Search

A weedy rye, Secale cereale subsp. segetale found in Xinjiang, China, possess strong stress tolerance, tillering capacity and many useful traits. The study aims to better understand the genetic diversity of segetale rye from China at the molecular level. The genetic diversity of 92 populations (bulked samples) and further 168 plants (individual samples from 14 populations) in the segetale rye were analyzed using 47 polymorphic EST-SSR (expressed sequence tags derived microsatellite) molecular markers. A total of 211 bands were amplified by 47 EST-SSR primers in the 92 populations. Among them, there were 190 polymorphic bands, with an average of 4.04 bands per primer and an average polymorphic ratio of 88.4%. The variation range of PIC (polymorphic information content) was 0.16–0.94 with the average 0.75, indicating abundant genetic diversity of weedy rye populations. The clustering analysis of 92 populations based on Nei's genetic distance showed that their average genetic distance was near 0.35, and 92 populations from different regions of Xinjiang were relatively scattered, generally close genetic distance between populations in the same region. Similar rule was found between individual plants in same population using clustering and principal coordinate analysis (PCoA). To 168 individual plants from 14 populations, analysis found that the average genetic differentiation among populations was 0.143, and the genetic diversity of the segetale rye populations mainly existed within populations (85.7%). Abundant genetic diversity was found within different regions and populations of segetale rye from China. The research provides a theoretical basis on the application of elite genes of segetale rye to the genetic improvement of rye and wheat. [ABSTRACT FROM AUTHOR]

Wheat leaf rust, caused by Puccinia triticina, is one of the most important fungal diseases of wheat in China. However, little is known about the dynamic changes of population structure and genetic diversity of P. triticina during a period of time. In this study, 247 isolates of P. triticina collected from Hebei Province from 2001 to 2010 were tested on 36 Thatcher near-isogenic lines for virulence diversity and detected by 21 pairs of Expressed Sequence Tag derived Simple Sequence Repeat (EST-SSR) primers for genetic diversity. A total of 204 isolates were successfully identified as 164 races, and THTT, THST, PHRT, THTS, and PHTT were the most common races in Hebei Province from 2001 to 2010. The cluster analysis based on virulence showed that P. triticina has a rich virulence polymorphism, which had a certain correlation with the years, while the cluster analysis based on EST-SSR showed that the genetic diversity of the P. triticina population was significantly different between years in Hebei Province from 2001 to 2010. In addition, the population structure of P. triticina may have changed greatly in 2007 and 2009, which was significantly different from that of 2001–2006 on either virulence or genetic characteristics. The variation frequency of the population structure had an increasing trend during this period. From 2001 to 2010, there was a certain degree of gene flow among the P. triticina populations. No significant correlation was found between virulence and molecular polymorphism. The genetic differentiation analysis of the 10 tested populations (each year as a population) showed that the coefficient of genetic differentiation (Gst) was 0.27, indicating that there was a certain genetic differentiation among or within populations of P. triticina in Hebei Province. The genetic variation within populations (73.08%) was higher than that among populations (26.92%), which indicated that the genetic variations were mainly found within populations. Our study provides the foundation for a better understanding of the population structure change and genetic diversity of P. triticina over a period in Hebei Province of China. [ABSTRACT FROM AUTHOR]

Albizia odoratissima is a unique rare timber tree specie in South China. In order to carry out group genetics research on its germplasm resources, this study designed and developed EST-SSR markers of A. odoratissima based on the transcriptome sequencing results. In addition, A. procera, A. falcataria, Acacia melanoxylon, Erythrophloeum fordii and other related species were selected for analysis of interspecific generality. The results were as follows:（1） Among the 243 pairs of developed primers, 171 pairs could be successfully amplified to the target bands, and the effective amplification rates in Albizia odoratissima, A. procera, A. falcataria, Acacia melanoxylon and Erythrophloeum fordii were 63.79%, 33.75%, 45.68%, 41.56% and 14.81%, respectively, and the polymorphism ratios in them were 23.87%, 12.20%, 9.01%, 3.96% and 2.78%, respectively. There were 18 pairs of primers commonly used among Albizia odoratissima, A. procera, A. falcataria, Acacia melanoxylon and Erythrophloeum fordii.（2） There were 37 SSR polymorphism markers of Albizia odoratissima were obtained, ten polymorphism markers of A. procera and A. falcataria, four polymorphism markers of Acacia melanoxylon, and there was one polymorphism mark of Erythrophloeum fordii.（3） The developed EST-SSR markers can meet the needs of population genetic studies of Albizia odoratissima, and have good transferability and practicability in A. procera and A. falcataria and other related tree species. In conclusion, EST-SSR markers can provide a reliable research tool for genetic diversity evaluation of germplasm resources, fingerprint construction of breeding materials, and population mating system analysis of Albizia odoratissima, A. procera, A. falcataria, Acacia melanoxylon and Erythrophloeum fordii. It is of great significance for the protection and utilization of Albizia odoratissima germplasm resource. [ABSTRACT FROM AUTHOR]

Pistacia chinensis Bunge (P. chinensis), a dioecious plant species, has been widely found in China. The female P. chinensis plants are more important than male plants in agricultural production, as their seeds can serve as an ideal feedstock for biodiesel. However, the sex of P. chinensis plants is hard to distinguish during the seedling stage due to the scarcity of available transcriptomic and genomic information. In this work, Illumina paired-end RNA sequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensis flower buds. In total, 50,925,088 and 51,470,578 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 83,370 unigenes with a mean length of 1.3 kb were screened. Overall, 64,539 unigenes (77.48%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG, and GO databases, 71 of which were putatively related to the floral development of P. chinensis. Additionally, 21,662 simple sequence repeat (SSR) motifs were identified in 17,028 unigenes of P. chinensis, and the mononucleotide motif was the most dominant type of repeats (52.59%) in P. chinensis, followed by dinucleotide (22.29%), trinucleotide (20.15%). The most abundant repeats were AG/CT (13.97%), followed by AAC/GTT (6.75%) and AT/TA (6.10%). Based on these SSR, 983 EST-SSR primers were designed, 151 of which were randomly chosen for validation. Of these validated EST-SSR markers, 25 SSR markers were found to be polymorphic between male and female plants. One SSR marker, namelyPCSSR55, displayed excellent specificity in female plants, which could clearly distinguish between male and female P. chinensis. Altogether, our findings not only reveal that the EST-SSR marker is extremely effective in distinguishing between male and female P. chinensis but also provide a solid framework for sex determination of plant seedlings. [ABSTRACT FROM AUTHOR]

As a unique tree species in the Salicaceae family, Chosenia arbutifolia is used primarily for construction materials and landscape planting in China. Compared with other Salicaceae species members, the genomic resources of C. arbutifolia are extremely scarce. Thus, in the present study, the full-length transcriptome of C. arbutifolia was sequenced by single-molecular real-time sequencing (SMRT) technology based on the PacBio platform. Then, it was compared against those of other Salicaceae species. We generated 17,397,064 subreads and 95,940 polished reads with an average length of 1812 bp, which were acquired through calibration, clustering, and polishing. In total, 50,073 genes were reconstructed, of which 48,174 open reading frames, 4281 long non-coding RNAs, and 3121 transcription factors were discovered. Functional annotation revealed that 47,717 genes had a hit in at least one of five reference databases. Moreover, a set of 12,332 putative SSR markers were screened among the reconstructed genes. Single-copy and special orthogroups, and divergent and conserved genes, were identified and analyzed to find divergence among C. arbutifolia and the five Salicaceae species. To reveal genes involved in a specific function and pathway, enrichment analyses for GO and KEGG were also performed. In conclusion, the present study empirically confirmed that SMRT sequencing realistically depicted the C. arbutifolia transcriptome and provided a comprehensive reference for functional genomic research on Salicaceae species. [ABSTRACT FROM AUTHOR]

Zelkova schneideriana Hand.-Mazz. of the Ulmaceae family is a Tertiary relict and economically deciduous tree species endemic to Central and Southern China. In this study, we performed a transcriptome sequencing of Z. schneideriana using high-throughput sequencing approach to detect polymorphic expressed sequence tag-simple sequence repeats (EST-SSR) markers. A total of 3,235 microsatellite loci were detected from 53,517 unigenes. A set of 30 microsatellite markers were randomly selected to validate in 41 individuals from three populations, of which 10 were polymorphic. The number of alleles per locus ranged from 3 to 11. The observed heterozygosity and expected heterozygosity ranged from 0.366 to 0.829 and 0.439 to 0.848, respectively. These polymorphic SSR primers showed good transferability across different Zelkova species, and are valuable for future studies on genetic diversity, conservation, phylogeography, and species delimitation in Z. schneideriana, as well as other Zelkova species. [ABSTRACT FROM AUTHOR]

Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii. [ABSTRACT FROM AUTHOR]

Picea neoveitchii Mast. is a rare and endangered evergreen coniferous tree species in China. P. neoveitchii grows within a specific ecological and geographical range. Here, we performed transcriptome sequencing of P. neoveitchii using the Illumina high-throughput deep sequencing technology with the following aims: (i) to perform de novo transcriptome assembly, (ii) to perform transcriptome assembly with functional annotation, (iii) to study the candidate genes involved in the biosynthesis of cellulose and lignin, (iv) to identify and analyse the transcription factors, and (v) to develop potential expressed sequence tag–simple sequence repeat (EST-SSR) markers for future population genomic and genome-wide association studies in P. neoveitchii. This is, to the best of our knowledge, the first study to provide a comprehensive transcriptome of P. neoveitchii. The transcriptome data contained 12.97 gigabase pairs (Gbp) for a total of 120,951 different transcripts belonging to 66,022 unigenes. In addition, we classified enzymes involved in the biosynthesis of cellulose and lignin and identified and analysed the transcription factors involved in stress responses, growth and development. Based on the larger than 1 kb unigenes, 1,814 EST-SSR markers were shown. Our results demonstrated that the transcriptome analysis is a valuable technology for non-model species with large genomes and this dataset will be an essential resource for future genetic and genomic research in P. neoveitchii. [ABSTRACT FROM AUTHOR]

Rehmannia glutinosa Libosch is a well-known medicinal plant in China. Despite its common use, very few molecular markers are available for this species, severely impeding any improvement of key agronomic traits. In this study, gene-based SSR (simple sequence repeat) markers were mined from the R. glutinosa transcriptome, assembled from leaf and root libraries, to obtain polymorphic information content (PIC). A total of 1,812 SSR (≥18 bp) loci were identified from 1,747 transcripts, in which 1,018 transcripts had significant homology to known proteins, and 35 transcripts were identified as non-coding RNA. Of all SSR loci, AG/GT was the most frequent SSRs repeat type, and bias of base composition presented SSRs loci from noncoding RNA. A set of 279 SSR primers (≥20 bp) were synthesized, of which 204 were successfully amplified in the Wen85-5 genome and 91 had a polymorphic information content between 0.33 and 0.90. Seven pairs of polymorphic SSR primers were selected to evaluate the genetic diversity of 36 R. glutinosa germplasms, and results demonstrated that cultivars are differ considerably from wild strains and that distinct genetic relationships exist among wild strains. The SSRs identified in this study provide critical information for future R. glutinosa breeding. [ABSTRACT FROM AUTHOR]

Spring orchid (Cymbidium goeringii), a valuable and endangered species in China, plays an important role as a potted flower. The genetic diversity of 129 spring orchid cultivars was evaluated with 13 selected EST-SSR markers and 120 alleles were identified, of which 111 alleles were polymorphic. The plum petal type, with 43 cultivars, contributed 102 polymorphic alleles out of the 111, while the colored flower type, with 3 cultivars, had 38 polymorphic alleles. Cluster analysis showed that these 129 spring orchid cultivars could be sorted into two groups, or three subgroups (A1, A2, B), based on the allelic data, and with all cultivars from three currently recognized variants intermingled with some cultivars from C. goeringii in the same subgroup, indicating that they should not be regarded as variants. Through principal coordinate analysis, only a weak correlation between DNA fingerprints and the horticultural types of the spring orchid was observed. However, common alleles existed in cultivars from the same horticultural type, for example, 15 common alleles were found in the 3 cultivars of the colored flower type, and the CY2-J allele existed in the 43 cultivars of the plum petal type. All these cultivars, except for Longzi and Lao Longzi, could be distinguished from each other using these EST-SSR markers. Moreover, a set of 102 out of the 129 cultivars had their own specific alleles, and therefore, with a single EST-SSR marker, each of these cultivars can be distinguished from all other cultivars. These findings can be valuable for taxonomy improvement as well as resource conservation and utilization, and the EST-SSR markers developed can also be a useful tool for cultivar identification which is frequently required commercially. [ABSTRACT FROM AUTHOR]

Tea plant ( Camellia sinensis (L.) O. Kuntze) originated from China, where distributed abundant genetic resources. It is of critical importance to well understanding of genetic diversity and population structure for effective collection, conservation, and utilization of tea germplasms. In this study, 96 new polymorphic EST-SSR markers were developed and used to analyze 450 tea accessions collected from 14 tea-producing regions across China. A total of 409 alleles were observed, and the gene diversity ( H) and polymorphic information content ( PIC) were estimated to be averagely 0.64 and 0.61, respectively, across all the tested samples. The higher level of genetic diversity was observed in original regions like Guangxi, Yunnan, and Guizhou provinces. The allele number, H, and PIC showed decreasing trend when the region was more and more away from origin center of tea plant, which gave us implications on the spreading route of tea plant in China. The clustering of 450 samples both showed a clear separation according to their geographic origin based on either model simulation or genetic distance. The genetic differentiation was further analyzed among five inferred populations represented different eco-geographic regions. The lowest F and the closest relationship were revealed between proximal populations, which indicated that gene exchanges occurred frequently between nearby regions than distance ones. The majority of genetic variation resulted from differentiation within population (81.36%) rather than among inferred (13.6%) and regional (5.04%) populations based on analysis of molecular variance. Our study also revealed that the lower diversity and simpler population structure were found in improved cultivars than wild teas and landraces, which indicated that genetic base of developed cultivars became narrow because of long-standing domestication and artificial selection. So more attentions should be focused to conserve and utilize the beneficial genes in wild teas and landraces to broaden genetic variation of new cultivars in future breeding of the tea plant. [ABSTRACT FROM AUTHOR]

Abstract: Chinese orchid (Cymbidium spp.) is an important potted flower with extremely high ornamental value in China. It is important to identify the genetic diversity of its germ plasma resources for development and evaluation of its cultivars. A set of 13 expressed sequence tag (EST)-derived simple sequence repeat (SSR) was used to analyze 103 cultivars of six species of Chinese orchid, namely Cymbidium goeringii, C. faberi, Cymbidium ensifolium, C. kanran, C. sinense and C. goeringii var. longibracteatum. The 13 SSR primer pairs generated a total of 168 polymorphic bands, with an average of 12.92 bands per primer and a range of 6–24 bands which clearly revealed the difference between cultivars inter- or intra-species of Chinese orchid. Cluster analysis based on UPGMA, NJ and PCoA method showed a dendrogram with three basic clusters and splitting feature of C. ensifolium and C. goeringii which partially congruent with the current taxonomic classification. [Copyright &y& Elsevier]

Background: Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew severely affects yield security wheat production in China. Understanding the virulence structure and genetic variations of this pathogen is important for breeding wheat lines resistant to wheat powdery mildew. However, information related to genes controlling resistance remains elusive. This study analyzes the virulence structure and the genetic diversity of pathogenic Bgt populations isolated from northeastern (Liaoning, Heilongjiang) and northwestern (Gansu) China, two representative wheat producing areas, on 37 wheat cultivars each carrying a known powdery mildew resistance (Pm) gene. Results: Bgt isolates from northeastern China show higher frequencies of virulence genes than populations from Gansu Province. Many of the known Pm genes failed to provide resistance in this study. However, Pm21 provided 100% resistance to all isolates from all three provinces, obtained during two consecutive years, while Pm13 provided 100% resistance in Gansu. Pm13, Pm16, Pm18, and Pm22 also showed partial resistance in northeastern China, while Pm16, Pm18, Pm22, Pm5 + 6 and Pm2 + 6 +? maintained some resistance in Gansu. Genetic diversity among populations in different regions was detected by cluster analyses using expressed sequence tag-simple sequence repeat (EST-SSR). When the genetic similarity coefficient is relatively high, populations from the same regional origin are mostly clustered into one group while populations from different regions exhibit large genetic differences. Conclusion: Pm21 remains the best choice for breeding programs to maintain resistance to Bgt. Only 58% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and frequency of virulence gene data. [ABSTRACT FROM AUTHOR]

Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars. [ABSTRACT FROM AUTHOR]

The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P < 0.01), which suggested that the clams carrying these two alleles have stronger resistance against vibrio. Clam individuals of 11-S were divided into three subgroups based on the survival time post-challenge, and the multi-dimensional scaling (MDS) analysis showed that clusters generated by genetic similarity revealed by the three SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding., (Copyright © 2013 Elsevier Ltd. All rights reserved.)