Phylogeographic analysis reveals extensive genetic variation of native grass Elymus nutans (Poaceae) on the Qinghai-Tibetan plateau

Introduction

Elymus nutans holds ecological and pastoral significance due to its adaptability and nutritional value, the Qinghai-Tibet Plateau (QTP) is a key hub for its genetic diversity. To conserve and harness its genetic resources in highland ecosystems, a thorough assessment is vital. However, a comprehensive phylogeographic exploration of E. nutans is lacking. The objective of this study was to unravel the genetic diversity, adaptation, and phylogenetics of E. nutans populations.

Methods

Encompassing 361 individuals across 35 populations, the species' genetic landscape and dynamic responses to diverse environments were decoded by using four chloroplast DNA (cpDNA) sequences and nine microsatellite markers derived from the transcriptome.

Results and discussion

This study unveiled a notable degree of genetic diversity in E. nutans populations at nuclear (I = 0.46, He = 0.32) and plastid DNA levels (Hd = 0.805, π = 0.67). Analysis via AMOVA highlighted genetic variation predominantly within populations. Despite limited isolation by distance (IBD), the Mekong-Salween Divide (MSD) emerged as a significant factor influencing genetic differentiation and conserving diversity. Furthermore, correlations were established between external environmental factors and effective alleles of three EST-SSRs (EN5, EN57 and EN80), potentially linked to glutathione S-transferases T1 or hypothetical proteins, affecting adaptation. This study deepens the understanding of the intricate relationship between genetic diversity, adaptation, and environmental factors within E. nutans populations on the QTP. The findings shed light on the species' evolutionary responses to diverse ecological conditions and contribute to a broader comprehension of plant adaptation mechanisms.

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.

Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

Virulence and molecular genetic diversity, variation, and evolution of the Puccinia triticina population in Hebei Province of China from 2001 to 2010

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.

Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium)

BACKGROUND

Lilium genus consists of approximately 100 species and numerous varieties, many of which are interspecific hybrids, which result in a complicated genetic background. The germplasm identification, genetic relationship analysis, and breeding of Lilium rely on exploiting genetic information among different accessions. Hence, an attempt was made to develop new EST-SSR markers and study the molecular divergence among 65 genotypes of Lilium.

METHODS AND RESULTS

A total of 5509 EST-SSRs were identified from the high-throughput sequencing database of L. 'Elodie'. After primer screening, six primer pairs with the most abundant polymorphic bands were selected from 100 primer pairs. Combined with the other 10 reported SSR primers, a total of 16 pairs detected genetic information with an average PIC value of 0.7583. The number of alleles per locus varied from four to 33, the expected heterozygosity varied from 0.3289 to 0.9231, and the observed heterozygosity varied from 0.2857 to 0.5122. Based on the phylogenic results, 22 Asiatic hybrids (A), seven Longiflorum × Asiatic hybrids (LA), as well as two native species were grouped. Eighteen Oriental hybrids (O) and nine Oriental × Trumpet (OT) hybrids, four native species, one LO, and one LL (L. pardalinum × L. longiflorum) variety were grouped.

CONCLUSIONS

Two major clusters were reported and a large number of genotypes were grouped based on UPGMA and STRUCTURE analysis methods. The PIC value as well as other parameters revealed that the EST-SSR markers selected were informative. In addition, the clustering pattern displayed better agreement with the cultivar's pedigree. The newly identified SSRs in this study provides molecular markers for germplasm characterization and genetic diversity for Lilium.

De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.

Genetic diversity and inferred ancestry of Asian lotus (Nelumbo nucifera) germplasms in Thailand and Vietnam

Tropical lotus (Nelumbo) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively. Higher genetic diversity was revealed in Thai lotus than in Vietnamese lotus. A Neighbor-Joining tree of five main clusters was constructed using combined EST-SSR and SRAP markers. Cluster I included 17 accessions of Thai lotus; cluster II contained three Thai accessions and 11 accessions from southern Vietnam; and cluster III was constituted by 13 accessions of seed lotus. Consistent with the results from the Neighbor-Joining tree, the genetic structure analysis showed that the genetic background of most Thai and Vietnamese lotus was pure, as artificial breeding has been rare in both countries. Furthermore, these analyses indicate that Thai and Vietnamese lotus germplasms belong to two different gene pools or populations. Most lotus accessions are genetically related to geographical distribution patterns in Thailand or Vietnam. Our findings showed that the origin or genetic relationships of some unidentified lotus sources can be evaluated by comparing morphological characteristics and the data of molecular markers. In addition, these findings provide reliable information for the targeted conservation of tropical lotus and parent selection in breeding novel cultivars of lotus.

ex Maxim using novel EST-SSR markers

Background

Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied.

Results

We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R² = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis.

Conclusions

As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08832-x.

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.

Comparative Transcriptomics and Metabolites Analysis of Two Closely Related Euphorbia Species Reveal Environmental Adaptation Mechanism and Active Ingredients Difference

Roots of Euphorbia fischeriana and Euphorbia ebracteolata are recorded as the source plant of traditional Chinese medicine "Langdu," containing active ingredients with anticancer and anti-AIDS activity. However, the two species have specific patterns in the graphic distribution. Compared with E. ehracteolata, E. fischeriana distributes in higher latitude and lower temperature areas and might have experienced cold stress adaptation. To reveal the molecular mechanism of environmental adaptation, RNA-seq was performed toward the roots, stems, and leaves of E. fischeriana and E. ehracteolata. A total of 6,830 pairs of putative orthologs between the two species were identified. Estimations of non-synonymous or synonymous substitution rate ratios for these orthologs indicated that 533 of the pairs may be under positive selection (Ka/Ks > 0.5). Functional enrichment analysis revealed that significant proportions of the orthologs were in the TCA cycle, fructose and mannose metabolism, starch and sucrose metabolism, fatty acid biosynthesis, and terpenoid biosynthesis providing insights into how the two closely related Euphorbia species adapted differentially to extreme environments. Consistent with the transcriptome, a higher content of soluble sugars and proline was obtained in E. fischeriana, reflecting the adaptation of plants to different environments. Additionally, 5 primary or secondary metabolites were screened as the biomarkers to distinguish the two species. Determination of 4 diterpenoids was established and performed, showing jolkinolide B as a representative component in E. fischeriana, whereas ingenol endemic to E. ebracteolate. To better study population genetics, EST-SSR markers were generated and tested in 9 species of Euphorbia. A total of 33 of the 68 pairs were screened out for producing clear fragments in at least four species, which will furthermore facilitate the studies on the genetic improvement and phylogenetics of this rapidly adapting taxon. In this study, transcriptome and metabolome analyses revealed the evolution of genes related to cold stress tolerance, biosynthesis of TCA cycle, soluble sugars, fatty acids, and amino acids, consistent with the molecular strategy that genotypes adapting to environment. The key active ingredients of the two species were quantitatively analyzed to reveal the difference in pharmacodynamic substance basis and molecular mechanism, providing insights into rational crude drug use.

Development and Application of Fruit Color-Related Expressed Sequence Tag-Simple Sequence Repeat Markers in Abelmoschus esculentus on the Basis of Transcriptome Sequencing

Abelmoschus esculentus is a medicinal and edible plant that contains large amounts of active ingredients, including anthocyanins, polysaccharides, flavonoids, and terpenoids. However, because of a relative lack of molecular research, there are few molecular markers applicable for this plant species. In this study, on the basis of A. esculentus fruit color-related transcriptome sequencing data, we analyzed the patterns of simple sequence repeats (SSRs) in differentially expressed genes (DEGs) and revealed the biological processes and metabolic pathways associated with the related genes. We also designed primers for SSR loci to develop SSR molecular markers. Primers were synthesized using a DEG associated with a protein-protein interaction network. Polymorphic SSR markers were screened for the subsequent examination of A. esculentus germplasm resources and fruit color association analysis. The results indicated that 24.98% of the unigenes contained SSR motifs. Single-base (mononucleotide) repeats were the main SSRs, followed by trinucleotide and dinucleotide repeats. We selected 47 expressed sequence tag (EST)-SSR primer pairs for the genotyping of 153 A. esculentus varieties/lines. We ultimately obtained 21 EST-SSR markers suitable for genotyping. A generalized linear model-based association analysis detected two EST-SSR markers significantly associated with A. esculentus fruit color. In conclusion, several EST-SSR and SSR molecular markers in A. esculentus were developed in this study. The fruit color-associated markers may be useful for the molecular marker-assisted breeding of new A. esculentus varieties.

Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.

EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski

Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei's gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.

Classification and Association Analysis of Gerbera (Gerbera hybrida) Flower Color Traits

Floral color plays a crucial role in plant life such as plant-pollinator interactions and modifying the abiotic environment of reproductive structures. In the current study, 123 gerbera accessions were divided into six color groups (white, yellow, orange, pink, red, and purple), based on Royal Horticultural Society Color Chart calibration and colorimeter measurement. Partial least squares discriminant analysis showed that the white group was mainly affected by L* value, a* value, C value, and total anthocyanin contents, while the yellow group was positively correlated with L* value, b* value, and total anthocyanin contents. Similarly, the orange group was mainly affected by b* value and total carotenoid contents, whereas the pink group was positively correlated with L* and h values. Furthermore, the red group was affected by L* value, a* value, C value, and total anthocyanin contents, whilst the purple group was mainly distributed by L* value, a* value, b* value, and total anthocyanin contents. Based on 'Jin Xiang' transcriptome data, 14,106 expressed sequence tag (EST)-SSR markers were identified and 48 pairs of primers (19 newly developed primers) were screened. Population genetic structure, neighbor-joining clustering, and principal coordinate analysis showed that 123 gerbera accessions could be divided into two groups. EST-SSR-based association analysis showed that 1, 1, 2, 1, 1, 2, and 1 significant loci were related to L*, a*, b*, C, and h, total carotenoid, and total anthocyanin contents, respectively. These results provide an important reference for flower color classification and genetic improvement of gerbera.

based on analysis of EST-SSR markers

Chrysanthemums (Chrysanthemum morifolium Ramat.) are ornamental flowers, which are famous worldwide. The mode of inheritance has great implications for the genetic analysis of polyploid species. However, genetic analysis of chrysanthemum has been hampered because of its controversial inheritance mode (disomic or hexasomic). To classify the inheritance mode of chrysanthemums, an analysis of three approaches was carried out in an F₁ progeny of 192 offspring using 223 expressed sequence tag-simple sequence repeat (EST-SSR) markers. The analysis included segregation analysis, the ratio of simplex marker alleles linked in coupling to repulsion, as well as the transmission and segregation patterns of EST-SSR marker alleles. After segregation analysis, 204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance, showing that marker alleles were inherited predominantly in a hexasomic manner. Furthermore, the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes. Additionally, the ratio of simplex marker alleles linked in coupling to repulsion was 1:0, further supporting hexasomic inheritance. Therefore, it could be inferred that chrysanthemum is a complete or near-complete hexasome.

(Ulmaceae)

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.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02968-5.

Identification of management units in threatened populations of Arnica mallotopus Makino (Asteraceae) using novel EST-SSR markers

Arnica mallotopus is a perennial herb endemic to the snowy regions of Japan. At the southern edge of its distribution, in Kyoto Prefecture, overgrazing by sika deer and decreased snowfall have resulted in the rapid decline of A. mallotopus populations. Therefore, there is an urgent need for a conservation genetic analysis of the remaining local populations. In this study, we first developed 13 EST-SSR markers to evaluate genetic variation in A. mallotopus. The average number of alleles per locus was 5.33. Genetic analysis using these markers showed that the investigated samples were classified into two groups corresponding to landscape structure. One group isolated from a tributary of the Yura River showed a strong population bottleneck signal, likely resulting from founder effects and subsequent drifts. On the other hand, the genetic diversity of the second group in the main distribution along the Yura River was higher and less inbred. Overall, our assessment suggested recognizing the two genetic groups as management units in conservation programs for the threatened populations.

EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)

High-throughput sequencing of the Phoebe bournei transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three P. bournei populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of P. bournei but also for phylogenetic studies.

Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers

Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.

Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

BACKGROUND

The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.

RESULTS

In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.

CONCLUSIONS

This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Chrysanthemums (Chrysanthemum morifolium Ramat.) are famous ornamental crops with high medicinal and industrial values. The inflorescence and leaf traits are key factors that affect the yield and quality of chrysanthemum. However, the genetic improvement of those traits is slow within chrysanthemum because of its hexaploidy, high heterozygosity and enormous genome. To study the genetic control of the important traits and facilitate marker-assisted selection (MAS) in chrysanthemum, it is desirable to populate the genetic maps with an abundance of transferrable markers such as microsatellites (SSRs). A genetic map was constructed with expressed sequence tag–simple sequence repeat (EST-SSR) markers in an F₁ progeny of 192 offspring. A total of 1000 alleles were generated from 223 EST-SSR primer pairs. The preliminary maternal and paternal maps consisted of 265 marker alleles arranged into 49 and 53 linkage groups (LGs), respectively. The recombined parental maps covered 906.3 and 970.1 cM of the genome, respectively. Finally, 264 polymorphic loci were allocated to nine LGs. The integrated map spanned 954.5 cM in length with an average genetic distance of 3.6 cM between two neighbouring loci. Quantitative trait loci (QTLs) analysis was performed using the integrated map for inflorescence diameter (ID), central disc flower diameter (CDFD), number of whorls of ray florets (NWRF), number of ray florets (NRF), number of disc florets (NDF), number of florets (NF), ray floret length (RFL), ray floret width (RFW), ray floret length/width (RFL/W), leaf length (LL), leaf width (LW) and leaf length/width (LL/W). Overall, 36 (21 major) QTLs were identified. The successful mapping of inflorescence and leaf traits QTL demonstrated the utility of the new integrated linkage map. This study is the first report of a genetic map based on EST-SSR markers in chrysanthemum. The EST-SSR markers, genetic map and QTLs reported here could be valuable resources in implementing MAS for chrysanthemums in breeding programs.

Development of EST-SSR markers and association mapping with floral traits in Syringa oblata

BACKGROUND

Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.

RESULTS

In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.

CONCLUSION

The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.

TIAs pathway genes and associated miRNA identification in Vinca minor: supporting aspidosperma and eburnamine alkaloids linkage via transcriptomic analysis

V. minor contains monomeric eburnamine-type of indole alkaloids having utilization as a neuro-medicinal plant. The biosynthetic pathway studies using miRNAs has been the focal point for plant genomic research in recent years and this technique is utilized to get an insight into a possible pathway level study in V. minor as understanding of genes in this prized medicinal plant is meagrely understood. The de novo transcriptomic analysis using Illumina Next gen sequencing has been performed in glasshouse shifted plant and transformed roots to elucidate the possible non confirmed steps of terpenoid indole alkaloids (TIAs) pathway in V. minor. A putative TIA pathway is elucidated in the study including twelve possible TIAs biosynthetic genes. The specific miRNA associated with TIAs pathway were identified and their roles were discussed for the first time in V. minor. The comparative analysis of transcriptomic data of glasshouse shifted plant and transformed roots showed that the raw reads of transformed roots were higher (83,740,316) compared to glasshouse shifted plant (67,733,538). The EST-SSR prediction showed the maximum common repeats among glasshouse shifted plant and transformed roots, although small variation was found in trinucleotide repeats restricted to glasshouse shifted plant. The study reveals overall 37 miRNAs which were observed to be true and can have a role in pathway as they can regulate the growth and alkaloid production. The identification of putative pathway genes plays an important role in establishing linkage between Aspidosperma and Eburnamine alkaloids.

In silico structural homology modelling of EST073 motif coding protein of tea Camellia sinensis (L)

Background

Tea (Camellia sinensis (L). O. Kuntze) is known as the oldest, mild stimulating caffeine containing non-alcoholic beverage. One of the major threats in south Asian tea industry is the blister blight leaf disease (BB), caused by the fungus Exobasidium vexans Masse. SSR DNA marker EST SSR 073 is used as a molecular marker to tag blister blight disease resistance trait of tea. The amino acid sequences were derived from cDNA sequences related to EST SSR 073 of BB susceptible (TRI 2023) and BB resistant (TRI 2043) cultivars. An attempt has been made to understand the structural characteristics and variations of EST SSR 073 locus that may reveal the factors influencing the BB resistance of tea with multiple bioinformatics tools such as ORF finder, ExPasy ProtParam tools, modeler V 9.17, Rampage server, UCSF-Chimera, and HADDOCK docking server.

Results

The primary, secondary, and tertiary structures of EST SSR 073 coding protein were analyzed using the amino acid sequences of both BB resistant TRI 2043 and BB susceptible TRI 2023 tea cultivars. The coding amino acid sequences of both the cultivars were homologous to photosystem I subunit protein (PsaD I) of Pisum sativum. The predicted 3D structures of proteins were validated and considered as an acceptable overall stereochemical quality. The BB resistant protein showed CT repeat extension and did not involve in topology of the PsaD I subunit. The C terminal truncation of BB resistance caused the formation of hydrogen bonds interacting with PsaD I and other subunits of photosystem I in the modeled three-dimensional protein structure.

Conclusions

Camellia sinensis EST 073 SSR motif coding protein was identified as the PsaD I subunit of photosystem I. The exact mechanism of PsaD I conferring the resistance for blister blight in tea needs to be further investigated.

DNA sequence-based mapping and comparative genomics of the genome of Pseudoroegneria spicata (Pursh) Á. Löve versus wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Bluebunch wheatgrass (referred to as BBWG) [Pseudoroegneria spicata (Pursh) Á. Löve] is an important rangeland Triticeae grass used for forage, conservation, and restoration. This diploid has the basic St genome that occurs also in many polyploid Triticeae species, which serve as a gene reservoir for wheat improvement. Until now, the St genome in diploid species of Pseudoroegneria has not been mapped. Using a double-cross mapping populations, we mapped 230 expressed sequence tag derived simple sequence repeat (EST-SSR) and 3468 genotyping-by-sequencing (GBS) markers to 14 linkage groups (LGs), two each for the seven homologous groups of the St genome. The 227 GBS markers of BBWG that matched those in a previous study helped identify the unclassified seven LGs of the St sub-genome among 21 LGs of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey. Comparisons of GBS sequences in BBWG to whole-genome sequences in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) revealed that the St genome shared a homology of 35% and 24%, a synteny of 86% and 84%, and a collinearity of 0.85 and 0.86, with ABD and H, respectively. This first-draft molecular map of the St genome will be useful in breeding cereal and forage crops.

Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum

The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of comprising high species diversity, morphological overlap and weak genetic barrier. In present study, expressed sequence tag (EST) data from Rhododendron catawbiense Michx (Subgenus Hymenanthes, Section Ponticum) and Rhododendron mucronatum var. ripense (Makino) E.H. Wilson (Subgenus Tsutsusi, Section Tsutsusi) were utilized for mining and identification of the SSRs for genetic diversity analysis of R. arboreum Smith (Subgenus Tsutsusi, Section Tsutsusi). A total of 249 SSRs were developed from 1767 contigs. Di-nucleotide was found to be most abundant repeat followed by tri- and tetra-nucleotide repeats. The motif AG/CT was most common di-nucleotide motif (31.73%), whereas, AAC/GTT (8.43%), ACG/CGT (8.03%), AAG/CTT (7.23%) and AGG/CCT (6.43%) were most abundant tri-nucleotide repeat motif. Among these SSRs, 168 sequences were only fit into the criteria to design flanking primer pairs. A total of 30 randomly selected primer pairs were utilized for validation and genetic diversity study in 36 genotypes of R. arboreum collected from western Himalayan region. In aggregate, 26 SSR markers (86.66%) produced good and repeatable amplifications. Expected heterozygosity (H_E) ranged from 0.322 to 0.841 and observed heterozygosity (H_O) ranged from 0.327 to 1.000 and PIC value ranged from 0.008 to 0.786. These primers were able to distinguish the geographic differences of occurrence based on cluster analysis. These developed EST-SSRs can be useful in future population genetics analysis and micro-evolutionary studies in Rhododendron species.

New EST-SSR Markers for Individual Genotyping of Opium Poppy Cultivars (Papaver somniferum L.)

High-quality simple sequence repeat (SSR) markers are invaluable tools for revealing genetic variability which could be utilized for many purposes, such as breeding new varieties or the identifying current ones, among other applications. Based on the analysis of 3.7 million EST sequences and 15 genomic sequences from bacterial artificial chromosome (BAC) libraries, 200 trinucleotide genic (EST)-SSR and three genomic (gSSR) markers were tested, where 17 of them fulfilled all criteria for quality markers. Moreover, the reproducibility of these new markers was verified by two genetics laboratories, with a mean error rate per allele and per locus equal to 0.17%. These markers were tested on 38 accessions of Papaver somniferum and nine accessions of another five species of the Papaver and Argemone genera. In total, 118 alleles were detected for all accessions (median = 7; three to ten alleles per locus) and 88 alleles (median = 5; three to nine alleles per locus) within P. somniferum alone. Multivariate methods and identity analysis revealed high resolution capabilities of the new markers, where all but three pair accessions (41 out of 47) had a unique profile and opium poppy was distinguished from other species.

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Auxin/Indole-3-Acetic Acid (Aux/IAA) genes are involved in auxin signaling pathway and play an important role in plant growth and development. However, many studies focus on Aux/IAA gene families and much less known in Bletilla striata. In this study, a total of 27 Aux/IAA genes (BsIAA1-27) were cloned from the transcriptome of Bletilla striata. Based on a phylogenetic analysis of the Aux/IAA protein sequences from B. striata, Arabidopsis thaliana and Dendrobium officinale, the Aux/IAA genes of B. striata (BsIAAs) were categorized into 2 subfamilies and 9 groups. While BsIAAs were more closer to those of D. officinale compared to A. thaliana. EST-SSR marker mining test showed that 4 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our results suggested that BsIAAs were involved in the process of tuber development and provided insights into functional roles of Aux/IAA genes in B. striata and other plants.

Characterization and Application of EST-SSR Markers Developed From the Transcriptome of Amentotaxus argotaenia (Taxaceae), a Relict Vulnerable Conifer

Amentotaxus argotaenia (Taxaceae) is a vulnerable coniferous species with preference for shade and moist environment. Accurate estimation of genetic variation is crucial for its conservation, especially in the context of global warming. In this study, we acquired a transcriptome from A. argotaenia leaves using Illumina sequencing and de novo assembled 62,896 unigenes, of which 5510 EST-SSRs were detected. Twenty-two polymorphic EST-SSRs were successfully developed and further used to investigate genetic variation, linkage disequilibrium, and bottleneck signatures of A. argotaenia. The results showed that A. argotaenia had moderate genetic variation and high genetic differentiation, which may provide raw material to protect against climatic changes and accelerate local adaptation, respectively. No bottlenecks were found to occur in A. argotaenia. Our study not only showed that these EST markers are very effective in population genetic analysis but also lay a solid foundation for further investigating adaptive evolution and conservation strategies of A. argotaenia.

Virulence structure and its genetic diversity analyses of Blumeria graminis f. sp. tritici isolates in China

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.

Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure

BACKGROUND

Sino-Vietnamese limestone karsts (SVLK) are a biodiversity hotspot rich in endemic plant species associated with caves and cave-like microhabitats. Based on phylogenetic studies of Begonia sect. Coelocentrum, a species-rich and characteristic SVLK clade, geographic isolation caused by extensive and continuous karstification was proposed as the major driving force triggering population diversification and geographic speciation. To test this proposition, population genetics and phylogeography of Begonia luzhaiensis were investigated using EST-SSR markers and the chloroplast trnC-ycf6 intergenic spacer.

RESULTS

F statistics, Bayesian clustering analysis, AMOVA, and PCoA of both data sets all indicated substantial population differentiation and significant isolation by distance. Nested clade phylogeographic analyses inferred that historical fragmentations have been prominent, congruent with Guangxi's geohistory of karstification as well as suggesting a mountain chain in northeastern Guangxi could have also acted as a major geographic barrier. A Bayesian skyline plot (BSP) indicated a slight decline in effective population size at 75,000 years ago (75 Kya), coinciding with the last glacial period during which the increased aridity in East Asia had retarded karstification, negatively affecting the populations of B. luzhaiensis. However, BSP detected a continuous and further population decline until the present time even though summer monsoons have resumed since the end of the last glacial maximum.

CONCLUSIONS

The microevolution patterns of B. luzhaiensis support that limited gene flow would have greatly enhanced the effects of random genetic drift and has been a major factor promoting diversification in Begonia, highly congruent with previous proposition. Based our study, we further propose that the arrival of Paleolithic Homo sapiens whose activities centered around limestone caves could have had further impacts on the populations of B. luzhaiensis, resulting in additional population decline. Further habitat destruction could have resulted from the transition from hunter gathering to food-producing societies ca. 20-10 Kya and the development of agriculture ca. 10 Kya in South China. Implications of the current study for SVLK plant conservation are also discussed.

Phenotypic and Genetic Variation of an Interspecific Centaurium Hybrid (Gentianaceae) and Its Parental Species

Interspecific hybridization is one of the major actuators of evolutionary changes in plants. As the result of allopolyploid hybridization, offspring may gain different ploidy levels in comparison to parental species, which can provide them instant reproductive isolation. Two tetraploid sister species, Centaurium erythraea and C. littorale, readily cross-fertilize, resulting in hybrids of various ploidy. In northern Serbia, two stable populations of a hexaploid taxon C. pannonicum have been documented. It has been proposed previously that this taxon emerged after an interspecific hybridization event between two tetraploid sister-species: C. erythraea and C. littorale subsp. compressum. The existing populations of the hybridogenic taxon, as well as neighboring populations of the two parental taxa were here characterized by both morphometrics and molecular markers (EST-SSR and trnL-F). Three leaf and two flower characteristics were found to be informative in delimitation of the parental taxa and in their discernment from hybrid individuals, the latter having intermediate values. Eight microsatellite markers were found to have good ability to distinguish studied taxa, placing C. pannonicum in closer relationship with C. erythraea. Conversely, trnL-F plastid marker nominated C. littorale subsp. compressum to be the donor of the C. pannonicum plastid DNA. Reproductive isolation of the hexaploid hybrid individuals from the parental species should be examined as the next logical step in describing the new species.

Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers

KEY MESSAGE

Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies.

ABSTRACT

Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq 500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500 bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.

Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)

Background

Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered.

Methods

In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions.

Results

Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant.

Discussion

Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

SRAPs and EST-SSRs provide useful molecular diversity for targeting drought and salinity tolerance in Indian mustard

Abiotic stress tolerance is one of the target trait in crop breeding under climate change scenario. Selection of suitable gene pools among available germplasm is first requisite for any crop improvement programme. Drought and salinity traits, being polygenic, are most difficult to target. The present investigation aimed at exploring and assessment of the genetic variability in Indian mustard at molecular level. A total of twenty-five genotypes and five related species were used. Sixty-three molecular markers including sequence related amplified polymorphism (SRAP) markers along with twenty-three expressed sequence tag-simple sequence repeats (EST-SSRs) were used for diversity analysis. Thirty-seven SRAPs and 18 EST-SSRs showed amplification producing a total of 423 alleles of which 422 were polymorphic. These markers gave an overall polymorphism of 99.78%, with 99.67% polymorphism in SRAPs and 100% polymorphism in EST-SSRs. The study revealed the genetic relationships among different genotypes of B. juncea and related species which could be used for Indian mustard improvement for targeting drought and salinity tolerance in future. Four SRAP and two EST-SSRs identified unique bands which may be related to abiotic stress tolerance. EST sequence BRMS-040 (IM7) was similar to Brassica and radish sequences related to PR-5 (pathogenesis-related) protein.

Comprehensive Analysis of Differentially Expressed Unigenes under NaCl Stress in Flax (Linum usitatissimum L.) Using RNA-Seq

Flax (Linum usitatissimum L.) is an important industrial crop that is often cultivated on marginal lands, where salt stress negatively affects yield and quality. High-throughput RNA sequencing (RNA-seq) using the powerful Illumina platform was employed for transcript analysis and gene discovery to reveal flax response mechanisms to salt stress. After cDNA libraries were constructed from flax exposed to water (negative control) or salt (100 mM NaCl) for 12 h, 24 h or 48 h, transcription expression profiles and cDNA sequences representing expressed mRNA were obtained. A total of 431,808,502 clean reads were assembled to form 75,961 unigenes. After ruling out short-length and low-quality sequences, 33,774 differentially expressed unigenes (DEUs) were identified between salt-stressed and unstressed control (C) flax. Of these DEUs, 3669, 8882 and 21,223 unigenes were obtained from flax exposed to salt for 12 h (N1), 24 h (N2) and 48 h (N4), respectively. Gene function classification and pathway assignments of 2842 DEUs were obtained by comparing unigene sequences to information within public data repositories. qRT-PCR of selected DEUs was used to validate flax cDNA libraries generated for various durations of salt exposure. Based on transcriptome sequences, 1777 EST-SSRs were identified of which trinucleotide and dinucleotide repeat microsatellite motifs were most abundant. The flax DEUs and EST-SSRs identified here will serve as a powerful resource to better understand flax response mechanisms to salt exposure for development of more salt-tolerant varieties of flax.

A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats

Understanding the genetic diversity and differentiation of the genetic resources of a species is important for the effective use and protection of forest tree resources. Ex situ development is a common method for the protection of genetic diversity and an essential resource for users who require ready access to a species’ germplasm. In this study, we collected seeds of black locust (Robinia pseudoacacia L.) from 19 provenances, covering most of its natural distribution; we randomly selected 367 tender leaves with well-grown and different maternal strains from this group for further analysis. Forty-eight simple sequence repeat (SSR) primers were successfully selected from 91 pairs of SSR primers using native-deformation polyacrylamide gel electrophoresis. In addition, we identified identical genotypes among all individuals and evaluated the quality of the markers. From this, 35 loci were confirmed for analyses of genetic diversity and differentiation of the black locust provenances, which contained 28 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and 7 genomic DNA-derived simple sequence repeats (G-SSRs). We observed high genetic diversity among the native black locust provenances, from which Wright’s fixation index and molecular variance suggested that a majority of the genetic differentiation variation could be attributed to within-provenance differences. The genetic distance and identity results indicated that geographic distance was not a dominating factor influencing the distribution of black locust. This is the first study to evaluate provenance genetic variation in native black locust samples using two types of SSR markers, which provides a comprehensive theoretical basis for ex situ conservation and utilization of genetic resources, with an emphasis on breeding applications.

Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers

In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2-6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079-1.753, 0.074-0.428 and 0.074-0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon (Cucumis melo var. momordica), muskmelon (Cucumis melo L.), pickling melon (Cucumis melo var. conomon) and wild muskmelon (Cucumis melo var. agrestis) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences]

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding.

Transcriptome dynamics provide insights into long-term salinity stress tolerance in Triticum aestivum cv. Kharchia Local

Kharchia Local, a wheat (Triticum aestivum) cultivar, is native to the saline-sodic soils of Pali district, Rajasthan, India and well known for its salinity stress tolerance. In the present study, we performed transcriptome sequencing to compare genome wide differential expression pattern between flag leaves of salinity stressed (15 EC) and control plants at anthesis stage. The 63.9 million paired end raw reads were assembled into 74,106 unigenes, of which, 3197 unigenes were found to be differentially expressed. Functional annotation analysis revealed the upregulation of genes associated with various biological processes including signal transduction, phytohormones signaling, osmoregulation, flavonoid biosynthesis, ion transport and ROS homeostasis. Expression pattern of fourteen differentially expressed genes was validated using qRT-PCR and was found to be consistent with the results of the transcriptome sequencing. Present study is the primary report on transcriptome profiling of Kharchia Local flag leaf under long-term salinity stress at anthesis stage. In conclusion, the data generated in this study can improve our knowledge in understanding the molecular mechanism of salinity stress tolerance. It will also serve as a valuable genomic resource in wheat breeding programs.

Development and characterization of EST-SSR markers via transcriptome sequencing in Brainea insignis (Aspleniaceae s.l.)

PREMISE OF THE STUDY

Brainea insignis (Aspleniaceae) is an endangered tree fern in China whose wild populations have been seriously damaged due to overexploitation. Expressed sequence tag-simple sequence repeat (EST-SSR) primers were developed to investigate its genetic diversity and provide resources for future conservation studies.

METHODS AND RESULTS

We obtained 72,897 unigenes of B. insignis using transcriptome sequencing and detected 15,006 SSRs in 12,058 unigenes. Based on these results, we designed 100 EST-SSR primer pairs and successfully amplified 52 of them in six individuals; 27 demonstrated polymorphisms after amplification against 72 individuals across three populations. Allele numbers ranged from three to 10, and the observed and expected heterozygosities ranged from 0.105 to 1.000 and from 0.523 to 0.865, respectively, in the tested populations. Most of these primers could be successfully amplified in two other fern species (Blechnumorientale and Chieniopteris harlandii).

CONCLUSIONS

These selected EST-SSRs are valuable for genetic diversity and conservation studies in B. insignis and other related fern species.

Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.

The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers

Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG), established in the years' 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries. In the present study, a set of 370 olive trees previously uncharacterized was screened with 10 standard simple sequence repeats (SSRs) and nine new EST-SSR markers, to correctly and thoroughly identify all genotypes, verify their representativeness of the entire cultivated olive variation, and validate the effectiveness of new markers in comparison to standard genotyping tools. The SSR analysis revealed the presence of 59 genotypes, corresponding to 72 well known cultivars, 13 of them resulting exclusively present in this collection. The new EST-SSRs have shown values of diversity parameters quite similar to those of best standard SSRs. When compared to hundreds of Mediterranean cultivars, the UNIPG olive accessions were splitted into the three main populations (East, Center and West Mediterranean), confirming that the collection has a good representativeness of the entire olive variability. Furthermore, Bayesian analysis, performed on the 59 genotypes of the collection by the use of both sets of markers, have demonstrated their splitting into four clusters, with a well balanced membership obtained by EST respect to standard SSRs. The new OLEST (Olea expressed sequence tags) SSR markers resulted as effective as the best standard markers. The information obtained from this study represents a high valuable tool for ex situ conservation and management of olive genetic resources, useful to build a common database from worldwide olive cultivar collections, also based on recently developed markers.

Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm

The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

Assessment of the Genetic Diversity Among Potato Cultivars from Different Geographical Areas Using the Genomic and EST Microsatellites

Background

Potato has a narrow genetic base which is due to its development, as it takes its genetic root from a few genotypes originated from South America.

Objectives

The objective of this study was to assess the genetic relationships among potato (Solanum tuberosum L.) genotypes originated from different geographical regions.

Materials and Methods

This study has rendered 25 useful SSRs and EST-SSRs that were located in pre-existing genetic maps, fingerprinted in a collection of the 47 potato genotypes from America, Europe and Iran.

Results

The number of alleles per locus ranged from 2 to 9 with an average of 6.22 alleles per locus. UPGMA dendrogram, constructed from microsatellite data based on Jaccard similarity coefficient slightly clustered the American and European potatoes according to their geographical distribution. Iranian genotype, "Istanbuli", joined to a group with American genotype. The results indicated that American genotypes show the highest expected heterozygosity compared to the European genotype. This result was expected due to the narrow genetic base of European potatoes considering their origin from a limited number of introductions.

Conclusions

It could be concluded that SSR is an appropriate marker for evaluating genetic diversity within and among potatoes from different geographical regions.

Intraspecific variations in cardamom (Elettaria cardamomum Maton): assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis

BACKGROUND

The main goal of the work was to analyse intraspecific variation in Elettaria cardamomum Maton (cardamom) using genome size, cytological studies and molecular marker data. Nuclear DNA content and molecular marker details furnish data on genome size and genetic diversity respectively among the studied accessions and both complement each other for evolutionary and taxonomic studies.

RESULTS

The relative 2C genome size and total number of base pairs of cardamom was determined through flow cytometric analysis using propidium iodide staining. The nuclear DNA content was estimated in various sections of the species representing individuals from wild and cultivar genotypes following Zea mays L. CE-777 (2C = 5.43 pg) as internal reference standard. Chromosome number from growing root tip was examined following standard protocols. Twenty-six ISSR primers that generated polymorphic bands were used for genetic diversity analysis of the thirty accessions of cardamom. Estimated nuclear 2C DNA content ranged from 2.57 to 3.22 pg demonstrating 1.25-fold variation. The mean amount of 2C nuclear DNA of the cardamom was calculated as 2.87 pg which is equivalent of 2806 Mbp as the diploid genome size. The chromosome number was found to be 2n = 48. Among the thirty accessions of cardamom studied using ISSR markers, C53 (feral from Bonacaud) showed a very prominent level of genetic diversity and was lowest for C96 (Avinash-I, a released variety from Indian Institute of Spices Research, Kozhikode).

CONCLUSION

These analyses revealed the existence of genetic variability within the studied cardamom accessions. The plant specimens also differed significantly in their genome size. However, the genetic variability parameters did not show any correlation with genome size.

De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified. As the interest in T. cordifolia is primarily due to its secondary metabolite constituents, the ESTs pertaining to terpenoids biosynthetic pathway were identified in the present study. Additionally, several ESTs were assigned to different transcription factor families. To validate our transcripts dataset, the novel EST-SSR markers were generated to assess the genetic diversity among germplasm of T. cordifolia. These EST-SSR markers were found to be polymorphic and the dendrogram based on dice similarity index revealed three distinct clustering of accessions. The present study demonstrates effectiveness in using both NEWBLER and MIRA sequence read assembler software for enriching transcript-dataset and thus enables better exploitation of EST resources for mining candidate genes and designing molecular markers.

In silico search, characterization and validation of new EST-SSR markers in the genus Prunus

BACKGROUND

Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions.

RESULTS

A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available Prunus reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in P. mume (mei) in comparison with the rest of species analyzed.

CONCLUSIONS

Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.

Development of EST-SSR markers for the invasive plant Tithonia diversifolia (Asteraceae)

PREMISE OF THE STUDY

Tithonia diversifolia (Asteraceae) is an invasive plant species that can outcompete natives and thus poses a great threat to biodiversity in introduced areas. Here, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized.

METHODS AND RESULTS

Sixteen polymorphic microsatellite loci were isolated from T. diversifolia using transcriptome sequencing and bioinformatic screening. The number of alleles per locus varied from two to four alleles in 48 individuals from three populations. Most of these primers also amplified in T. rotundifolia and some even in Parthenium hysterophorus.

CONCLUSIONS

These markers are useful for investigating the genetic structure and evolutionary process of T. diversifolia, which may provide important information for better management.