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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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Dai Y, Su W, Yang C, Song B, Li Y, Fu Y. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding. Genes (Basel) 2017; 8:genes8110325. [PMID: 29149037 PMCID: PMC5704238 DOI: 10.3390/genes8110325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 01/02/2023] Open
Abstract
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotuseryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Wenying Su
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Chentao Yang
- China National GeneBank, Environmental Genomics, Beijing Genomics Institute, Shenzhen 518083, China.
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
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Sorkheh K, Prudencio AS, Ghebinejad A, Dehkordi MK, Erogul D, Rubio M, Martínez-Gómez P. In silico search, characterization and validation of new EST-SSR markers in the genus Prunus. BMC Res Notes 2016; 9:336. [PMID: 27389023 PMCID: PMC4937603 DOI: 10.1186/s13104-016-2143-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/30/2016] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran
| | - Angela S Prudencio
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain
| | - Azim Ghebinejad
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran
| | - Mehrana Kohei Dehkordi
- Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran, Iran
| | - Deniz Erogul
- Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100, Izmir, Turkey
| | - Manuel Rubio
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain.
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De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) Using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PLoS One 2014; 9:e106438. [PMID: 25184704 PMCID: PMC4153635 DOI: 10.1371/journal.pone.0106438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/29/2014] [Indexed: 12/14/2022] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then de novo assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and Z. mauritiana Lam and Z. acidojujuba as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in Z. jujuba. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.
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Qian G, Ping J, Zhang Z, Xu D. Sequencing and comparative genomics analysis in Senecio scandens Buch.-Ham. Ex D. Don, based on full-length cDNA library. BIOTECHNOL BIOTEC EQ 2014; 28:805-812. [PMID: 26740776 PMCID: PMC4684062 DOI: 10.1080/13102818.2014.956461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/10/2014] [Indexed: 11/23/2022] Open
Abstract
Senecio scandens Buch.-Ham. ex D. Don, an important antibacterial source of Chinese traditional medicine, has a widespread distribution in a few ecological habitats of China. We generated a full-length complementary DNA (cDNA) library from a sample of elite individuals with superior antibacterial properties, with satisfactory parameters such as library storage (4.30 × 106 CFU), efficiency of titre (1.30 × 106 CFU/mL), transformation efficiency (96.35%), full-length ratio (64.00%) and redundancy ratio (3.28%). The BLASTN search revealed the facile formation of counterparts between the experimental sample and Arabidopsis thaliana in view of high-homology cDNA sequence (90.79%) with e-values <1e - 50. Sequence similarities to known proteins indicate that the entire sequences of the full-length cDNA clones consist of the major of functional genes identified by a large set of microarray data from the present experimental material. For other Compositae species, a large set of full-length cDNA clones reported in the present article will serve as a useful resource to facilitate further research on the transferability of expressed sequence tag-derived simple sequence repeats (EST-SSR) development, comparative genomics and novel transcript profiles.
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Affiliation(s)
- Gang Qian
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Junjiao Ping
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Zhen Zhang
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
| | - Delin Xu
- Department of Cell Biology and Genetics, Zunyi Medical College, Zunyi, Guizhou, P.R. China
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Qian G, Ping J, Lu J, Zhang Z, Wang L, Xu D. Construction of Full-Length cDNA Library and Development of EST-Derived Simple Sequence Repeat (EST-SSR) Markers in Senecio scandens. Biochem Genet 2014; 52:494-508. [DOI: 10.1007/s10528-014-9662-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
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Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map. BMC Genet 2014; 15 Suppl 1:S1. [PMID: 25078672 PMCID: PMC4118613 DOI: 10.1186/1471-2156-15-s1-s1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mei, Prunus mume Sieb. et Zucc., is an ornamental plant popular in East Asia and, as an important member of genus Prunus, has played a pivotal role in systematic studies of the Rosaceae. However, the genetic architecture of botanical traits in this species remains elusive. This paper represents the first genome-wide mapping study of quantitative trait loci (QTLs) that affect stem growth and form, leaf morphology and leaf anatomy in an intraspecific cross derived from two different mei cultivars. Genetic mapping based on a high-density linkage map constricted from 120 SSRs and 1,484 SNPs led to the detection of multiple QTLs for each trait, some of which exert pleiotropic effects on correlative traits. Each QTL explains 3-12% of the phenotypic variance. Several leaf size traits were found to share common QTLs, whereas growth-related traits and plant form traits might be controlled by a different set of QTLs. Our findings provide unique insights into the genetic control of tree growth and architecture in mei and help to develop an efficient breeding program for selecting superior mei cultivars.
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Sun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M. Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC Genet 2013; 14:98. [PMID: 24093913 PMCID: PMC3851432 DOI: 10.1186/1471-2156-14-98] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 09/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume ‘Fenban’ and Prunus mume ‘Kouzi Yudie’ to identify high-quality polymorphic markers between the two cultivars on a large scale. Results A total of 1464.1 Mb and 1422.1 Mb of ‘Fenban’ and ‘Kouzi Yudie’ sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent’s SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny. Conclusions A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between ‘Fenban’ and ‘Kouzi Yudie’ using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, 100083 Beijing, P,R, China.
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Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.). PLoS One 2013; 8:e59562. [PMID: 23555708 PMCID: PMC3610739 DOI: 10.1371/journal.pone.0059562] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 02/19/2013] [Indexed: 11/19/2022] Open
Abstract
Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.
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Li WJ, Ma H, Li ZH, Wan YM, Liu XX, Zhou CL. Thirty-four Musa (Musaceae) expressed sequence tag-derived microsatellite markers transferred to Musella lasiocarpa. GENETICS AND MOLECULAR RESEARCH 2012; 11:2094-8. [PMID: 22911593 DOI: 10.4238/2012.august.6.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We assembled 31,308 publicly available Musa EST sequences into 21,129 unigenes; 4944 of them contained 5416 SSR motifs. In all, 238 unigenes flanking SSRs were randomly selected for primer design and then tested for amplification in Musella lasiocarpa. Seventy-eight primer pairs were found to be transferable to this species, and 49 displayed polymorphism. A set of 34 polymorphic SSR markers was analyzed in 24 individuals from four wild M. lasiocarpa populations. The mean number of alleles per locus was 3.0, ranging from 2 to 7. The observed and expected heterozygosities per marker ranged from 0.087 to 0.875 (mean 0.503) and from 0.294 to 0.788 (mean 0.544), respectively. These markers will be of practical use for genetic diversity and quantitative trait loci analysis of M. lasiocarpa.
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Affiliation(s)
- W J Li
- Biotechnology Department, Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, China
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Wang XC, Guo L, Shangguan LF, Wang C, Yang G, Qu SC, Fang JG. Analysis of expressed sequence tags from grapevine flower and fruit and development of simple sequence repeat markers. Mol Biol Rep 2012; 39:6825-34. [DOI: 10.1007/s11033-012-1507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Ghangal R, Raghuvanshi S, Sharma PC. Expressed sequence tag based identification and expression analysis of some cold inducible elements in seabuckthorn (Hippophae rhamnoides L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 51:123-8. [PMID: 22153248 DOI: 10.1016/j.plaphy.2011.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 10/14/2011] [Indexed: 05/24/2023]
Abstract
A cDNA library was constructed from the mature leaves of seabuckthorn (Hippophae rhamnoides). Expressed Sequence Tags (ESTs) were generated by single pass sequencing of 4500 cDNA clones. We submitted 3412 ESTs to dbEST of NCBI. Clustering of these ESTs yielded 1665 unigenes comprising of 345 contigs and 1320 singletons. Out of 1665 unigenes, 1278 unigenes were annotated by similarity search while the remaining 387 unannotated unigenes were considered as organism specific. Gene Ontology (GO) analysis of the unigene dataset showed 691 unigenes related to biological processes, 727 to molecular functions and 588 to cellular component category. On the basis of similarity search and GO annotation, 43 unigenes were found responsive to biotic and abiotic stresses. To validate this observation, 13 genes that are known to be associated with cold stress tolerance from previous studies in Arabidopsis and 3 novel transcripts were examined by Real time RT-PCR to understand the change in expression pattern under cold/freeze stress. In silico study of occurrence of microsatellites in these ESTs revealed the presence of 62 Simple Sequence Repeats (SSRs), some of which are being explored to assess genetic diversity among seabuckthorn collections. This is the first report of generation of transcriptome data providing information about genes involved in managing plant abiotic stress in seabuckthorn, a plant known for its enormous medicinal and ecological value.
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Affiliation(s)
- Rajesh Ghangal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector-16C, Dwarka, New Delhi 110075, India
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