Markers For Population Genetic Studies Research Articles

Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis.

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from -0.9643 to 1.0000. The global Fst value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.

Novel microsatellite markers suggest significant genetic isolation in the Eastern Pacific sponge Aplysina gerardogreeni

BackgroundThe Eastern Tropical Pacific (ETP) harbors a great diversity of Porifera. In particular, the Aplysina genus has acquired biotechnological and pharmacological importance. Nevertheless, the ecological aspects of their species and populations have been poorly studied. Aplysina gerardogreeni is the most conspicuous verongid sponge from the ETP, where it is usually found on rocky-coralline ecosystems. We evaluated the polymorphism levels of 18 microsatellites obtained from next-generation sequencing technologies. Furthermore, we tested the null hypothesis of panmixia in A. gerardogreeni population from two Mexican-Pacific localities.Methods and resultsA total of 6,128,000 paired reads were processed of which primer sets of 18 microsatellites were designed. The loci were tested in 64 specimens from Mazatlan, Sinaloa (N = 32) and Isabel Island, Nayarit (N = 32). The microsatellites developed were moderately polymorphic with a range of alleles between 2 and 11, and Ho between 0.069 and 0.785. Fifteen loci displayed significant deviation from the Hardy–Weinberg equilibrium. No linkage disequilibrium was detected. A strong genetic structure was confirmed between localities using hierarchical Bayesian analyses, principal coordinates analyses, and fixation indices (FST = 0.108*). All the samples were assigned to their locality; however, there was a small sign of mixing between localities.ConclusionsDespite the moderate values of diversity in microsatellites, they showed a strong signal of genetic structure between populations. We suggest that these molecular markers can be a relevant tool to evaluate all populations across the ETP. In addition, 17 of these microsatellites were successfully amplified in the species A. fistularis and A. lacunosa, meaning they could also be applied in congeneric sponges from the Caribbean Sea. The use of these molecular markers in population genetic studies will allow assessment of the connectivity patterns in species of the Aplysina genus.

De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer.

Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.

Visualization of the Linear and Spatial Organization of Chromosomes in Mosquitoes.

Mosquitoes are vectors of dangerous human diseases such as malaria, dengue, Zika, West Nile fever, and lymphatic filariasis. Visualization of the linear and spatial organization of mosquito chromosomes is important for understanding genome structure and function. Utilization of chromosomal inversions as markers for population genetics studies yields insights into mosquito adaptation and evolution. Cytogenetic approaches assist with the development of chromosome-scale genome assemblies that are useful tools for studying mosquito biology and for designing novel vector control strategies. Fluorescence in situ hybridization is a powerful technique for localizing specific DNA sequences within the linear chromosome structure and within the spatial organization of the cell nucleus. Here, we introduce protocols used in our laboratories for chromosome visualization and their application in mosquitoes.

The Complete Chloroplast Genomes of Primula obconica Provide Insight That Neither Species nor Natural Section Represent Monophyletic Taxa in Primula (Primulaceae).

The genus Primula (Primulaceae) comprises more than 500 species, with 300 species distributed in China. The contradictory results between systematic analyses and morphology-based taxonomy make taxonomy studies difficult. Furthermore, frequent introgression between closely related species of Primula can result in non-monophyletic species. In this study, the complete chloroplast genome of sixteen Primula obconica subsp. obconica individuals were assembled and compared with 84 accessions of 74 species from 21 sections of the 24 sections of the genus in China. The plastome sizes of P. obconica subsp. obconica range from 153,584 bp to 154,028 bp. Genome-wide variations were detected, and 1915 high-quality SNPs and 346 InDels were found. Most SNPs were detected in downstream and upstream gene regions (45.549% and 41.91%). Two cultivated accessions, ZP1 and ZP2, were abundant with SSRs. Moreover, 12 SSRs shared by 9 accessions showed variations that may be used as molecular markers for population genetic studies. The phylogenetic tree showed that P. obconica subsp. obconica cluster into two independent clades. Two subspecies have highly recognizable morphological characteristics, isolated geographical distribution areas, and distinct phylogenetic relationships compared with P. obconica subsp. obconica. We elevate the two subspecies of P. obconica to separate species. Our phylogenetic tree is largely inconsistent with morphology-based taxonomy. Twenty-one sections of Primula were mainly divided into three clades. The monophyly of Sect. Auganthus, Sect. Minutissimae, Sect. Sikkimensis, Sect. Petiolares, and Sect. Ranunculoides are well supported in the phylogenetic tree. The Sect. Obconicolisteri, Sect. Monocarpicae, Sect. Carolinella, Sect. Cortusoides, Sect. Aleuritia, Sect. Denticulata, Sect. Proliferae Pax, and Sect. Crystallophlomis are not a monophyletic group. The possible explanations for non-monophyly may be hybridization, polyploidization, recent introgression, incorrect taxonomy, or chloroplast capture. Multiple genomic data and population genetic studies are therefore needed to reveal the evolutionary history of Primula. Our results provided valuable information for intraspecific variation and phylogenetic relationships within Primula.

Evidence for two domestication lineages supporting a middle-eastern origin for Brassica oleracea crops from diversified kale populations.

Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.

Genetic diversity, population structure and demographic history of the tropical eel Anguilla bicolor pacifica in Southeast Asia using mitochondrial DNA control region sequences

The tropical catadromous eel, Anguilla bicolor pacifica, an important fishery resource in Southeast Asia, is under threat due to overexploitation (especially of its glass eel phase) and the limited information on their current genetic status which is necessary for resource management. Mitochondrial DNA (mtDNA) control region sequences, a useful marker for population genetic studies in many aquatic organisms, were used to investigate the genetic diversity, population structure and demographic history of A. bicolor pacifica in the region. A total of 151 specimens were collected from three sites in Southeast Asia, namely: Phu Yen, Vietnam (n = 48); General Santos, Philippines (n = 52); and, Palu, Indonesia (n = 51). A total of 138 haplotypes were identified using the mtDNA control region sequences. In spite of the lack of shared haplotypes, low and non-significant FST values, high haplotype diversity in concurrence with relatively low nucleotide diversity, a haplotype network with no phylogeographic structuring indicate no significant genetic population structuring among the eel samples from Vietnam, Philippines and Indonesia. Population expansion of A. bicolor pacifica was also suggested based on the results of the neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Taken together, a joint management strategy for A. bicolor pacifica must involve countries in Southeast Asia particularly Vietnam, Philippines and Indonesia for its sustainable use.

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

The scope of Rp EPIC markers in population genetic studies: a preliminary study with dengue vectors

Most genetic markers carry numerous limitations which question their credibility. Ribosome protein Exon Primed Intron Crossing (Rp EPIC) markers claimed to effectively overcome some of these limitations. Hence, the present study was aimed at demonstrating the scope of Rp EPIC markers in population genetics in comparison to conventional microsatellites, using the dengue vectors; Aedes aegypti and Aedes albopictus. A total of 62 Ae. aegypti and 51 Ae. Albopictus samples were genotyped for two Rp EPIC markers; RpS20b and RpL30a and two microsatellite markers; AC7 and BbH08 for Ae. aegypti and Alb-tri 03 & Alb-tri 25 for Ae. Albopictus. The Rp EPIC markers were successfully transferred among the two species, while differentiating them based on F statistics. Total size variants ( electromorphs ) observed for the two markers, RpS20b and RpL30a were 14 (3 for Ae. aegypti; 13 for Ae. albopictus; shared: 2) and 7 (3 for Ae. aegypti; 4 for Ae. albopictus; shared: 0) with many more alleles uncovered through sequencing (RpS20b:74 and RpL30a:54). In contrast, microsatellites produced 6 (AC7) and 3 (BbH08) size variants for Ae. aegypti and 8 (Alb- tri 03 ) and 7 (Alb- tri 25 ) for Ae. albopictus. Both marker types detected genetic structure among Ae. albopictus populations while a genetic structure among Ae. aegypti was detected only with microsatellites and not with Rp EPIC size variants. The combined data of microsatellites and Rp EPIC size variants as well as sequence analysis did not support the presence of a genetic structure among the studied Ae. aegypti populations. It is possible that microsatellites tend to infl ate genetic differentiation among the studied Ae. aegypti populations, which has been counteracted by the Rp EPIC markers.

Development of microsatellite loci and optimization of a multiplex assay for Latibulus argiolus (Hymenoptera: Ichneumonidae), the specialized parasitoid of paper wasps

Microsatellite loci are commonly used markers in population genetic studies. In this study, we present 40 novel and polymorphic microsatellite loci elaborated for the ichneumonid parasitoid Latibulus argiolus (Rossi, 1790). Reaction condition optimisation procedures allowed 14 of these loci to be co-amplified in two PCRs and loaded in two multiplex panels onto a genetic analyser. The assay was tested on 197 individuals of L. argiolus originating from ten natural populations obtained from the host nests of paper wasps. The validated loci were polymorphic with high allele numbers ranging from eight to 27 (average 17.6 alleles per locus). Both observed and expected heterozygosity values were high, ranging between 0.75 and 0.92 for HO (mean 0.83) and from 0.70 to 0.90 for HE (mean 0.85). The optimized assay showed low genotyping error rate and negligible null allele frequency. The designed multiplex panels could be successfully applied in relatedness analyses and genetic variability studies of L. argiolus populations, which would be particularly interesting considering the coevolutionary context of this species with its social host.

Transferability of heterologous microsatellite primers in Leiarius marmoratus

The Amazonian Jundiá (Leiarius marmoratus) (Siluliformes: Pimelodidae) is a species of catfish with social and economic importance in some South American countries such as Brazil and Colombia. Genetic evaluation of this species is limited due to the lack of specific molecular markers, hindering studies on genetic diversity and structure in animals under captive conditions or in natural populations. The objective of the present study was to evaluate the transferability of heterologous microsatellite markers in Leiarius marmoratus. Thirty-two heterologous primers were tested in L. marmoratus. The primers that presented the best standards were applied to 20 specimens, and the number of alleles (Na), number of effective alleles (Ne), gene diversity per Locus (GdL) and percentage of amplification failure (Md) were calculated. Eleven primers demonstrated satisfactory transferability patterns, all from the fish of the Pimelodidae family, of which, seven were monomorphic and four polymorphic. The eleven markers presented low percentage of Md (mean was 5.9% samples per locus). Na varied from one to two alleles per locus, revealing low polymorphism in the evaluated samples. The mean Ne and GdL numbers were 1.77 and 0.32, respectively. The transferability of the heterologous microsatellite loci in L. marmoratus was shown to be possible. However, further tests are needed to apply these markers in population genetic studies.

Characterisation of arginine kinase intron regions and their potential as molecular markers for population genetic studies of Bithynia snails (Gastropoda: Bithyniidae) in Thailand

ABSTRACT Three taxa of Bithynia snails, Bithynia funiculata, B. siamensis siamensis and B. siamensis goniomphalos, are currently recognised in Thailand. They serve as first intermediate hosts for the liver fluke Opisthorchis viverrini sensu lato. This study aims to characterise the arginine kinase gene intron regions (AKInt) for further use as molecular markers to explore the genetic variation and differentiation of Bithynia snails in Thailand. Four intron regions belonging to the AK gene, namely AK intron 1 (AKInt1) to AK intron 4 (AKInt4) were characterised for B. funiculata, B. s. siamensis and B. s. goniomphalos. Of these, AKInt1 showed a high level of genetic variability and was the most appropriate region for reliably examining the genetic variation of Bithynia species/subspecies and discriminating between them. Two different forms of AKInt1, namely AKInt1-long containing a long fragment (∼341–351 bp) and a short fragment (∼213–229 bp), and AKInt1-short containing only a short fragment, were observed. Insertions/deletions (indels) were commonly found within AKInt1 leading to observed heterozygosity. This study revealed that nucleotide polymorphism was high in the long fragment, which was observed in some specimens. The short fragment was common in all samples and can potentially be used to discriminate between Bithynia taxa.

Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.

BackgroundHimalayan balsam Impatiens glandulifera Royle (Balsaminaceae) is a highly invasive annual species native of the Himalayas. Biocontrol of the plant using the rust fungus Puccinia komarovii var. glanduliferae is currently being implemented, but issues have arisen with matching UK weed genotypes with compatible strains of the pathogen. To support successful biocontrol, a better understanding of the host weed population, including potential sources of introductions, of Himalayan balsam is required.MethodsIn this molecular study, two new complete chloroplast (cp) genomes of I. glandulifera were obtained with low coverage whole genome sequencing (genome skimming). A 125-year-old herbarium specimen (HB92) collected from the native range was sequenced and assembled and compared with a 2-year-old specimen from UK field plants (HB10).ResultsThe complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.

Effect of growth hormone gene polymorphism on growth traits in migratory Gaddi goats of Western Himalayas, India.

Goat production under migratory system is foremost meat resource in Western Himalayan region of India. Thus, selection of goats for superior growth rate is rewarding. Growth hormone (GH) gene is identified as main regulator of post-natal growth and development. The objective of this study was to identify GH gene variants in Gaddi goats reared under migratory system via polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and single-strand conformation polymorphism (SSCP). Blood samples from 63 animals from different migratory flocks registered under All India Coordinated Research Project, Himachal Pradesh Agricultural University (HPAU), Palampur, were subjected to DNA isolation. A total of 422, 116, 389 and 181-bp amplicons were generated on amplification of four targeted regions of GH gene. GH1 and GH2 fragments were analysed using PCR-RFLP (HaeIII RE) that revealed three variants (AA, AB and BB) for GH1 having frequency as 0.27, 0.52 and 0.31, respectively whereas, two variants (AB and BB) were revealed for GH2 fragment having frequency of 0.24 and 076, respectively. GH3 and GH4 fragments were subjected to PCR-SSCP that detected three genotypes (AB, BB and AA) for GH3 with respective genotype frequency as 0.57, 0.21 and 0.22 respectively; however, GH4 was found to be monomorphic. The polymorphism information content values for GH1, GH2 and GH3 were 0.37, 0.36 and 0.34, respectively, which suggested the median level of polymorphism at studied loci and also indicated the effectiveness of the studied marker for population genetic studies. Significant associations (P ≤ 0.05) were detected for GH1 with 9-month body weight, GH2 with 9 and 12-month heart girth and GH3 with 6-month body weight, body height and body length, respectively. From the present study, it was concluded that SNPs and their association with some body measurements may be employed as useful markers for ongoing phenotypic selection programme.

Characterization of the complete plastid genome of Butia eriospatha (Arecaceae).

Butia eriospatha is an endemic palm species from the Atlantic Rainforest in Brazil, a biodiversity hotspot. This species is currently listed in the IUCN red list as vulnerable and lacks specific plastid markers for population genetics studies. In addition, the evolutionary relationship within the genus Butia is not yet well resolved. Here, we sequenced and characterized the complete plastid genome (plastome) sequence of B. eriospatha. The complete plastome sequence is 154,048 bp in length, with the typical quadripartite structure. This plastome length and genes content is consistent with other six species from tribe Cocoseae. However, the Inverted Repeat (IR) borders show some variation among the analyzed species from this tribe. Species from the Bactridinae (Astrocaryum and Acrocomia) and Elaeidinae (Elaeis) subtribes present the rps19 gene completely duplicated in the IR region. In contrast, all plastomes sequenced from the subtribe Attaleinae (Butia, Cocos, Syagrus) present one complete CDS of rps19 and one partial copy of rps19. The difference in the IR/LSC junctions between Attaleinae and the sister clades Bactridinae + Elaeidinae might be considered an evolutionary signal and the plastome sequence of B. eriopatha may be used in future studies of population genetics and phylogeny.

Genome Resource for Neocamarosporium betae (syn. Pleospora betae), the Cause of Phoma Leaf Spot and Root Rot on Beta vulgaris.

Neocamarosporium betae (syn. Phoma betae, Pleospora betae) is the cause of Phoma leaf spot and root decay on Beta vulgaris worldwide. Despite the economic importance of the pathogen, many aspects of its life cycle and population biology remain unknown. The first genome assembly of N. betae was constructed to facilitate identification of mating-type loci and development of microsatellite markers for population genetics studies. The de novo assembled genome is provided as a resource for future genetic studies to understand the genetic mechanisms underlying disease development and host-pathogen interactions.

Polymorphic microsatellite loci and partial mitogenome for the Chestnut-bellied Seed-finch Sporophila angolensis (Aves, Passeriformes) using next generation sequencing.

Brazil is one of the major contributors to international trade in wildlife and species of the bird genus Sporophila are currently under threat due to illegal trade. Microsatellite loci and mitochondrial DNA constitute important molecular markers for population genetics studies and parentage analyses, and hold great potential to help authorities manage illegal trafficking and control commercial breeders. We describe and characterize 19 polymorphic microsatellite loci and recover part of the mitochondrial genome for Sporophila angolensis using massive parallel sequencing with the Illumina platform. DNA sequencing resulted in a dataset with 2,379,295 paired reads, of which 392 were mapped to the mitogenome of S. maximiliani, resulting in a partial mitogenome of 16,785bp for S. angolensis. The microsatellite search identified a total of 4737 loci, from which 27 primer pairs were tested on 24 individuals of unknown geographic origin. Nineteen of the 27 loci were successfully amplified and exhibited high levels of genetic variation, with a mean of 11.2 alleles per locus, a mean observed heterozygosity of 0.588 and a mean expected heterozygosity of 0.852. About half of the loci showed significant evidence for the presence of a null allele and significant deviation from Hardy-Weinberg equilibrium; the remaining eight loci had high paternity exclusion probabilities and low identity probabilities. The high levels of polymorphism for these loci, as well as their high paternity exclusion probability and low identity probability, indicate that they hold potential for parentage analyses and population genetics studies of S. angolensis.

Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species

Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping.

Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree.

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America

A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a MassARRAY® iPLEX™ platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studies