Fourteen polymorphic microsatellite markers were developed to study the clonal diversity of the sugarcane aphid Melanaphis sacchari from a repeat-enriched genomic library. Allelic diversity was estimated on aphids collected on sugarcane originating from nine locations. The number of alleles per locus ranged from two to five. Six multilocus genotypes were identified. Population genetic parameters were computed from a population from Reunion and revealed features that are common for parthenogenetic aphid species: (i) observed heterozygosity ranged from 0.94 to 1 and exceeded significantly expectations for all loci and (ii) significant linkage disequilibrium was found for all pairwised loci comparisons.
[Show abstract][Hide abstract] ABSTRACT: An integrated parental linkage map of guava (Psidium guajava L., 2n = 22) based on AFLP and SSR markers has been constructed for the mapping population MP1 derived from a cross between two heterozygous guava cultivars (¿Enana¿ x ¿N6¿). A total of 1103 segregating AFLP markers obtained from 119 AFLP primer combinations were produced for linkage mapping. In addition, 171 SSR maker loci were analysed which generated 258 allelic fragments. In total 1364 AFLP and SSR markers were available for linkage mapping. The integrated linkage map of MP1 contains 578 markers (452 AFLPs, 126 SSRs) distributed on 11 linkage groups corresponding to the 11 chromosomes of the haploid guava genome. This map has a length of 2179 cM and an average linkage group length of 198 cM. In addition, a total of 126 so-called RF0 markers and 146 so-called associated markers were determined. The current MP1 map will be completed by the integration of the individual maps derived from other available guava mapping populations. This represents a decisive step towards a saturated genetic reference map of P. guajava in support of accelerated breeding in guava by marker-assisted selection.
[Show abstract][Hide abstract] ABSTRACT: The development and application of molecular genetic markers provide the opportunity to establish and evaluate measures for the quality of genetic resources collections. In particular, DNA-based polymorphisms are a powerful tool for the assessment of genetic diversity. Among the various molecular markers, RFLPs were the first to be used for plant genome studies, mapping and diversity analysis. However, RFLPs are labour-intensive, timeconsuming, and depend on large quantities of DNA which in instances such as some species requires purification by ultracentrifugation. PCR-based techniques can be readily used to detect polymorphisms with small amounts of DNA and are, therefore, convenient for genetic analysis of plants at early stages of development. Among the various PCR-based techniques, the simple sequence repeats (SSRs or microsatellites) are characterized by the codominant mode of inheritance which permits easy transfer of markers between genetic maps of different crosses in contrast to dominant PCR markers types such as RAPD or AFLP. Microsatellites detect multiple alleles at a single locus and a high level of polymorphisms within cultivars; thus they are a powerfull tool for the estimation of heterozygosity. A method for establishing genomic libraries enriched for microsatellites was developed, and results obtained on Psidium guava will be presented. Designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries.SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. The SAT Web application is available at http://sat.cirad.fr/sat.
[Show abstract][Hide abstract] ABSTRACT: Theobroma cacao, is a tropical understorey tree that is a major economic resource to several tropical countries. However, the crop is under
increased threat from several diseases that are responsible for 30% loss of harvest globally. Although QTL data related to
the genetic determinism of disease resistance exist in cocoa, QTL mapping experiments are heterogeneous, thus making comparative
QTL mapping essential for marker assisted selection (MAS). Sixteen QTL experiments were analysed, and the 76 QTLs detected
were projected on a progressively established consensus map. Several hot spots, with QTLs related to different Phytophthora species and other diseases, were observed. The likely number of “real” QTLs was estimated by using a meta-analysis implemented
in BioMercator software. There was a twofold reduction in average confidence interval observed when compared to the confidence
interval of individual QTLs. This alternative approach confirms the existence of several sources of resistance to different
diseases of cocoa which could be cumulated in new varieties to increase the sustainability of cocoa resistance using MAS strategies.
[Show abstract][Hide abstract] ABSTRACT: The native Theobroma cacao L. population from Ecuador, known as Nacional, is famous for its fine cocoa flavour. From the beginning of the twentieth
century, however, it has been subjected to genetic erosion due principally to successive introductions of foreign germplasm
whose hybrid descendants gradually replaced the native plantations, implying a decrease in cocoa quality. We attempted to
trace this native cacao within a wide pool of modern Ecuadorian cacao population. Three hundred and twenty-two cacao accessions
collected from different geographical areas along the pacific coast of Ecuador and maintained in two living collections were
analysed using 40 simple-sequence repeat markers. Most of Ecuadorian cacao accessions displayed a high diversity and heterozygosity
level. A factorial analysis of correspondence (FAC) showed a continuous variation among them, with a few ones, grouped at
an extreme side of the FAC cloud, showing higher levels of homozygosity and lower introgression level by foreign cacaos. A
paternity analysis revealed that these highly homozygous individuals are the most probable ancestors of the modern Nacional
hybrid pool. These particular accessions studied could represent the native Nacional cacao present in Ecuador before the foreign
introductions. Their identification will help to conserve valuable genetic material and to improve cocoa quality in new cacao
[Show abstract][Hide abstract] ABSTRACT: The genus Calliptamus (Orthoptera, Acrididae) includes locusts and grasshoppers, spread mainly throughout the Mediterranean Basin and as far as the southern part of Siberia. Some species are of substantial economic importance, such as C. italicus (Linné, 1758). Despite many studies on their taxonomy and biology, the identification of many species remains difficult, particularly for females and nymphs. Furthermore, in spite of their economic importance, dispersion capabilities which could have an impact in outbreak as demonstrated for other locusts - are not well understood. In order to clarify both aspects – identification and dispersion capabilities - we tried to develop molecular tools for various species of this genus distributed in Southern France. We focused our studies on C. italicus, C. barbarus (Costa, 1836) and C. wattenwylianus (Pantel, 1896). In order to facilitate the identification process, we developed a multiplex PCR assays to discriminate - quickly and inexpensively – any specimen collected in the field at the species level. Then, we developed new microsatellite markers to be used for further studies on dispersion capabilities. Seven markers were obtained for C. barbarus, six for C. italicus, three of them cross amplified on C. wattenwylianus. Genetic analyses were performed on two sampling seasons, at different geographic scales: the first study at an individual level (on two sites of 72 km2 and 40 km apart, in Southern France), the second at a population level at different localities throughout the Mediterranean Basin. Analyses are in progress and results will be provided during the congress.
10th International Congress of Orthopterology, Antalya, Turkey, June 21-25, 2009, Antalya, Turkey; 06/2009
[Show abstract][Hide abstract] ABSTRACT: We developed 13 new polymorphic microsatellite loci in the house sparrow (Passer domesticus), which exhibited from 2 to 15 alleles. Observed and expected heterozygosities ranged from 0.17 to 0.77 and from 0.35 to 0.85, respectively. We detected no linkage disequilibrium between loci. Allele frequencies supported Hardy-Weinberg equilibrium for 8 loci out of 13 after Bonferroni correction. Combined with loci previously isolated in the house sparrow, these new microsatellite markers provide valuable tools to study population genetics of this species.