Genic Simple Sequence Repeat Markers Research Articles

Utilization of conserved genic SSR markers for phylogenetic analysis of Nigerian Ipomoea species

Ipomoea, with enormous economic importance, is a large genus with species that are highly evolutionarily diverged. There is dearth of information regarding the phylogenetic relationships of the Nigerian species of the genus Ipomoea. It is therefore imperative to use contemporary taxonomic evidences to understand the diversity of its distribution in a region and provide enhanced delimitation of the taxa. In this study, 6 genic simple sequence repeat (SSR) markers whose cross transferability have been established among the plant species were selected to appraise their level of polymorphism and used to study the phylogenetic relationships among 11 indigenous Nigerian Ipomoea species. The 6 SSR loci showed varying levels of polymorphism among the genotypes of all 11 species assessed and demonstrated 100% polymorphism when examined across the 11 species. A total of 55 alleles were produced. The PIC of the primers ranged between 0.2223 and 0.874 with an average value of 0.71885. Phylogenetic analysis clustered species into 3 major and 6 sub clusters wherein the species were clearly separated. This study has shown the effectiveness of developed genic SSR markers for establishing phylogenetic relationship in Ipomoea species.

Development of Genic Simple Sequence Repeat Markers as Novel Genomic Resources in Dolichos Bean (Lablab purpureus L.)

Development of Genic Simple Sequence Repeat Markers as Novel Genomic Resources in Dolichos Bean (Lablab purpureus L.)

Development of Genic SSR Markers from Transcriptome Sequences of Baeckea frutescens (Cucur Atap) for Genetic Diversity Assessment

Baeckea frutescens or Cucur Atap, is a medicinal plant that has been traditionally used as herbal medicine and has great potential for pharmaceutical application due to its biological properties. The increasing demand for B. frutescens herbal medicinal products has led to its over-exploitation. Therefore, it is crucial to generate baseline genetic information in order to formulate conservation and breeding programmes for this species. In this study, a total of 26 polymorphic simple sequence repeat (SSR) markers have been developed in B. frutescens based on the leaf transcriptome sequence data obtained via next generation sequencing (NGS) technology. These markers were evaluated using 32 individuals from Forest Research Institute Malaysia Research Station in Setiu, Terengganu. The mean number of alleles was two and the average expected (HE) and observed heterozygosity (HO) were 0.484 and 0.900, respectively. Cluster analysis revealed high genetic similarity among the individuals, whereby many of them were of the same clones. It is essential to assess more individuals from other populations for better understanding on the genetic diversity of this useful medicinal plant.

Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas.

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry.

Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average length of 717bp. After functional annotation and prediction, there were 47,058 unigenes; of these, 26,861 had a gene ontology annotation, with 14,264 SSR loci. Mononucleotide SSRs were the predominant repeat type (47.20%, n = 6724), followed by di- (32.50%, n = 4641), tri- (19.10%, n = 2729), tetra- (0.90%, n = 132), hexa- (0.2%, n = 21), and penta- (0.10%, n = 16) nucleotide repeats. The most frequent di-, tri-, and tetra-nucleotide repeats were AG/CT, AAG/CTT, and AAAG/CTTT, respectively. PCR amplification with 105 SSR primer pairs yielded four bands specific to red flowers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142, and UgRFsr54608; corresponding 4 trait-specific markers were found to co-segregate with white and red flower color in hybrid population, demonstrating that the genic SSR marker is useful to discriminate between white and red flowers in strawberry. Markers to discriminate flower color in red-flowered strawberry will be useful for early selection of progeny and for breeding management.

Development and Characterization of Genic Microsatellites for the Ornamental Plant Green and Gold (Chrysogonum virginianum)

The genus Chrysogonum is native to the eastern United States. Three entities have been recognized—either as three varieties of Chrysogonum virginianum or as two species, one of them with two varieties. The current study suggests that a fourth entity should be recognized. Several forms of the complex are in commercial trade as ornamentals. As very limited molecular information on Chrysogonum is available, we developed a set of genic simple sequence repeat markers (eSSRs) from de novo transcriptome sequencing. We tested a set of 17 eSSRs on a collection of C. virginianum genomic DNA samples from the three botanical varieties, and a new putative type observed in Tennessee, dubbed “Ocoee-type” for its geographic origin. The polymerase chain reaction and capillary electrophoresis analyses with downstream population genetics tools verified the usefulness of the eSSRs. By applying this approach, we showed recognizable variation within Chrysogonum, although it did not correspond exactly to previous infraspecific classifications. Finally, as demonstrated for the commercial cultivar Pierre included in the study, the eSSRs can be used for enhancing the future breeding or hybridization efforts of this ornamental plant.

Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers

Finger millet (Eleusine coracana (L.) Geartn.) is one of the important small millets serves as a food security crop because of its high nutritional values. The complex tetraploid genome of finger millet requires a large number of informative, functional DNA markers for different applications in genetics and breeding. Yet, less number of simple sequence repeat (SSR) markers have been developed from expressed sequence tags in finger millet. In the present study, 56 new genic SSR markers were developed from publicly available drought related ESTs. The 43 polymorphic markers were used to evaluate polymorphism, revealed a range of PIC value 0.41 to 0.79. Our results suggest that, analyzed genotypes have high genetic diversity with an average gene diversity (h) of 0.176 and Shannon's information index (I) of 0.315. We conclude that there was a higher gene exchange within populations, by the value of overall gene flow (Nm) of 0.7721. The unweighted pair group method with arithmetic mean and neighbor joining dendrogram generated three main clusters to differentiate genotypes and these results were also confirmed by PCA and PCoA analysis. The high genetic diversity (77%) was found within the populations in the analysis of molecular variance. A Bayesian model-based cluster analysis evidenced a high extent of admixture between the gene pools from the different geographical origins. Population based cluster analyses pointed out a strong pattern of ‘isolation by distance’. Overall, these results underscored that this study showed a significantly high level of polymorphism, adequate genetic diversity and population structure which expand the modern genetic resources and its utility in various applications in genetics and genomics including association mapping and breeding.

Genic simple sequence repeat markers for measuring genetic diversity in a native food crop: a case study of Australian Kunzea pomifera F.Muell. (muntries)

Kunzea pomifera F.Muell. (muntries) is a native food crop in Australia that produces spicy apple-flavoured berries. Orchards were established in the 1990s using a variety of wild-collected selections. No published records are currently available of formal plant breeding although the Rivoli Bay selection is the most widely planted. DNA markers are needed to reliably assess genetic diversity and validate plant selections, however genomic resources of K. pomifera are not available. Initially, based on the large MYB gene family, eight MYB gene fragments were amplified and cloned using a degenerate PCR primer strategy. Targeted amplicon sequencing was subsequently used to evaluate diversity of 19 K. pomifera plants and this revealed the presence of single nucleotide polymorphisms and simple sequence repeats (SSRs). Three genic SSR markers were developed from K. pomifera MYB gene fragments and another three genic SSRs were successfully transferred from K. pulchella (Lindl.) A. S. George. A high transfer rate (75%) was obtained due to selecting SSRs in genic regions (introns or intergenic regions) and using Eucalyptus grandis W.Hill sequences to identify conserved regions. The six SSRs were highly polymorphic with observed heterozygosity (Ho) (average Ho = 0.63) and polymorphic information content (PIC) (average PIC = 0.54). Using the six genic SSRs, 15 unique genotypes were identified from the K. pomifera collections in two orchards. Importantly, plants in a new diversity panel were genotyped and suspected mis-labeling events confirmed. The genic SSRs and approach developed will benefit marker assisted selection programs by increasing the proportion of genic markers that could be linked to important horticultural traits.

De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites

The pen shell (Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes (18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats (SSRs) were identified, of them the most abundant type was mono-nucleotide repeats (12902, 55.01%), which was followed by di-nucleotide (8132, 34.68%), tri-nucleotide (2010, 8.57%), tetra-nucleotide (401, 1.71%), and penta-nucleotide (7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.

De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development

BackgroundCowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus.ResultsApproximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions.ConclusionsThis transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae).

Premise of the study:Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers.Methods:Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated.Results:In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups.Discussion:A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.

Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection

Cowpea (Vigna unguiculata) is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat (SSR) markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content (PIC) value was 0.3615. The average PIC of genomic SSRs (0.3996) was higher than that of genic SSRs (0.3235), and most of the polymorphic genomic SSRs were composed of di- and trinucleotide repeats (51.9% and 37.0% of all loci, respectively). The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.

Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale

Dendrobium officinale is a critically endangered and valuable medicinal herb. In this study, two transcriptome libraries were constructed from 2-year-old stems of two cultivated varieties and sequenced with the Ion Torrent PGM™ platform. A total of 51,683 all-transcripts with average length of 505 bp, and 40,405 all-unigenes with N50 of 644 bp were achieved. Totally, 8527 potential genic simple sequence repeats (SSRs) were identified from 7332 (18.15%) unigene sequences, of which 1023 (2.53%) unigenes contained more than one SSR. Finally, 68 locus-specific primer pairs were designed, and 17 of them produced polymorphic products in D. officinale individuals. The number of alleles per locus ranged from 2 to 15, the observed and expected heterozygosity estimates ranged from 0.194 to 0.903 and from 0.360 to 0.893, respectively. These loci were further tested for cross-species transferability to D. huoshanense. All the 17 primer pairs were successfully amplified to yield locus-specific PCR products in D. huoshanense. Due to their high level of polymorphism and transferability, these genic SSR markers are valuable tools not only for germplasm conservation of this species but also for phylogenetic studies of Dendrobium.

Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon)

AbstractDongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers.

Chinese sweetgum (Liquidambar formosana) is a relatively fast-growing ecological pioneer species. It is widely used for multiple purposes. To assess the genetic diversity and genetic differentiation of the species, genic SSR markers were mined from transcriptome data for subsequent analysis of the genetic diversity and population structure of natural populations. A total of 10645 potential genic SSR loci were identified in 80482 unigenes. The average frequency was one SSR per 5.12 kb, and the dinucleotide unit was the most abundant motif. A total of 67 alleles were found, with a mean of 6.091 alleles per locus and a mean polymorphism information content of 0.390. Moreover, the species exhibited a relatively moderate level of genetic diversity (He = 0.399), with the highest was found in population XY (He = 0.469). At the regional level, the southwestern region displayed the highest genetic diversity (He = 0.435) and the largest number of private alleles (n = 5), which indicated that the Southwestern region may be the diversity hot spot of L. formosana. The AMOVA results showed that variation within populations (94.02%) was significantly higher than among populations (5.98%), which was in agreement with the coefficient of genetic differentiation (Fst = 0.076). According to the UPGMA analysis and principal coordinate analysis and confirmed by the assignment test, 25 populations could be divided into three groups, and there were different degrees of introgression among populations. No correlation was found between genetic distance and geographic distance (P > 0.05). These results provided further evidence that geographic isolation was not the primary factor leading to the moderate genetic differentiation of L. formosana. As most of the genetic diversity of L. formosana exists among individuals within a population, individual plant selection would be an effective way to use natural variation in genetic improvement programs. This would be helpful to not only protect the genetic resources but also attain effective management and exploit genetic resources.

Genetic relationships of boxwood (Buxus L.) accessions based on genic simple sequence repeat markers

Boxwoods (Buxus L., Buxaceae) are popular woody landscape shrubs grown for their diverse forms and broad-leaved evergreen foliage. We used genic simple sequence repeat (genic-SSR) markers to assess genetic diversity and relatedness of 275 accessions from the National Boxwood Collection at the U.S. National Arboretum. Flow cytometry was conducted to determine the relative ploidy of each accession. Genic-SSR loci were highly variable among the accessions, detecting an average of 6.7 alleles per locus based on 17 primer pairs. Data were analyzed with a distance matrix based on Jaccard’s similarity index, followed by Unweighted Pair Group Method with Arithmetic Mean clustering. Two major clusters were identified, with four subclusters consisting of individual accessions from B. balearica Lam., B. bodinieri Levl., B. harlandii Hance, B. microphylla Siebold et Zuccarini, B. sempervirens L., B. sinica (Rehd. et Wils.) M. Cheng, and their putative interspecific hybrids. The accessions generally clustered by cultivar, provenance, or species. Clustering within each group typically reflected breeding pedigrees, when known, and the clusters were supported by bootstrap results. This information will be used for breeding programs and collection management, and for identifying possible sources of disease tolerance for boxwood blight and other diseases and pests.

Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).

Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.

Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)

Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and dinucleotide (14.57%). A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89%) showed high levels of polymorphism. The average polymorphism information content (PIC) value and the number of alleles (Na) were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future.

Development of twenty-seven genic SSR markers and screening for their association with resistance to Aeromonas hydrophila infection in rohu (Labeo rohita, Hamilton)

A set of 221 contigs containing simple sequence repeats (SSR) that were identified from mRNA-seq data of rohu (Labeo rohita) generated twenty-seven polymorphic SSRs out of which 17 had significant homology to known genes. The number of alleles per locus and observed heterozygosity (Ho) ranged from 2 to 6 and 0.066–0.846, respectively whereas the expected heterozygosity ranged from 0.129 to 0.768. Two loci (58391f4r4 and 57246f4r4) deviated from Hardy–Weinberg Equilibrium (HWE) (P < 0.05). Line specific allele segregation study of these markers in Aeromonas hydrophila resistant and susceptible lines of rohu revealed allelic variation in one SSR locus (58391f4r4). Expression analysis of this revealed the presence of detectable transcripts in skin, muscle, liver, intestine, kidney, spleen, brain, heart, stomach and eye tissues of rohu juveniles without showing any expression in gill tissue. It also exhibited 1.8-fold higher expression in skin tissue of resistant line over susceptible line. However, there was no significant difference noticed in its expression in muscle tissues between the lines. The contig didn't show homology to any known genes. The present study reports a putative marker linked to resistance to aeromoniasis in rohu, which could be exploited further for marker assisted breeding program.

Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.