[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.
Full-text · Article · Nov 2013 · Journal of Applied Entomology
[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.
[Show abstract][Hide abstract] ABSTRACT: Nine microsatellite markers were isolated from unfed larvae of Ixodes ricinus and were tested on two populations of nymphs collected on roe deer (N=21) and birds (N=39) in a French suburban forest. All markers were polymorphic, with limited evidence for deviations from linkage equilibrium. In accordance with previous markers developed for this species, we found large heterozygote deficits for six of the nine loci. Deficits were of the same order of magnitude within a tick infrapopulation, suggesting that population-level estimates were not due to a Wahlund effect among individual hosts, but more likely to technical problems (i.e., null alleles due to mutations in the flanking regions of the microsatellites). Although micro-geographic substructure (e.g., homogamy within infrapopulations) can not be ruled out, it is possible that null alleles could be an inherent problem associated with this tick species and specific genome-level studies are called for. Despite the possible presence of null alleles, the precision of population genetic estimates was improved by the addition of the newly-developed markers making them a useful addition for studying the population ecology of I. ricinus.
[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.
Full-text · Article · Mar 2012 · Conservation Genetics Resources
[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.
No preview · Article · Mar 2012 · Conservation Genetics Resources
[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.
[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–
Full-text · Article · Oct 2011 · Conservation Genetics Resources
[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
No preview · Article · Aug 2011 · Tree Genetics & Genomes
[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: Guava (Psidium guajava L.) belongs to the Myrtaceae family and is native to the tropical and subtropical regions of America. It produces a fruit of high nutritional value due to its mineral and vitamin content. During the past 2 decades, classical methods to evaluate genetic variation have been complemented by molecular DNA techniques. There is a great potential for the application of these molecular markers to fruit crops. The objective of this research was to compare results derived from individual versus combined data sets for varietal identification and diversity estimation in guava germplasm by different DNA markers. AFLP data permitted the discrimination of all the accessions evaluated, but diversity groups were not observed. Microsatellite (SSR) markers detected seven diversity groups, although all the accessions could not be differentiated. The combined AFLP and SSR data offered similar results only when AFLP markers were used. Although coincidences were identified in individuals and combined dendrograms, the integration of the information derived by each marker system individually permitted a more accurate estimation of guava germplasm diversity. This corroborates the strengths and constraints of each data set. Thus, the congruence or correspondence among the results derived from individual data sets is the most important point to consider before combining different types of data.
No preview · Article · Jan 2010 · Acta horticulturae
[Show abstract][Hide abstract] ABSTRACT: Integrated parental linkage maps have been constructed in three guava mapping populations ('Enana' × "N", 'Enana' × 'Suprema Roja' and 'Enana' × 'Belic L-207') based on AFLP and SSR markers. Between 102 and 119 AFLP primer combinations (PCs) were analysed in each population, generating between 684 and 1163 segregating AFLP fragments. The distribution of parent-specific and common markers indicated that 'Enana' is less heterozygous than the other parents and that all parents share a considerable gene pool. In addition, between 28 and 171 SSR PCs were analysed for linkage mapping in these populations. Initially parent specific linked fragments were arranged into linkage groups. In all mapping population, 11 linkage groups (LGs) corresponding to the 11 chromosomes of the haploid guava genome were obtained for each parent. Based on the available SSR markers, combined parental linkage maps of each mapping population were produced using as anchor points allelic SSR fragments and common AFLP fragments. These integrated maps contain between 408 and 850 markers and have lengths of 1885 to 2179 cM, respectively. Average linkage group lengths in these maps vary between 160 and 198 cM and contain on average between 37 and 77 markers. Several identical SSR markers were mapped in various progenies, and potential associations of linkage groups from different populations were detected. In the future, the number of common SSR markers has to be increased in order to achieve full alignment of all individual linkage maps into a high-density reference molecular linkage map of guava.
No preview · Article · Jan 2010 · Acta horticulturae
[Show abstract][Hide abstract] ABSTRACT: Guava (Psidium guajava L.) is one of the economically most important fruit trees of the Myrtaceae. Until nowadays, guava breeding programs in Cuba have been limited to the selection and introduction of genotypes with important agronomic characteristics, but focussed studies on genetic diversity which is very important for the identification of potential parents for breeding programs, had not been undertaken. The utilization of microsatellite (SSR) markers for guava germplasm characterization and gene bank management was the main objective of this work. A total of 34 different SSR alleles ranging from three to seven per locus were detected in the examined genotypes with an average number of putative alleles per locus of 4.57. Out of these, twenty-four alleles were classified as common alleles, out of which 10 were widespread and 14 sporadic. Ten alleles were classified as rare, from which 7 were sporadic and 3 localised. For all SSR loci, a major number of homozygote genotypes were identified, except for the SSR locus mPgCIR09. This result reflected the medium to low levels of heterozygosis detected, which ranged from 0.08 to 0.54 with 0.38 as the total average for this parameter. Genotypes showing cultivar-specific markers were 'Darío 19-2'; 'Belic L-98'; 'BG 76-23'; 'Belic L-205' and 'Microguayaba'. These could be important materials for conservation purposes. The high number of common alleles detected suggested that most of the plant material analyzed shares a common genetic ancestor. The microsatellites evaluated could play an important role in the identification of guava accessions representing an interesting gene pool for ex situ maintenance.
No preview · Article · Jan 2010 · Acta horticulturae
[Show abstract][Hide abstract] ABSTRACT: Agro-morphologic traits and molecular markers were compared in terms of their polymorphism level, discriminating power, and informativeness for 23 genotypes assembled in the Cuban guava germplasm collection. AFLP and SSR markers were powerful techniques for guava discrimination and variety identification, but the high level of polymorphic loci detected by the dominant AFLP marker highlights the discriminating capacity of this genetic marker. With a single AFLP primer combination all of the individuals were identified, while only a few genotypes can be differentiated with a single SSR primer combination or by morphological variables. The higher values of expected heterozygosity were detected by SSR. This value doubled the one obtained with AFLP, and reflects the high level of informativeness of this marker, due to the multiallelic and co-dominant nature of SSR; which makes them suitable for diversity studies. The morphologic diversity index provided a good estimate of diversity among guava accessions when phenotypic traits of high heritability were used, and it was comparable with the expected heterozygosity scored with DNA markers. The value of this index was the lowest. The assay efficiency index (Ai) and marker index (MI) had the same pattern of variation than discrimination capacity (D), number of banding pattern (I), number of unique banding pattern (Iu) and number of effective pattern (P) for both molecular markers. Then, these indexes are probably indicators of the discriminating capacity in guava.
No preview · Article · Jan 2010 · Acta horticulturae