[Genetic background of lily germplasm resources based on SSR markers]

To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.

The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress

Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants.

The chickpea WIP2 gene underlying a major QTL contributes to lateral root development

Lateral roots are a major component of root system architecture, and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRCs was genotyped by sequencing, and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13-32% of the LRC trait variation. A single- nucleotide polymorphism tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2), orthologous to NO TRANSMITTING TRACT/WIP domain protein 2 (NTT/WIP2) gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low versus high LRC parents and mapping individuals, suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong expression in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in the Arabidopsis wip2wip4wip5 mutant rescued its rootless phenotype to produce more lateral roots than the wild-type plants, and led to formation of amyloplasts in the columella. CaWIP2 expression also induced the expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful for developing drought-tolerant, high-yielding chickpea varieties.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

A simple sequence repeats marker of disease resistance in shrimp Litopenaeus vannamei and its application in selective breeding

The polymorphism of the simple sequence repeat (SSR) in the 5' untranslated coding region (5'-UTR) of the antiviral gene IRF (LvIRF) has been shown to be implicated in the resistance to viral pathogens in shrimp Litopenaeus vannamei (L. vannamei). In this study, we explored the potential of this (CT)n-SSR marker in disease resistance breeding and the hereditary property of disease resistance traits in offspring. From 2018 to 2021, eight populations were generated through crossbreeding by selecting individuals according to microsatellite genotyping. Our results demonstrated that shrimp with the shorter (CT)n repeat exhibited higher resistance to white spot syndrome virus (WSSV) or Decapod iridescent virus 1 (DIV1); meanwhile, these resistance traits could be inherited in offspring. Interestingly, we observed that the longer (CT)n repeats were associated with bacterial resistance traits. Accordingly, shrimp with longer (CT)n repeats exhibited higher tolerance to Vibrio parahaemolyticus infection. Taken together, these results indicate that the single (CT)n-SSR marker could be used to selective breeding for both resistance to virus and bacteria in shrimps.

Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review

Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.

Genetic Analysis of Mutagenesis That Induces the Photoperiod Insensitivity of Wild Cotton Gossypium hirsutum Subsp. purpurascens

Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a genetic analysis of morphological, cytological, and genomic changes from radiation-mediated mutagenesis that induced plant photoperiod insensitivity in the wild cotton of Gossypium hirsutum. Several morphological and agronomical traits were found to be highly inheritable using the progeny between the wild-type G. hirsutum subsp. purpurascens (El-Salvador) and its mutant line (Kupaysin). An analysis of pollen mother cells (PMCs) revealed quadrivalents that had an open ring shape and an adjoining type of divergence of chromosomes from translocation complexes. Using 336 SSR markers and 157 F₂ progenies that were grown with parental genotypes and F₁ hybrids in long day and short night conditions, five quantitative trait loci (QTLs) associated with cotton flowering were located on chromosomes At-05, At-11, and Dt-07. Nineteen candidate genes related to the flowering traits were suggested through molecular and in silico analysis. The DNA markers associated with the candidate genes, upon future functional analysis, would provide useful tools in marker-assisted selection (MAS) in cotton breeding programs for early flowering and maturity.

Classification of Southeast Asian mints (Mentha spp.) based on simple sequence repeat markers

Mentha is a complex genus encompassing many species as a consequence of their interspecific hybridization and polyploidy. Southeast Asian mints have been poorly distinguished though they are widely used for culinary and medical purposes. In this study, we have analyzed Southeast Asian mints and known varieties as well as a related Lamiaceae species (Nepeta sp.) using simple sequence repeat (SSR) markers and leaf morphology. Two types of mints were clearly distinguished based on their venation pattern and leaf shape index. We developed 12 SSR markers that allowed good amplification in the Mentha and another Lamiaceae species. In the SSR-based phylogram, the Mentha lines could be delimited into groups I-VI. The Southeast Asian mints divided into groups I and II, and the phylogram separated most of the available species, with groups I and II containing the known species M. × cordifolia and M. arvensis, respectively. The separation of the two groups was supported by a population structure analysis. The SSR markers developed in this study enabled the simultaneous classification of mints and will help improve our understanding of the genetic composition of known mint varieties and as yet unclassified Southeast Asian mints.

Parentage analysis of tea cultivars in Japan based on simple sequence repeat markers

Tea cultivars have been bred by individual selection of landraces and by crossbreeding, but the validation of the parentage is limited. In this study, we performed parentage analysis of 79 tea cultivars in Japan based on SSR markers to confirm or identify the parent-offspring relationships among them. The effectiveness of nine SSR markers for parentage analysis was validated by comparing them to the existing cleaved amplified polymorphic sequence markers. The former markers were detectable more alleles than the latter. Simulation of parentage analysis of the tea cultivars predicted biparental origins for 12 cultivars ('Houshun', 'Mie ryokuhou no. 1', 'Surugawase', 'Tenmyo', 'Yamanoibuki', 'Harumidori', 'Koushun', 'Minekaori', 'Okumusashi', 'Saemidori', 'Sofu', and 'Toyoka'), in the first five of which candidate parents of yet-to-be-defined pedigree were newly identified. Comparisons of a total of 41 SSR genotypes confirmed the newly-identified parentages of 'Asahi' for 'Tenmyo', 'Rokurou' for 'Houshun', 'Surugawase', and 'Yamanoibuki', and 'Yamatomidori' for 'Mie ryokuhou no. 1'. The maternity of seven cultivars out of the 12 was also confirmed with chloroplast DNA sequences. Uniparental origins were confirmed for 25 cultivars. This parentage analysis has improved our knowledge of tea pedigrees and will aid in the development of new cultivars.

Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel)

Simple Summary

In this study, a full-length transcriptome was analyzed with single-molecule real-time (SMRT) sequencing, which was first used to discover simple sequence repeat (SSR) genetic markers from B. dorsalis. Moreover, SSR markers from isoforms were screened for the identification of species diversity. These results could provide molecular biology methods for further population research.

Abstract

Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.

A novel (ATC)n microsatellite locus is associated with litter size in an indigenous Chinese pig

Simple sequence repeats (SSRs) are an important part of the genome and have become powerful auxiliary DNA markers in animal breeding using marker-assisted selection (MAS). Based on previous sequencing data of Qinghai Bamei pigs, a total of three novel candidate SSR loci were analysed in this study. Time-of-flight mass spectrometry (TOF-MS) was used for SSR genotyping, and association analyses between SSRs and the litter size of Qinghai Bamei sows was also performed. The results of genotyping showed that the (ATC)_n -P1, (AC)_n -P2 and (AC)_n -P3 loci had 2, 3 and 18 genotypes, respectively; 2, 3 and 8 alleles were also identified at these loci. Except for the (AC)_n -P2 locus, the polymorphism information content (PIC) values of other loci were greater than 0.25. Association analyses indicated that only the (ATC)_n -P1 locus was significantly associated with the litter size of Qinghai Bamei sows (p = .047). Compared to 189-/189- genotype, individuals with the 189-/195- genotype had the senior litter size, which was 9.04 ± 0.21. Our results enrich the data on SSRs in Qinghai Bamei pigs and indicate that (ATC)_n -P1 is a candidate locus for MAS in the pig industry.

Autochthonous Austrian Varieties of Prunus avium L. Represent a Regional Gene Pool, Assessed Using SSR and AFLP Markers

Sweet cherry production faces new challenges that necessitate the exploitation of genetic resources such as varietal collections and landraces in breeding programs. A harmonized approach to characterization is key for an optimal utilization of germplasm in breeding. This study reports the genotyping of 63 sweet cherry accessions using a harmonized set of 11 simple sequence repeat (SSR) markers optimized in two multiplexed PCR reactions. Thirty-eight distinct allelic profiles were identified. The set of SSR markers chosen proved highly informative in these germplasm; an average of 6.3 alleles per locus, a PIC value of 0.59 and above-average expected and observed heterozygosity levels were detected. Additionally, 223 amplified fragment length polymorphism (AFLP) markers derived from eight selective primer combinations were employed to further differentiate 17 closely related accessions, confirming the SSR analysis. Genetic relationships between internationally known old cultivars were revealed: SSR fingerprints of “Schneiders Späte Knorpelkirsche” and “Germersdorfer” were found to be identical to those of the standard cultivar “Noire de Meched”, among others, whereas four accessions known as “Hedelfinger Riesenkirsche” and four known as “Große Schwarze Knorpelkirsche” showed allelic differences at various loci. The genetic diversity of locally-grown cultivars worldwide might be currently underestimated. Several autochthonous Austrian sweet cherry germplasm accessions were genotyped for the first time and their genetic relationships analyzed and discussed. Interestingly, seven Austrian sweet cherry landraces were shown to be clearly genetically separated from international and modern varieties, indicating that Austrian germplasm could include valuable genetic resources for future breeding efforts.

Two cytotype niche shifts are of different magnitude in Solidago gigantea

PREMISE

Polyploidy may serve to contribute to range size if autopolyploid cytotypes are adapted to differing ecological conditions. This study aims to establish the geographic distribution of cytotypes within the giant goldenrod (Solidago gigantea), and to assess whether cytotypes exhibit differing ecological tolerances and morphology.

METHODS

A range-wide set of 629 Solidago gigantea individuals was obtained through field collecting, sampling from herbarium specimens, and incorporating existing chromosome counts. Cytotype of each unknown sample was estimated by observing allele numbers at twelve microsatellite loci, a strategy that was assessed by comparing estimated to known cytotype in 20 chromosome-counted samples. Abiotic ecological differentiation was assessed for two transitions: diploid-tetraploid and tetraploid-hexaploid. Morphological differentiation among cytotypes was assessed.

RESULTS

Microsatellite repeat variation accurately estimated cytotype in 85% of samples for which ploidy was known. Applying this approach to samples of unknown ploidy established that the three cytotypes are non-randomly distributed. Although niche modeling and MANOVA approaches identified significant differences in macro-climatic conditions for both cytotype transitions, the tetraploid to hexaploid transition was more substantial. Leaf length and width did not differ among cytotypes. Although leaf vestiture exhibited strong trends, no absolute differences were observed among cytotypes.

CONCLUSIONS

With the largest such study to date, we established niche transitions among giant goldenrod cytotypes of differing magnitudes. Collectively, this suggests that whole-genome duplication has contributed to Solidago gigantea's large range.

Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

Classification of "Kintoki ninjin" and other groups of carrot (Daucus carota) based on simple sequence repeat markers

Carrot (Daucus carota) is cultivated in temperate regions for its taproot. Eastern and Western types have been differentiated. In Japan, the former type is categorized into Kintoki, Takinogawa oonaga, and Toso, with a few local cultivars. However, their genetic relationships are unclear because of the paucity of reports. We classified the Japanese Eastern and selected Western types based on simple sequence repeat (SSR) markers. Field traits, including root weight, length, diameter, and skin color, were also examined. Our field tests showed clear differences between the Kintoki and Western-type cultivars, confirming their differentiation. A phylogram based on nine SSRs classified 24 cultivars into groups I and II. Group I included all Eastern-type carrots examined (Kintoki and Toso groups, plus two local and two foreign cultivars), with the exception of an Indian cultivar ('Pusa rudhira red'). Among them, red carrots including Kintoki were clustered into two subgroups. Western-type, Eastern-Western hybrid, and 'Pusa rudhira red' were included in group II. A population structure analysis revealed the split between the Eastern and the other types. This study elucidates the genetic characteristics of the Eastern type of carrot, which will be valuable information for carrot breeding, especially when using the Eastern type as a source.

Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).

Are buffalograss (Buchloë dactyloides) cytotypes spatially and ecologically differentiated?

PREMISE

Although autopolyploidy is common among dominant Great Plains grasses, the distribution of cytotypes within a given species is typically poorly understood. This study aims to establish the geographic distribution of cytotypes within buffalograss (Buchloë dactyloides) and to assess whether individual cytotypes have differing ecological tolerances.

METHODS

A range-wide set of 578 B. dactyloides individuals was obtained through field collecting and sampling from herbarium specimens. The cytotype of each sample was estimated by determining allele numbers at 13 simple sequence repeat loci, a strategy that was assessed by comparing estimated to known cytotype in 79 chromosome-counted samples. Ecological differentiation between the dominant tetraploid and hexaploid cytotypes was assessed with analyses of macroclimatic variables.

RESULTS

Simple sequence repeat variation accurately estimated cytotype in 89% of samples from which a chromosome count had been obtained. Applying this approach to samples of unknown ploidy established that diploids and pentaploids are rare, with the common tetraploid and hexaploid cytotypes generally occurring in sites to the north/west (tetraploid) or south/east (hexaploid) portions of the species range. Both MANOVA and niche modeling approaches identified significant but subtle differences in macroclimatic conditions at the set of locations occupied by these two dominant cytotypes.

CONCLUSIONS

Incorporating chromosome count vouchers and cytotype-estimated herbarium records allowed us to perform the largest study of cytotype niche differentiation to date. Buffalograss cytotypes differ greatly in frequency, the common tetraploid and hexaploid cytotypes are non-randomly distributed, and these two cytotypes are subtly ecologically differentiated.

Characterization of 15 nuclear microsatellite markers for Afzelia africana (Fabaceae) and related species

PREMISE

Afzelia africana (Fabaceae) is a valuable, internationally vulnerable tree species in tropical Africa. The development of specific simple sequence repeat (SSR) loci is necessary for population genetic studies in this tree species and its closest relatives.

METHODS AND RESULTS

Fifteen new polymorphic microsatellite markers were developed for A. africana using Illumina next-generation sequencing. We tested the polymorphism of the 15 loci in three populations in Benin, West Africa. The number of expressed alleles per locus varied from one to 12. The levels of observed and expected heterozygosity ranged from 0.100 to 1.000 and from 0.095 to 0.882, respectively. Most markers successfully amplified in the closely related species A. quanzensis and A. bipindensis, but less so in A. bipindensis.

CONCLUSIONS

Because of their cross-amplification ability, these newly developed loci will serve as useful tools for future molecular analyses on A. africana and related species.

Classification of "nabana" (Brassica rapa) cultivars and landraces based on simple sequence repeat markers

Brassica rapa or B. napus vegetables for eating as young inflorescences and stalks are called "nabana". Japanese nabana includes "flower-bud type" and "stem-and-leaf type". Chinese and European types are also known (cai-xin, zicaitai, and broccoletto). We classified nabana belonging to B. rapa and other B. rapa vegetables. In a simple sequence repeat-based phylogram, 49 ingroup samples were classified into four groups (I-IV). Flower-bud and stem-and-leaf types were separated into groups I and III, respectively, with a slight overlap in group II. Cai-xin and non-heading Chinese cabbages were included in group IV. Broccoletto was placed in group III, close to turnips. Zicaitai cultivars were included in group II. We tested for clubroot resistance (CR) and its marker genotypes in nabana because of their agronomical importance. Ten cultivars were resistant to group 4 pathogen but not to group 2. Most of the CR cultivars had heterozygous resistance alleles in the CRb and Crr1 loci, consistent with inoculation tests. Our results suggest that Japanese nabana lines and foreign types were differentiated according to their consumption parts and cultivar origins, respectively. This study elucidates the relationships and CR properties of nabana and provides valuable information for the breeding of nabana cultivars.

Microsatellite markers for the prized matsutake mushroom (Tricholoma matsutake, Tricholomataceae)

PREMISE OF THE STUDY

Novel and cost-effective microsatellite markers were developed to explore the population genetics, biogeographic structure, and evolutionary history of the prized Euro-Asian wild edible ectomycorrhizal fungus Tricholoma matsutake (Tricholomataceae).

METHODS AND RESULTS

Eighteen new polymorphic simple sequence repeat loci, detected from a microsatellite-enriched genomic library, were used to characterize 131 individuals from eight T. matsutake populations. The number of alleles ranged from two to 10, with averages of 1.42 to 3.22. Levels of observed and expected heterozygosity ranged from 0.00-1.00 and from 0.00-0.83, with mean values of 0.21 and 0.26, respectively. In total, 50% of the loci showed interspecific transferability and polymorphism in the related species T. equestre.

CONCLUSIONS

These newly developed markers will aid research into the genetic diversity and population structure of T. matsutake. They can also be used in other species of Tricholoma.

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

PREMISE OF THE STUDY

Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.

METHODS

In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results.

RESULTS

The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates.

DISCUSSION

Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.

Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides

Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection

Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study's findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.

Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10⁻40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.

Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants

Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation. Genome-related research in ornamentals plants has been relatively slow to develop because of their heterozygosity or polyploidy. Advances in analytical instruments, such as next-generation sequencers and information processing technologies have revolutionized biology, and have been applied in a large number and variety of species, including ornamental plants. Recently, high-quality whole genome sequences have been reported in plant genetics and physiology studies of model ornamentals, such as those in genus Petunia and Japanese morning glory (Ipomoea nil). In this review, whole genome sequencing and construction of high-density genetic linkage maps based on SNP markers of ornamentals will be discussed. The databases that store this information for ornamentals are also described.

Reduced incompatibility in the production of second generation hybrids between two Magnolia species revealed by Bayesian gene dispersal modeling

PREMISE OF THE STUDY

Hybrid zones are areas where gene flow between related species is currently occurring, so information on the compatibility between related species and their hybrids is essential for predicting the dynamics of such zones generated by introgressive hybridization. In this study, we quantified the compatibility among Magnolia stellata, M. salicifolia, and their hybrids in a hybrid zone using gene dispersal modeling.

METHODS

After determining the genealogical classes of adult trees in the hybrid zone, the paternity of 574 open-pollinated seeds from 37 known maternal trees was analyzed with microsatellite markers. A neighborhood-based Bayesian gene dispersal model developed by us for estimating compatibility was then applied to the paternity data.

KEY RESULTS

When M. stellata or M. salicifolia were mothers, interspecific mating to produce F₁ hybrids yielded significant incompatibility, but backcrossing with F₁ hybrids did not. Furthermore, when F₁ hybrids became mothers, no significant incompatibility resulted from backcrossing to parental species or intra-F₁ mating to produce F₂ hybrids. The estimated proportion of F₁ hybrids in the outcrossed seeds (1.7%) in the hybrid zone was much lower than that in the adult trees (14.0%).

CONCLUSIONS

While it is difficult to obtain F₁ hybrids, their low incompatibility makes it easy to produce advanced generation hybrids, once they have been successfully obtained. Although the production of F₁ seeds is rare, heterosis and/or weak selection pressure in an empty niche between the parental species' niches may have contributed to the increased proportion of adult F₁ hybrids in the hybrid zone.

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

Development of User-Friendly Method to Distinguish Subspecies of the Korean Medicinal Herb Perilla frutescens Using Multiplex-PCR

Perilla (Perilla frutescens) is an economically and culturally important plant in East Asia. Plant breeding between cultivars has enhanced the genetic diversity of perilla overall, but means that functionally diverse subspecies are more difficult to identify and distinguish. In this study, we developed gene-based DNA markers to distinguish between the Korean herbal medicinal perilla varieties. We identified informative simple sequence repeat (SSR) regions on the promoter regions of the Myb-P1 and dihydroflavonol 4-reductase (DFR) genes, as well as a large insertion-deletion (indel) region in the limonene synthase (LS) gene, and developed markers to characterize the distinct subspecies differences (PfMyb-P1pro, PfDFRpro, and PfLS, respectively). Using the PfLS primers, a 430-bp region could be amplified from P. frutescens var. acuta, crispa, and f. viridis (known as Jasoyeop, Jureum-soyeop, and Chungsoyeop, respectively), but not from P. frutescens var. japonica (Dlggae). The PfMybpro primers resulted in PCR products of 314 or 316, 330, 322, and 315 bp from Dlggae, Jasoyeop, Jureum-soyeop, and Chungsoyeop, respectively, and the PfDFRpro primers resulted in products of 189 or 202, 187 or 189, 185 or 189, and 193bp, respectively, for the four perilla subspecies. Combining these three reactions into a single multiplex PCR approach resulted in subspecies-specific PCR band patterns for six common types of commercial perilla, distinguishing between three varieties of Dlggae (Cham-Dlggae, Ip-Dlggae, and Bora-Dlggae), as well as identifying Jasoyeop, Jureum-soyeop, and Chungsoyeop. These user-friendly markers will be valuable as a simple and efficient method for identifying the Korean medicinal herb Jasoyeop, as well as distinguishing between other functionally distinct subspecies, which may have broad applications in the Korean herbal industry.

Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae), based on RAD sequencing

PREMISE OF THE STUDY

Lancea tibetica (Phrymaceae), a Tibetan medicinal plant, is endemic to the Qinghai-Tibet Plateau. The over-exploitation of wild L. tibetica has led to the destruction of many populations. To enhance protection and management, biological research, especially population genetic studies, should be carried out on L. tibetica. Simple sequence repeat (SSR) markers of L. tibetica were developed to analyze population diversity.

METHODS AND RESULTS

Four thousand four hundred and forty-one SSR loci were identified for L. tibetica based on restriction-site associated DNA (RAD) sequencing on the Illumina HiSeq platform. One hundred SSR loci were arbitrarily selected for primer design, and 38 of them were successfully amplified. These markers were tested on 56 individuals from three populations of L. tibetica, and 10 markers displayed polymorphisms. The total number of alleles per locus ranged from three to eight, and observed and expected heterozygosities ranged from 0.200 to 1.000 and 0.683 to 0.879, respectively. We tested for cross-amplification of these 10 markers in the related species L. hirsuta and found that nine could be successfully amplified.

CONCLUSIONS

The SSR markers characterized here are the first to be developed and tested in L. tibetica. They will be useful for future population genetic studies on L. tibetica and closely related species.

Polymorphic microsatellite markers in Anthoxanthum (Poaceae) and cross-amplification in the Eurasian complex of the genus

PREMISE OF THE STUDY

Nonplastid microsatellite primers were developed for the first time in the Euro-Siberian complex of Anthoxanthum (Poaceae), a genus of temperate grasses in which reticulate evolution is common.

METHODS AND RESULTS

A microsatellite-enriched genomic DNA library allowed the detection of 500 fragments containing a microsatellite motif. Fifteen primer pairs were selected for an extended primer test. A preliminary analysis was conducted on the Eurasian diploid lineages of Anthoxanthum, with special emphasis on three populations of the Mediterranean A. aristatum-A. ovatum complex. Thirteen out of 15 markers tested were polymorphic in the complex, with successful cross-amplification in A. odoratum (93% polymorphic loci), A. amarum (73% polymorphic), A. alpinum (73% polymorphic), and A. maderense (60% polymorphic).

CONCLUSIONS

These microsatellite markers will enable the analysis of evolution and phylogeography in diploid and polyploid lineages of this important genus.

A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes

PREMISE OF THE STUDY

The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.

METHODS AND RESULTS

Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.

CONCLUSIONS

We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes

PREMISE OF THE STUDY

The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.

METHODS AND RESULTS

Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.

CONCLUSIONS

We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

Inheritance and Molecular Mapping of an All-Stage Stripe Rust Resistance Gene Derived from the Chinese Common Wheat Landrace "Yilongtuomai"

Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating foliar disease that affects common wheat (Triticum aestivum L.) around the world. In China, common wheat landraces are potential sources of disease and abiotic stress resistance genes for wheat improvement. Yilongtuomai (YL), a wheat landrace from Yilong County, Sichuan Province, shows high levels of resistance against most Chinese Pst races. In this study, the resistance of YL to stripe rust disease was examined in detail. Parent strains, YL and Taichung 29, a variety susceptible to Pst race CYR32, and their F1, F2, and F2:3 offspring, were inoculated with CYR32 during the seedling stage in the field or adult-plant stage in the greenhouse. Results indicated that resistance to CYR32 in YL is conferred by a single dominant gene, designated YrYL The segregating F2 population (352 plants), was analyzed in terms of its resistance locus using simple sequence repeats (SSRs), resistance gene analog polymorphisms (RGAPs), and sequence-related amplified polymorphism (SRAP). A linkage group of 6 SSRs, 2 RGAPs, and 1 SRAP was constructed for the YrYL gene. Using the identified SSRs associated with physical mapping of RGAP using Chinese Spring nullisomic-tetrasomic stocks, the YrYL gene was localized to the short arm of chromosome 7D. The gene was flanked by 1 SSR marker, Xbarc92, and 1 RGAP marker, CLRRfor/Ptokin4, at genetic distances of 5.35 and 9.86 cM, respectively. The YrYL gene was compared to other stripe rust resistance genes reported on chromosome 7D by evaluating its reaction patterns to CYR32 and its pedigree relationship. Our results suggest that the YrYL gene is a new stripe rust resistance gene.

Polymorphic microsatellite loci for Haumania danckelmaniana and transferability to H. liebrechtsiana (Marantaceae)

PREMISE OF THE STUDY

Microsatellite markers were developed for the species Haumania danckelmaniana (Marantaceae) from central tropical Africa.

METHODS AND RESULTS

Microsatellite isolation was performed simultaneously on three different species of Marantaceae through a procedure that combines multiplex microsatellite enrichment and next-generation sequencing. From 80 primers selected for initial screening, 20 markers positively amplified in H. danckelmaniana, of which 10 presented unambiguous amplification products within the expected size range and eight were polymorphic with four to nine alleles per locus. Positive transferability with the related species H. liebrechtsiana was observed for the same 10 markers.

CONCLUSIONS

The polymorphic microsatellite markers are suitable for studies in genetic diversity and structure, mating system, and gene flow in H. danckelmaniana and the closely related species H. liebrechtsiana.

DNA microsatellite markers for Swartzia glazioviana (Fabaceae), a threatened species from the Brazilian Atlantic Forest

PREMISE OF THE STUDY

Development and characterization of a set of DNA microsatellite markers for Swartzia glazioviana (Fabaceae), a naturally rare and threatened tree species, were carried out to investigate its conservation genetics.

METHODS AND RESULTS

Through an enriched genomic library procedure, 10 DNA microsatellite loci were isolated and characterized for the species. The mean expected heterozygosity was 0.776 (0.424-0.894). Cross-species amplifications of these loci were successfully tested for six congener taxa (S. apetala var. apetala, S. flaemingii, S. langsdorffii, S. macrostachya, S. myrtifolia var. elegans, and S. simplex var. continentalis).

CONCLUSIONS

The 10 polymorphic microsatellite markers developed are quite informative and will provide a valuable resource to study the population and conservation genetics of S. glazioviana and other Swartzia species.

Microsatellites for Carpotroche brasiliensis (Flacourtiaceae), a useful species for agroforestry and ecosystem conservation

PREMISE OF THE STUDY

We developed microsatellite markers for Carpotroche brasiliensis (Flacourtiaceae), a dioecious tree that is used as a food resource by midsize animals of the Brazilian fauna.

METHODS AND RESULTS

We designed 30 primer pairs using next-generation sequencing and classified 25 pairs as polymorphic. Observed heterozygosity ranged from 0.5 to 1.0, and expected heterozygosity ranged from 0.418 to 0.907. The combined probability of exclusion was greater than 0.999 and the combined probability of identity was less than 0.001, indicating that these microsatellites are appropriate for investigations of genetic structure, individual identification, and paternity testing.

CONCLUSIONS

The developed molecular tools may contribute to future studies of population genetics, answering ecological and evolutionary questions regarding efficient conservation strategies for C. brasiliensis.

Characterization of nuclear microsatellite markers for Rumex bucephalophorus (Polygonaceae) using 454 sequencing

PREMISE OF THE STUDY

Nuclear microsatellite markers were developed in Rumex bucephalophorus subsp. canariensis (Polygonaceae) to investigate its genetic diversity and structure.

METHODS AND RESULTS

Sixteen polymorphic microsatellite markers were obtained using 454 next-generation sequencing with di-, tri-, and tetranucleotide repeats. The average number of alleles was 5.688 and 3.813 for R. bucephalophorus subsp. canariensis var. canariensis and var. fruticescens, respectively. Slightly higher levels of mean genetic diversity were found in var. canariensis (expected heterozygosity = 0.600) than in var. fruticescens (expected heterozygosity = 0.514). Cross-amplifications in related taxa within R. bucephalophorus showed good amplification and polymorphic patterns.

CONCLUSIONS

These 16 novel nuclear microsatellite markers are the first in the genus Rumex and may serve as valuable tools to carry out studies on genetic diversity and structure as well as progeny studies.

Microsatellite markers isolated from Cabomba aquatica s.l. (Cabombaceae) from an enriched genomic library

PREMISE OF THE STUDY

Microsatellite primers were designed for the submersed aquatic plant Cabomba aquatica s.l. (Cabombaceae) and characterized to estimate genetic diversity parameters.

METHODS AND RESULTS

Using a selective hybridization method, we designed and tested 30 simple sequence repeat loci using two natural populations of C. aquatica s.l., resulting in 13 amplifiable loci. Twelve loci were polymorphic, and alleles per locus ranged from two to four across the 49 C. aquatica s.l. individuals. Observed heterozygosity, expected heterozygosity, and fixation index varied from 0.0 to 1.0, 0.0 to 0.5, and -1.0 to -0.0667, respectively, for the Manaus population and from 0.0 to 1.0, 0.0 to 0.6, and -1.0 to 0.4643 for the Viruá population.

CONCLUSIONS

The developed markers will be used in further taxonomic and population studies within Cabomba. This set of microsatellite primers represents the first report on rapid molecular markers in the genus.

Development and characterization of 25 microsatellite primers for Ilex chinensis (Aquifoliaceae)

PREMISE OF THE STUDY

To evaluate genetic variation and structure of Ilex chinensis (Aquifoliaceae), a dioecious evergreen tree, we developed 25 microsatellite markers from its nuclear genome.

METHODS AND RESULTS

Based on the biotin-streptavidin capture method, 10 polymorphic and 15 monomorphic microsatellite markers were developed. Ten polymorphic loci were characterized by 87 individuals sampled from three populations located in Zhejiang Province and Shanghai, China. The number of alleles per locus varied from two to 12. The observed and expected heterozygosities were 0.0435-0.9032 and 0.3121-0.8343, respectively.

CONCLUSIONS

These microsatellite markers can be useful for further genetic studies of I. chinensis populations, and so contribute to forest restoration and management.

Microsatellite markers for studies with the carnivorous plant Philcoxia minensis (Plantaginaceae)

PREMISE OF THE STUDY

Microsatellite markers were developed for the critically endangered carnivorous species Philcoxia minensis (Plantaginaceae) for further population genetic studies aiming at its conservation.

METHODS AND RESULTS

We identified 29 clones containing 40 microsatellites from a genomic enriched library. A total of 27 primer pairs were developed and evaluated in 30 individuals of a natural P. minensis population. Seventeen markers successfully presented amplification products within the expected size range, of which 12 were polymorphic. The expected and observed heterozygosities ranged from 0.03 to 0.65 and from 0.00 to 0.77, respectively. Positive transferability with the related species P. bahiensis was observed for the same 17 markers.

CONCLUSIONS

The 12 polymorphic microsatellite markers are suitable for studies in genetic diversity and structure, mating system, and gene flow in P. minensis and also may be useful for similar issues regarding the related species P. bahiensis.

New microsatellite markers for Campanula pyramidalis (Campanulaceae) and cross-amplification in closely related species

PREMISE OF THE STUDY

Microsatellite markers were identified and characterized to study the genetic diversity and structure, conservation status, taxonomy, and biogeography of subspecific taxa and populations of Campanula pyramidalis (Campanulaceae).

METHODS AND RESULTS

Eleven microsatellite markers were developed from genomic libraries enriched for di- and trinucleotide repeats. A total of 80 alleles were observed in the tested natural population. The number of alleles per locus, observed heterozygosity, and expected heterozygosity ranged from four to 13, 0.217 to 0.913, and 0.521 to 0.895, respectively.

CONCLUSIONS

The new microsatellite markers will be useful for studying genetic diversity and structure as well as for better assessing the conservation status of subspecific taxa and populations of C. pyramidalis. Furthermore, a set of seven loci was successfully cross-amplified in C. secundiflora and C. versicolor and will be of great value for addressing unsolved taxonomic and biogeographic issues within the C. pyramidalis species complex.

New microsatellite markers for Campanula scheuchzeri (Campanulaceae), with cross-amplification in C. rotundifolia

PREMISE OF THE STUDY

We developed new microsatellite primers for the alpine bellflower Campanula scheuchzeri. Allelic polymorphisms will be used to study differentiation along elevation gradients of C. scheuchzeri populations and in the co-occurring sister-species C. rotundifolia in the Alps.

METHODS AND RESULTS

We analyzed C. scheuchzeri from three high-elevation sites and C. rotundifolia from two low-elevation sites in Switzerland. Campanula scheuchzeri was found to be tetraploid (2n = 68 = 4x), and up to 22 alleles were found per locus and population. Of the 15 polymorphic loci developed for C. scheuchzeri, 10 loci were tested, all of which amplified in C. rotundifolia, with similar amplicon length. Campanula rotundifolia individuals also showed tetraploid signals.

CONCLUSIONS

We speculate that C. scheuchzeri and C. rotundifolia share a common gene pool and evolve under vicariance. This presents a testable hypothesis that will be evaluated through future work. Our developed primers might also amplify in other related Campanula taxa.

De novo transcriptome analysis of a medicinal fungi Phellinus linteus and identification of SSR markers

The aim of this study was to facilitate gene discovery for functional genome studies and to identify simple sequence repeat (SSR) markers for molecular-assisted selection in Phellinus linteus. The transcriptome of Phellinus linteus was sequenced using а high-throughput RNA sequencing system - the Illumina Hiseq 2000. A total of 16,383,818 clean sequencing reads, 35,532 contigs and 25,811 unigenes were postulated. Based on similarity searches with known proteins, 19,350 genes (74.97% of the unigenes) were annotated. In the present research, 19,266, 10,978 and 7831 unigenes were mapped in Nr, Swiss-Prot and clusters of orthologous groups (COG) classifications, respectively. Of all unigenes, 6845 were categorized into three functional groups, namely biological process, cellular components and molecular function and 11,088 were annotated to 108 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 1129 SSRs were identified in these unigenes. In addition, 23 candidate genes, potentially involved in sterol biosynthesis, were identified and were worthy of further investigation.

Microsatellite primers for the gynodioecious grassland perennial Saxifraga granulata (Saxifragaceae)

PREMISE OF THE STUDY

Nine polymorphic and 12 monomorphic microsatellite loci (simple sequence repeats [SSRs]) were isolated and characterized for the gynodioecious grassland perennial Saxifraga granulata. •

METHODS AND RESULTS

Based on genomic screening of leaf material of four individuals from four populations, a total of 21 microsatellite primer pairs were designed for S. granulata. Nine loci were polymorphic and were optimized into two PCR multiplex reactions and tested on 100 individuals from five riparian populations from central Belgium. The number of alleles of the polymorphic loci ranged from three to 18, and gametic heterozygosity ranged from 0.26 to 0.94. •

CONCLUSIONS

The markers that are presented here are the first microsatellite markers reported for S. granulata and will be used to assess how river systems shape the spatial genetic structure and diversity of riparian populations of this species.

Microsatellite primers in Agave utahensis (Asparagaceae), a keystone species in the Mojave Desert and Colorado Plateau

PREMISE OF THE STUDY

Utah agave (Agave utahensis) and its putative subspecies, A. utahensis subsp. kaibabensis and A. utahensis subsp. utahensis, are keystone species of the Mojave Desert and Colorado Plateau in the southwestern United States. Here we developed microsatellite markers to study population structure and genetic diversity of the two subspecies of A. utahensis. •

METHODS AND RESULTS

We analyzed 22,386 454-pyrosequencing large contigs (>400 bp), derived from a genome reduction experiment consisting of A. utahensis accessions, for putative microsatellites. The use of unique multiplex barcodes for each of the Agave accessions allowed for the identification of putatively polymorphic microsatellites based solely on sequence alignment analysis. We report the characteristics of 11 polymorphic microsatellite loci based on a panel of 104 individuals from the two subspecies. The number of alleles per locus varied from three to eight, with an average of 5.5 alleles per locus. Observed and expected heterozygosity values ranged from 0.038 to 0.777 and 0.038 to 0.707, respectively. •

CONCLUSIONS

The microsatellites identified here will be invaluable for future studies of population structure, polyploidy, and genetic diversity across the species.

Genetic diversity and genetic relationships of japonica rice varieties in Northeast Asia based on SSR markers

Genetic diversity and the relationship among nine japonica rice groups consisting of 288 landraces and varieties in different geographical origins of Northeast Asia (China, Japan, Korea, Democratic People's Republic of Korea) and the Russian Far East district of the Russian Federation were evaluated with 154 simple sequence repeat (SSR) markers. A total of 823 alleles were detected. The observed allele numbers (Na) per locus, Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 2 to 9, 0.061 to 0.869 and 0.060 to 0.856, with an average of 5.344, 0.624 and 0.586, respectively. Five SSR loci, RM1350, RM1369, RM257, RM336 and RM1374, provided the highest PIC values and are potential for exploring the genetic diversity of rice cultivars in Northeast Asia. Molecular variance analysis showed that a significant difference existed both among groups (91.6%) and within each group (8.4%). The low genetic variation within each group indicated that the gene pool is narrow and alien genetic variation should be introduced into the rice breeding program in Northeast Asia. Based on the He and PIC values, the nine groups were ranked in a descending order: Heilongjiang landraces, Jilin landraces, Japanese improved varieties, Heilongjiang improved varieties, Russian Far East district of the Russian Federation improved varieties, Liaoning improved varieties, Jilin improved varieties, Korean improved varieties and Democratic People's Republic of Korea improved varieties. The nine groups were further divided into three subgroups and the 288 varieties into five clusters. This study provided information for parent selection in order to broaden the gene pool of the japonica rice germplasm in Northeast Asia.

Microsatellite markers for the invasive species Bidens alba (Asteraceae)

PREMISE OF THE STUDY

Microsatellite markers were developed in the invasive species Bidens alba (Asteraceae) to assess its population structure and to facilitate tracking its expansion in China. •

METHODS AND RESULTS

Using 454 pyrosequencing, 20 microsatellite primer sets were developed for B. alba. The markers were tested on one population of B. alba (30 individuals) and one population of the closely related B. pilosa (30 individuals) in China. For B. alba, all of the markers were polymorphic, and the number of alleles per locus ranged from three to 32. The expected heterozygosity values were from 0.3787 to 0.9284, and the Shannon-Wiener index was from 0.6796 to 2.8401. •

CONCLUSIONS

These markers will be useful for investigating the genetic structure, genetic diversity, and invasion dynamics of B. alba and will also be useful in studies of B. pilosa.

Isolation and characterization of microsatellite loci in Byrsonima cydoniifolia (Malpighiaceae) and cross-amplification in B. crassifolia

PREMISE OF THE STUDY

Microsatellite markers were developed and characterized in Byrsonima cydoniifolia (Malpighiaceae) to allow further investigation of genetic variation in natural populations. Cross-amplification was tested in the related species B. crassifolia. •

METHODS AND RESULTS

Seventeen microsatellite markers were isolated by a microsatellite-enriched library protocol. Fourteen polymorphic and three monomorphic loci were identified in B. cydoniifolia. The mean number of alleles in the three populations were 6.5, 6.5, and 8.2, ranging from three to 17 for different loci and populations. Mean observed and expected heterozygosities were 0.706 and 0.727, respectively. The fixation index was close to zero for all but two loci. Nine microsatellite loci were successfully cross-amplified in B. crassifolia. •

CONCLUSIONS

This new set of microsatellite markers will be a useful tool for genetic studies of B. cydoniifolia, supporting strategies for maintaining the genetic diversity of this species and possibly that of many related species.

Isolation and characterization of nine polymorphic microsatellite loci in Piper solmsianum (piperaceae)

PREMISE OF THE STUDY

Nine microsatellite (simple sequence repeat [SSR]) loci were characterized for natural populations of Piper solmsianum, a potential source of bioactive secondary metabolites, and analyzed to assess the levels of genetic diversity in this species. •

METHODS AND RESULTS

Based on an enriched library using the oligonucleotides (CT)8 and (GT)8, a total of 19 pairs of SSR primers were designed and nine of them were highly polymorphic after screening of 37 specimens from two populations. The number of alleles per locus ranged from one to six while the observed heterozygosity for polymorphic loci ranged from 0.000 to 0.875. •

CONCLUSIONS

The SSR regions characterized were informative, and the genetic markers will be useful to assess the genetic diversity and gene flow in populations of P. solmsianum.