Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N _A), expected heterozygosity (H _E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N _m = 1.252) and high genetic differentiation (F _st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.

Seventeen new microsatellites for Tamarix gallica and cross-amplification in Tamarix species

PREMISE

Microsatellite markers were developed for the western Mediterranean tree Tamarix gallica (Tamaricaceae) as part of a study of its genetic diversity and structure.

METHODS AND RESULTS

Seventeen microsatellite markers were developed for T. gallica, 14 of which were polymorphic. These microsatellites have di-, tri-, and tetranucleotide repeats with 1-13 alleles per locus and population. Levels of observed and expected heterozygosity ranged from 0.000 to 0.900 and from 0.000 to 0.863, respectively. Six microsatellites showed significant deviations from Hardy-Weinberg equilibrium in at least one population. Cross-amplification in 19 Tamarix species showed a wide transferability to other species of the genus.

CONCLUSIONS

The 14 new polymorphic microsatellite markers will be used to assess the genetic diversity and population genetic structure of T. gallica. Additionally, the successful cross-species amplification suggests their potential usefulness for investigating species delimitation and population genetics in the genus Tamarix.

Optimizing depth and type of high-throughput sequencing data for microsatellite discovery

PREMISE

Simple sequence repeat (SSR) markers (microsatellites) are a mainstay of many labs, especially when working on a limited budget, carrying out preliminary analyses, and in teaching. Whether SSRs mined from plant genomes or transcriptomes are preferred for certain applications, and the depth of sequencing needed to allow efficient SSR discovery, has not been tested.

METHODS

I used genome and transcriptome high-throughput sequencing data at a range of sequencing depths to compare efficacy of SSR identification. I then tested primers from tomato for amplification, polymorphism, and transferability to related species.

RESULTS

Small assemblies (two million read pairs) identified ca. 200-2000 potential markers from the genome assemblies and ca. 600-3650 from the transcriptome assemblies. Genome-derived contigs were often short, potentially precluding primer design. Genomic SSR primers were less transferable across species but exhibited greater variation (partially explained by being composed of more repeat units) than transcriptome-derived primers.

DISCUSSION

Small high-throughput sequencing resources may be sufficient for identification of hundreds of SSRs. Genomic data may be preferable in species with low polymorphism, but transcriptome data may result in longer loci (more amenable to primer design) and primers may be more transferable to related species.

Development and characterization of microsatellite markers in Campomanesia adamantium, a native plant of the Cerrado ecoregions of South America

PREMISE

A novel set of nuclear microsatellite markers was developed and characterized for Campomanesia adamantium (Myrtaceae) and tested for cross-amplification in the related species C. sessiliflora.

METHODS AND RESULTS

Forty-one primer pairs were designed for simple sequence repeat loci, of which 36 successfully amplified and were polymorphic. The number of alleles ranged from two to 14, with an average of 8.14 alleles per locus. Additionally, cross-amplification was tested in C. sessiliflora; more than 55.5% of the microsatellite loci amplified, confirming the use of these microsatellite markers in a related species.

CONCLUSIONS

We developed a set of microsatellite markers that will be useful for future studies of genetic diversity and population structure of C. adamantium and a closely related species, which will aid in future conservation efforts.

Development and characterization of genomic SSR markers for Tamarix chinensis (Tamaricaceae)

PREMISE OF THE STUDY

We developed a set of microsatellite markers to study the population genetic structure, mating system, and interspecific hybridization of Tamarix chinensis (Tamaricaceae), an alkali- and salt-tolerant shrub endemic to China, Korea, and Japan.

METHODS AND RESULTS

Using Illumina sequencing, we developed 10 polymorphic and 11 monomorphic microsatellite primers. High levels of polymorphism were detected in four T. chinensis populations. Allele numbers ranged from two to 11, and the levels of observed and expected heterozygosity ranged from 0.182 to 0.846 and from 0.165 to 0.794, respectively. The polymorphism information content values ranged from 0.201 to 0.803. Cross-species amplification showed two to 15 alleles per locus in 24 individuals from one natural population of the congener T. ramosissima, and the levels of observed and expected heterozygosity ranged from 0.042 to 0.864 and from 0.041 to 0.892, respectively.

CONCLUSIONS

These markers should be useful for exploring the population genetic structure, mating system, and gene flow of T. chinensis.

Molecular markers for Nassella trichotoma (Poaceae) to study genetic variation in New Zealand

PREMISE OF THE STUDY

Simple sequence repeat (SSR) markers were developed for the study of genetic diversity of New Zealand Nassella trichotoma (Poaceae) and to support future studies in its native range.

METHODS AND RESULTS

Genomic DNA was extracted from N. trichotoma leaf material and subjected to Roche 454 sequencing. From a total of 745 putative SSRs, 48 with di- to pentanucleotide repeats were screened, 32 primer pairs were designed, and 15 polymorphic markers were optimized for multiplex PCR on 105 N. trichotoma samples from four New Zealand regions. Each locus resulted in two to six alleles per locus, and four of the loci cross-amplified in N. tenuissima. The mean observed and expected heterozygosity ranged from 0.00 to 0.90 and 0.00 to 0.50 per locus, respectively.

CONCLUSIONS

The novel SSR markers are valuable for the study of genetic diversity of N. trichotoma and might also be useful for closely related species.

Development of 15 microsatellite markers in Acer triflorum (Aceraceae) and cross-amplification in congeneric species

PREMISE OF THE STUDY

Acer (Aceraceae) is an important genus in forest ecosystems in the Northern Hemisphere. In China, 151 species have been reported, and approximately 61 species are endemic. Thus, China is considered to host the greatest diversity of Acer, but markers are needed to evaluate the genetic structure and genetic diversity of these populations of wild Acer species.

METHODS AND RESULTS

Using an enriched genomic library, we developed and characterized 15 microsatellite primers for A. triflorum, 10 of which were polymorphic. The number of alleles varied from one to nine. The levels of observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 1.000 and 0.000 to 0.826, respectively. Most primers also successfully amplified in A. ginnala, A. griseum, A. mandshuricum, A. pseudosieboldianum, A. sinopurpurascens, A. tegmentosum, and A. ukurunduense.

CONCLUSIONS

These markers from A. triflorum will provide an opportunity to study genetic diversity and genetic structure in the genus Acer.

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.

Simple sequence repeat markers for kānuka (Kunzea spp.; Myrtaceae) present in New Zealand

PREMISE OF THE STUDY

We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on kānuka (Kunzea spp.; Myrtaceae).

METHODS AND RESULTS

A shotgun sequencing library was constructed from leaf material of K. robusta using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand Kunzea species. Each of these loci cross-amplified in all tested species. The amplified di-, tri-, and pentanucleotide repeats resulted in eight to 24 alleles per locus for a total of 220 specimens. The mean observed and expected heterozygosity per locus ranged from 0.18 to 0.77 and 0.33 to 0.82, respectively.

CONCLUSIONS

The SSR markers we produced are valuable for phylogenetic and population studies on all endemic Kunzea spp. and may also be useful for studies on closely related Kunzea species from Australia.

Sorghum Landrace Collections from Cooler Regions of the World Exhibit Magnificent Genetic Differentiation and Early Season Cold Tolerance

Cold temperature is an important abiotic stress affecting sorghum production in temperate regions. It reduces seed germination, seedling emergence and seedling vigor thus limiting the production of the crop both temporally and spatially. The objectives of this study were (1) to assess early season cold temperature stress response of sorghum germplasm from cooler environments and identify sources of tolerance for use in breeding programs, (2) to determine population structure and marker-trait association among these germplasms for eventual development of marker tools for improving cold tolerance. A total of 136 sorghum accessions from cooler regions of the world were phenotyped for seedling growth characteristics under cold temperature imposed through early planting. The accessions were genotyped using 67 simple sequence repeats markers spanning all ten linkage groups of sorghum, of which 50 highly polymorphic markers were used in the analysis. Genetic diversity and population structure analyses sorted the population into four subpopulations. Several accessions distributed in all subpopulations showed either better or comparable level of tolerance to the standard cold tolerance source, Shan qui red. Association analysis between the markers and seedling traits identified markers Xtxp34, Xtxp88, and Xtxp319 as associated with seedling emergence, Xtxp211 and Xtxp304 with seedling dry weight, and Xtxp20 with seedling height. The markers were detected on chromosomes previously found to harbor QTLs associated with cold tolerance in sorghum. Once validated these may serve as genomic tools in marker-assisted breeding or for screening larger pool of genotypes to identify additional sources of cold tolerance.

Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe

PREMISE OF THE STUDY

Polyploidy may generate novel variation, leading to adaptation and species diversification. An excellent natural system to study polyploid evolution in a comparative framework is Veronica (Plantaginaceae), which comprises several parallel, recently evolved polyploid series.

METHODS

Over 105 million Illumina paired-end sequence reads were generated from cDNA libraries of leaf tissue from eight individuals representing three European and four New Zealand species. Forty-eight simple sequence repeat (SSR) and 48 low-copy nuclear (LCN) markers were developed and validated with Fluidigm microfluidic PCR and Illumina MiSeq amplicon sequencing on 48 different individuals each.

RESULTS

Individual Trinity assemblies were similar regarding annotated transcripts (13,009-14,271), mean contig length (635-742 bp), N50 value (916-1133 bp), E90N50 value (1099-1308 bp), contigs with positive BLAST hits (42-63%), and gene ontology terms. Analyses of 29,738 single-nucleotide polymorphisms (8746 phylogenetically informative) mined from these transcriptomes plus two outgroups (Picrorhiza kurrooa and Plantago ovata) showed moderate to high bootstrap support for all branches and reticulation among sampled European Veronica.

DISCUSSION

The transcriptome sequences themselves, as well as the validated SSR (40/48) and LCN (11/48) markers derived from them, show inter- and intraspecific genetic variation. These resources will be invaluable for future population genetic, phylogenetic, and functional genetic investigations in polyploid Veronica.

Development of microsatellite markers for buffalograss (Buchloë dactyloides; Poaceae), a drought-tolerant turfgrass alternative

PREMISE OF THE STUDY

Buchloë dactyloides (Poaceae) is an important component of Great Plains prairies and a popular drought-tolerant turfgrass alternative in North America. This species comprises an autopolyploid series, and microsatellite primers were developed to understand the distribution of genetic variation among cytotypes and across its large geographic range.

METHODS AND RESULTS

Fifteen microsatellite loci were designed and successfully amplified in six B. dactyloides populations. Within-population genetic diversity was comparatively high, consistent with B. dactyloides' life history. Allelic variation at 13 loci was consistent with the cytotype established in chromosome-counted samples.

CONCLUSIONS

This variable, interpretable set of loci allows for the determination of multilocus genotype in B. dactyloides individuals of varying cytotype. Data such as these from a range-wide sample set can provide important insights for germplasm conservation and crop improvement in this ecologically and economically important species.

Identification and characterization of microsatellite markers in Penstemon scariosus (Plantaginaceae)

PREMISE OF THE STUDY

Penstemon scariosus var. albifluvis (Plantaginaceae) has been proposed to be federally listed as threatened due to its unique, geologically oil-rich habitat. Developing simple sequence repeat (SSR) markers to study its genetic diversity would be most useful.

METHODS AND RESULTS

Using genomic reduction in combination with next-generation sequencing, we identified SSR motifs with five to 15 perfect repeats in 1067 P. scariosus contigs. After multiple qualifying tests, 16 SSRs were selected for their robust polymorphic reliability across 12 taxa with as high as 21 alleles in a given taxon. With the exception of two monomorphic loci, the observed and expected heterozygosity values ranged from 0.083 to 1.000 and 0.398 to 0.920, respectively.

CONCLUSIONS

These microsatellite markers will directly aid in studies of the genetic diversity and relatedness of P. scariosus, P. comarrhenus, P. compactus, P. cyananthus var. cyananthus, P. fremontii var. fremontii, P. fremontii var. glabrescens, P. gibbensii, P. strictus, and P. subglaber.

Microsatellite markers for the Pilosella alpicola group (Hieraciinae, Asteraceae) and their cross-amplification in other Hieraciinae genera

PREMISE OF THE STUDY

Microsatellite markers were developed for the Pilosella alpicola group (Asteraceae), comprising four closely related species distributed in subalpine areas of Europe. These species are believed to have diverged recently, but display contrasting cytogeographic patterns and variation in breeding systems, representing a promising model system for studying plant speciation, adaptation, and recent polyploidization.

METHODS AND RESULTS

We developed 17 microsatellite markers for the P. alpicola group using 454 sequencing. Sixteen markers were polymorphic, with the number of alleles per locus ranging from seven to 16 and observed and expected heterozygosity ranging from 0.45 to 0.84 and 0.72 to 0.92, respectively. Ten and five loci amplified in the related species, P. echioides and P. officinarum, respectively, but only two in Andryala and one in Hieracium s. str.

CONCLUSIONS

The developed microsatellite markers have high potential to become useful tools to study microevolutionary processes in the P. alpicola group and related Pilosella species.

Novel microsatellites for Calibrachoa heterophylla (Solanaceae) endemic to the South Atlantic Coastal Plain of South America

PREMISE OF THE STUDY

Calibrachoa heterophylla (Solanaceae) is a petunia species restricted to the South Atlantic Coastal Plain of South America and presents a recent history of colonization from continental to coastal environments and diversification following the formation of the Coastal Plain during the Quaternary period.

METHODS AND RESULTS

This study reports a suite of 16 microsatellite loci for C. heterophylla. The applicability of these markers was assessed by genotyping 57 individuals from two natural populations. Of the 16 described loci, 12 were found to be polymorphic. Successful cross-amplification tests were obtained using 12 Calibrachoa species.

CONCLUSIONS

The development of microsatellite markers will be useful to recover the contemporary history of the colonization of the Coastal Plain and to provide information for the conservation of this endemic species.

Highly polymorphic microsatellite markers in Pulsatilla vulgaris (Ranunculaceae) using next-generation sequencing

PREMISE OF THE STUDY

We developed novel microsatellite markers for the perennial plant Pulsatilla vulgaris (Ranunculaceae) to investigate the effects of fragmentation on gene flow in this imperiled species.

METHODS AND RESULTS

We identified microsatellites and developed primers based on 454 shotgun sequences. We identified 14 markers that were polymorphic and produced clean bands. Of these, eight could be analyzed as diploids. Genotyping of 97 individuals across two populations revealed these markers to be highly polymorphic with seven to 17 alleles per locus and observed heterozygosity from 0.41 to 0.83.

CONCLUSIONS

The markers are highly informative and will be used to test if the reintroduction of shepherding in southern Germany improves genetic connectivity among fragmented populations of P. vulgaris. The combination of diploid and tetraploid markers presented here will be useful in resolving the polyploidization history of this and related species.

Characterization of microsatellite loci for an Australian epiphytic orchid, Dendrobium calamiforme, using Illumina sequencing

PREMISE OF THE STUDY

Microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon.

METHODS AND RESULTS

Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ∼80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380.

CONCLUSIONS

These novel markers will serve as valuable tools for investigation of levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history.

Development of 18 polymorphic microsatellite markers for Vinca minor (Apocynaceae) via 454 pyrosequencing

PREMISE OF THE STUDY

Polymorphic microsatellite markers were developed in Vinca minor (Apocynaceae) to evaluate the level of clonality, population structure, and genetic diversity of the species within its native and introduced range.

METHODS AND RESULTS

A total of 1371 microsatellites were found in 43,565 reads from 454 pyrosequencing of genomic V. minor DNA. Additional microsatellite loci were mined from publicly available cDNA sequences. After several rounds of screening, 18 primer pairs flanking di-, tri-, or tetranucleotide repeats were identified that revealed high levels of genetic diversity in two native Italian populations, with two to 11 alleles per locus. Clonal growth predominated in two populations from the introduced range in Germany. Five loci successfully cross-amplified in three additional Vinca species.

CONCLUSIONS

The novel polymorphic microsatellite markers are promising tools for studying clonality and population genetics of V. minor and for assessing the historical origin of Central European populations.

Genus-wide microsatellite primers for the goldenrods (Solidago; Asteraceae)

PREMISE OF THE STUDY

Microsatellite primers were developed for studies of polyploid evolution, ecological genetics, conservation genetics, and species delimitation in the genus Solidago. •

METHODS AND RESULTS

Illumina sequencing of a shotgun library from S. gigantea identified ca. 1900 putative single-copy loci. Fourteen loci were subsequently shown to be amplifiable, single-copy, and variable in a broad range of Solidago species. •

CONCLUSIONS

The utility of these markers both across the genus and in herbarium specimens of a wide age range will facilitate numerous inter- and intraspecific studies in the ca. 120 Solidago species.

Microsatellite markers for Russian olive (Elaeagnus angustifolia; Elaeagnaceae)

PREMISE OF THE STUDY

Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. •

METHODS AND RESULTS

Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. •

CONCLUSIONS

These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion.

Development of SSR markers for the tropical alpine tree species Leptospermum recurvum (Myrtaceae) on Mount Kinabalu in Borneo

PREMISE OF THE STUDY

Nuclear microsatellite (simple sequence repeat [SSR]) markers were developed for the woody species Leptospermum recurvum found on Mount Kinabalu, Borneo, to facilitate investigation of the genetic structure and patterns of gene flow in relation to leaf phenotypic polymorphisms. •

METHODS AND RESULTS

Eleven primer pairs were developed using the compound SSR marker technique. Ten of the 11 loci were polymorphic and their expected heterozygosity ranged from 0.04 to 0.83. Neither linkage disequilibrium nor departure from Hardy-Weinberg equilibrium were detected. All primer pairs also amplified the SSR loci of L. polygalifolium. •

CONCLUSIONS

These findings suggest the utility of these primers for investigating genetic structure and gene flow in L. recurvum and indicate their applicability to another species of Leptospermum.

Identificaiton of a clubroot resistance locus conferring resistance to a Plasmodiophora brassicae classified into pathotype group 3 in Chinese cabbage (Brassica rapa L.)

In Chinese cabbage (Brassica rapa), the clubroot resistance (CR) genes Crr1 and Crr2 are effective against the mild Plasmodiophora brassicae isolate Ano-01 and the more virulent isolate Wakayama-01, but not against isolate No. 14, classified into pathotype group 3. 'Akiriso', a clubroot-resistant F(1) cultivar, showed resistance to isolate No. 14. To increase the durability of resistance, we attempted to identify the CR locus in 'Akiriso'. CR in 'Akiriso' segregated as a single dominant gene and was linked to several molecular markers that were also linked to CRb, a CR locus from cultivar 'CR Shinki'. We developed additional markers around CRb and constructed partial genetic maps of this region in 'Akiriso' and 'CR Shinki'. The positions and order of markers in the genetic maps of the two cultivars were very similar. The segregation ratios for resistance to isolate No. 14 in F(2) populations derived from each of the two cultivars were also very similar. These results suggest that the CR locus in 'Akiriso' is CRb or a tightly linked locus. The newly developed markers in this study were more closely linked to CRb than previously reported markers and will be useful for marker-assisted selection of CRb in Chinese cabbage breeding.