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Journal articles on the topic 'Genic-SSRs'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Sharma, Arti, and Rajinder Singh Chauhan. "Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis inJatropha curcas." Comparative and Functional Genomics 2011 (2011): 1–9. http://dx.doi.org/10.1155/2011/286089.

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Castor bean andJatrophacontain seed oil of industrial importance, share taxonomical and biochemical similarities, which can be explored for identifying SSRs in the whole genome sequence of castor bean and utilized inJatropha curcas. Whole genome analysis of castor bean identified 5,80,986 SSRs with a frequency of 1 per 680 bp. Genomic distribution of SSRs revealed that 27% were present in the non-genic region whereas 73% were also present in the putative genic regions with 26% in 5′UTRs, 25% in introns, 16% in 3′UTRs and 6% in the exons. Dinucleotide repeats were more frequent in introns, 5′UT

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Duhan, Naveen, and Rakesh Kaundal. "LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement." International Journal of Molecular Sciences 22, no. 21 (2021): 11350. http://dx.doi.org/10.3390/ijms222111350.

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Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one

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Wang, Qinglang, Xing’er Chen, Yue Meng, et al. "The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants." International Journal of Molecular Sciences 25, no. 4 (2024): 2084. http://dx.doi.org/10.3390/ijms25042084.

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Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significan

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Li, Shengnan, Jiao Xu, Yipu Hu, et al. "Variation in SSRs at different genomic regions and implications for the evolution and identification of Armillaria gallica." PLOS ONE 19, no. 10 (2024): e0312114. http://dx.doi.org/10.1371/journal.pone.0312114.

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Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysi

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Hanai, Luiz Ricardo, Tatiana de Campos, Luis Eduardo Aranha Camargo, et al. "Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources." Genome 50, no. 3 (2007): 266–77. http://dx.doi.org/10.1139/g07-007.

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Microsatellites or SSRs (single sequence repeats) have been used to construct and integrate genetic maps in crop species, including Phaseolus vulgaris . In the present study, 3 cDNA libraries generated by the Bean EST project ( http://lgm.esalq.usp.br/BEST/ ), comprising a unigene collection of 3126 sequences and a genomic microsatellite-enriched library, were analyzed for the presence of SSRs. A total of 219 expressed sequence tags (ESTs) were found to carry 240 SSRs (named EST-SSR), whereas 714 genomic sequences contained 471 SSRs (named genomic-SSR). A subset of 80 SSRs, 40 EST-SSRs, and 40

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Dang, Zhenhua, Lei Huang, Yuanyuan Jia, Peter J. Lockhart, Yang Fong, and Yunyun Tian. "Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica." Genes 11, no. 3 (2020): 322. http://dx.doi.org/10.3390/genes11030322.

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Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in ge

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Liu, Yan, Xiaoyan Xiao, Guangzhu Li, et al. "Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes." Genes 13, no. 9 (2022): 1518. http://dx.doi.org/10.3390/genes13091518.

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Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regi

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Bassil, Nahla V., B. Gilmore, J. M. Oliphant, K. E. Hummer, and J. A. Henning. "Genic SSRs for European and North American hop (Humulus lupulus L.)." Genetic Resources and Crop Evolution 55, no. 7 (2008): 959–69. http://dx.doi.org/10.1007/s10722-007-9303-9.

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9

Pushpavalli, SNCVL, T. Rajeshwar Reddy, B. Pranitha, C. Sudhakar, C. Sudharani, and P. Satish. "Assessment of Molecular Diversity in Popular Pigeonpea Genotypes using Genic Microsatellite Markers." Journal of Advances in Biology & Biotechnology 27, no. 8 (2024): 1203–11. http://dx.doi.org/10.9734/jabb/2024/v27i81244.

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Fusarium wilt is an important soil borne disease of pigeonpea causing significant yield losses in susceptible cultivars throughout the pigeonpea growing areas. Thirty one diverse pigeonpea genotypes were screened for wilt resistance and analyzed using 14 genic SSRs which included five SSR markers that were reported to differentiate resistant and susceptible genotypes. Polymorphic information content ranged from 0.69 to 0.90 and SSR marker ASSR-352 displayed the highest PIC value of 0.90. Dissimilarity coefficient ranged from 0.4 to 0.93. Earlier studies have identified ASSR 352 as one of the h

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Sarac, Zorica, Jelena Aleksic, Tanja Dodos, Nemanja Rajcevic, Srdjan Bojovic, and Petar Marin. "Cross-species amplification of nuclear EST-microsatellites developed for other Pinus species in Pinus nigra." Genetika 47, no. 1 (2015): 205–17. http://dx.doi.org/10.2298/gensr1501205s.

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Due to the current lack of nuclear microsatellites (simple sequence repeats - SSRs) specifically developed for Pinus nigra, an important European coniferous species, we cross-species amplified 12 EST-SSRs (expressed sequence tagged SSRs) developed for other Pinus species in P. nigra in order to delineate loci which can be used for assessing levels of genetic diversity and genetic structuring in this species. We amplified these loci in individuals from seven populations from the central Balkans representing four recognized infraspecific taxa of P. nigra (ssp. nigra, var. gocensis, ssp. pallasia

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Kaur, Rajinder, Shilpa, Era Vaidya, and Krishan Kumar. "Development, Characterization and Transferability of Peach Genic SSRs to some Rosaceae species." Advances in Research 3, no. 2 (2015): 165–80. http://dx.doi.org/10.9734/air/2015/8804.

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Duhan, Naveen, Simardeep Kaur, and Rakesh Kaundal. "ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health." Genes 14, no. 7 (2023): 1481. http://dx.doi.org/10.3390/genes14071481.

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Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the gen

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Oliveira, K. M., L. R. Pinto, T. G. Marconi, et al. "Characterization of new polymorphic functional markers for sugarcane." Genome 52, no. 2 (2009): 191–209. http://dx.doi.org/10.1139/g08-105.

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Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarc

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Idrees, Muhammad, Muhammad Irshad, Mitra Lal Pathak, Akash Tariq, and Rehan Naeem. "Assessment of Microsatellite Markers (SSRs) For Genetic Diversity in Asparagus Officinalis L. And Allied Species." Bangladesh Journal of Botany 50, no. 3 (2021): 595–602. http://dx.doi.org/10.3329/bjb.v50i3.55839.

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The present study was hypothesized to evaluate a set of SSRs for the assessment of genetic variations in Asparagus officinalis L. and their allied species. Nine genic SSR markers were especially developed for Asparagus genome and employed for DNA profiling studies of Asparagus species. These SSRs markers have revealed the allelic polymorphism ranging from 1.0 to 2.0. Allele frequency was found highest for psbD-trnL (1.0), petB (1.0) and AG7 (1.0), while it was lowest for ZHD1 (0.1). Polymorphism Information content (PIC) was highest for TC7 (0.9) while it was lowest (0.0) for psbD-trnL, petB a

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15

Li, Wei, Cuiping Zhang, Xinqiang Jiang, Qingchao Liu, Qinghua Liu, and Kuiling Wang. "De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus." Forests 9, no. 12 (2018): 748. http://dx.doi.org/10.3390/f9120748.

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Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag–simple sequence repeats (EST–SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential ES

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16

Singh, Binay K., Dwijesh C. Mishra, Sushma Yadav, et al. "Identification, characterization, validation and cross-species amplification of genic-SSRs in Indian Mustard (Brassica juncea)." Journal of Plant Biochemistry and Biotechnology 25, no. 4 (2016): 410–20. http://dx.doi.org/10.1007/s13562-016-0353-y.

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17

Li, Xiaobai, Weirui Li, Chenlu Di, et al. "Development of Genic Simple Sequence Repeat Panels for Population Classification of Chinese Cymbidium Species." Journal of the American Society for Horticultural Science 141, no. 2 (2016): 125–30. http://dx.doi.org/10.21273/jashs.141.2.125.

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Chinese cymbidiums (Cymbidium sp.) are important ornamental plants because of their foliage, flower shape, and fragrance. Well-known Chinese cymbidiums mainly include Cymbidium goeringii, Cymbidium faberi, Cymbidium ensifolium, Cymbidium kanran, and Cymbidium sinense. The population genetics of Chinese cymbidiums can be efficiently analyzed using small-scale marker panels with high discriminatory power. In this study, we tested several genic simple sequence repeats (SSRs) and built six genic SSR panels. The panels included several robust markers, which can rapidly assign Chinese cymbidium acce

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18

Gailing, Oliver, and C. Dana Nelson. "Genetic variation patterns of American chestnut populations at EST-SSRs." Botany 95, no. 8 (2017): 799–807. http://dx.doi.org/10.1139/cjb-2016-0323.

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The objective of this study is to analyze patterns of genetic variation at genic expressed sequence tag – simple sequence repeats (EST-SSRs) and at chloroplast DNA markers in populations of American chestnut (Castanea dentata Borkh.) to assist in conservation and breeding efforts. Allelic diversity at EST-SSRs decreased significantly from southwest to northeast along the Appalachian range, suggesting repeated founder events during postglacial migration. Comparatively high allelic diversity in Ontario, northwest of the Appalachian range, suggested more recent long-distance dispersal. Clinal var

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Haq, Shamshad ul, Rohit Jain, Meenakshi Sharma, Sumita Kachhwaha, and S. L. Kothari. "Identification and Characterization of Microsatellites in Expressed Sequence Tags and Their Cross Transferability in Different Plants." International Journal of Genomics 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/863948.

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Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through

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20

Li, Zhiting, Yongda Zhong, Faxin Yu, and Meng Xu. "Novel SSR marker development and genetic diversity analysis of Cinnamomum camphora based on transcriptome sequencing." Plant Genetic Resources: Characterization and Utilization 16, no. 6 (2018): 568–71. http://dx.doi.org/10.1017/s147926211800014x.

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AbstractCinnamomum camphora (Lauraceae) is a well-known multipurpose tree with aromatic oils, insect-repellent effects and ornamental value. In this study, a total of 74,289 simple sequence repeats (SSRs) were found in 56,124 unigenes, of which 14,225 unigenes contained more than one SSR locus. Among these SSR loci, the mono-nucleotide repeats were the most frequent, with a frequency of 61.14%, followed by 24.87% di-nucleotide repeats and 12.87% tri-nucleotide repeats. Twenty-one polymorphic SSR markers were developed and validated in 45 camphor trees. The 21 loci were further examined for cro

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Jun, T. H., M. A. R. Mian, K. Freewalt, O. Mittapalli, and A. P. Michel. "Development of genic-SSRs markers from soybean aphid sequences generated by high-throughput sequencing of cDNA library." Journal of Applied Entomology 136, no. 8 (2011): 614–25. http://dx.doi.org/10.1111/j.1439-0418.2011.01697.x.

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V.S.K. Chakravarthy, B. Sarkar, Y. Varalaxmi S.K. Yadav, and M. Vanaja M. Maheswari. "Genetic Diversity among Pigeonpea (Cajanus cajan L. Millsp.) Genotypes Using Genic SSRs with Putative Function for Drought Tolerance." International Journal of Current Microbiology and Applied Sciences 6, no. 4 (2017): 1804–14. http://dx.doi.org/10.20546/ijcmas.2017.604.216.

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23

Zorrilla-Fontanesi, Yasmín, Amalia Cabeza, Ana M. Torres, et al. "Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily." Molecular Breeding 27, no. 2 (2010): 137–56. http://dx.doi.org/10.1007/s11032-010-9417-1.

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Sharma, Devender, Jai Prakash Jaiswal, Navin Chander Gahtyari, et al. "Population structure, marker-trait association and identification of candidate genes for terminal heat stress relevant traits in bread wheat (Triticum aestivum L. em Thell)." Plant Genetic Resources: Characterization and Utilization 18, no. 3 (2020): 168–78. http://dx.doi.org/10.1017/s1479262120000131.

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AbstractGenetic improvement along with widened crop base necessitates for the detailed understanding of the genetic diversity and population structure in wheat. The present investigation reports the discovery of a total of 182 alleles by assaying 52 simple sequence repeats (SSRs) on 40 genotypes of bread wheat. Unweighted neighbour-joining method grouped these genotypes into two main clusters. Highly heat tolerant and intermediate tolerant cultivars were grouped in the same cluster, whereas remaining genotypes, particularly sensitive ones, were assigned different cluster. Similarly, the entire

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Rojas G., Salvador, Doriani Rodrigues, Marcicleide Lima, and Spartaco Astolfi Fhilo. "Desenvolvimento e mapeamento de microssatélites gênicos (EST-SSRs) de camu-camu (Myrciaria dubia [H.B.K.] McVaugh)." Corpoica Ciencia y Tecnología Agropecuaria 9, no. 1 (2008): 14. http://dx.doi.org/10.21930/rcta.vol9_num1_art:100.

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<p>Descrevemos o desenvolvimento marcadores de nucleotídeos repetidos em tandem de seqüências expressas (EST-SSRs) o microssatélites gênicos de camu-camu, a qual é uma pequena fruta nativa da Amazônia que cotem o mais alto conteúdo de vitamina C natural de qualquer fruteira conhecida no mundo. Dois mil seqüências da biblioteca de ESTs de camu-camu foram analisadas e 219 EST-SSRs para o desenvolvimento de marcadores moleculares foram identificadas e analisadas. Dos 219 EST-SSRs 74,2% foram perfeitos simples e 22,7% perfeitos interrompidos. Os EST-SSRs foram 13% trinucleotídeos e 87% dinuc

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Gayathri, M., M. Pitchaimuthu, and Kundapura Ravishankar. "SSR marker development in Abelmoschus esculentus (L.) Moench using transcriptome sequencing and genetic diversity studies." Journal of Horticultural Sciences 16, no. 2 (2022): 206–14. http://dx.doi.org/10.24154/jhs.v16i2.1251.

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Okra [Abelmoschus esculentus (L.) Moench] also known as bhindi or lady’s finger is an important vegetable crop in India, West Africa, South Africa, Brazil, USA and Turkey. It belongs to the family Malvaceae. Okra is mainly grown in tropics and subtropics of the world. The studies regarding the molecular marker development are very limited; still there is no SSR development from comprehensive transcriptome data in this crop. This study presents the first comprehensive transcriptome data, using RNA from different parts of okra such as root, stem, leaf, bud, flower, different stages of developing

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Satya, Pratik, Avrajit Chakraborty, Sourav Jana, et al. "Identification of genic SSRs in jute (Corchorus capsularis, Malvaceae) and development of markers for phenylpropanoid biosynthesis genes and regulatory genes." Plant Breeding 136, no. 5 (2017): 784–97. http://dx.doi.org/10.1111/pbr.12514.

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Choudhary, Shashi Bhushan, Suresh Chandra Gurjar, Binay Kumar Singh, et al. "Morphology and genic-SSRs-based diversity analysis and georeferencing of economic traits in natural populations of Jack (Artocarpus heterophyllus Lam.) from Eastern India." Scientia Horticulturae 295 (March 2022): 110852. http://dx.doi.org/10.1016/j.scienta.2021.110852.

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Singh, Binay K., Shashi Bhushan Choudhary, Sushma Yadav, et al. "Genetic structure identification and assessment of interrelationships between Brassica and allied genera using newly developed genic-SSRs of Indian Mustard ( Brassica juncea L.)." Industrial Crops and Products 113 (March 2018): 111–20. http://dx.doi.org/10.1016/j.indcrop.2018.01.023.

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Rukmangada, M. S., R. Sumathy, and Vorkady Girish Naik. "Functional annotation of mulberry (Morus spp.) transcriptome, differential expression of genes related to growth and identification of putative genic SSRs, SNPs and InDels." Molecular Biology Reports 46, no. 6 (2019): 6421–34. http://dx.doi.org/10.1007/s11033-019-05089-8.

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Liu, Xiaofeng, Junjia Luo, Mingke Zhang, et al. "Phylogenomic Analysis of Two Species of Parasenecio and Comparative Analysis within Tribe Senecioneae (Asteraceae)." Diversity 15, no. 4 (2023): 563. http://dx.doi.org/10.3390/d15040563.

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The genus of Parasenecio (Senecioneae) comprises about 70 species of high medicinal value. In this study, the plastomes of Parasenecio palmatisectus and P. latipes were newly sequenced using high-throughput sequencing technology and compared with those of eight other species in Senecioneae. The complete chloroplast (cp) genomes were 151,185 bp in P. latipes with 37.5% GC and 151,263 bp in P. palmatisectus with 37.5% GC. We predicted 133 genes, including 37 tRNA genes, 86 protein-coding genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). A comparative genomic analysis showed that the compl

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Bhad, Poonam G., Suvendu Mondal, and Anand M. Badigannavar. "Genetic diversity in groundnut (Arachis hypogaea L.) genotypes and detection of marker trait associations for plant habit and seed size using genomic and genic SSRs." Journal of Crop Science and Biotechnology 19, no. 3 (2016): 203–21. http://dx.doi.org/10.1007/s12892-016-0060-1.

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Kim, Hyun Jung, Jungsu Jung, Myung-Shin Kim, Je Min Lee, Doil Choi, and Inhwa Yeam. "Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum." Genome 58, no. 10 (2015): 441–51. http://dx.doi.org/10.1139/gen-2015-0017.

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Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First,

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Ramesh, S. V., K. B. Hebbar, M. K. Rajesh, P. Abhin Sukumar, K. P. Gangaraj, and Athul Bobby. "Transcriptome Analysis of Cocos nucifera L. Seedlings Having Contrasting Water-Use Efficiency (WUE) under Water-Deficit Stress: Molecular Insights and Genetic Markers for Drought Tolerance." Biology and Life Sciences Forum 4, no. 1 (2020): 73. http://dx.doi.org/10.3390/iecps2020-08853.

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Perennials utilize complex adaptive strategies and molecular mechanisms to cope with water-deficit conditions. Hence, in order to gain molecular insights regarding water-deficit stress, two-year-old coconut seedlings of the varieties Kalpa Sree and Kalpatharu were subjected to soil water-deficit regimes (25% of available of soil moisture and control). The biochemical, physiological and growth parameters underlying water-deficit stress revealed the differential enzymatic anti-oxidants, lipid peroxidation status and water use efficiency traits between the genotypes investigated. The entire plant

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Al-Qurainy, Fahad, Aref Alshameri, Abdel-Rhman Gaafar, et al. "Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop." International Journal of Genomics 2019 (October 8, 2019): 1–14. http://dx.doi.org/10.1155/2019/7295859.

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The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina

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Evangelistella, Chiara, Alessio Valentini, Riccardo Ludovisi, et al. "De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock." Biotechnology for Biofuels 10, no. 1 (2017): 138. https://doi.org/10.1186/s13068-017-0828-7.

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<strong>Background: </strong> <i>Arundo donax</i> has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.<strong>Results: </strong>We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the <i>A. donax</i> leaf transcriptome. The s

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Kutlu, Imren, Sadettin Çelik, Yaşar Karaduman, and Özcan Yorgancılar. "Phenotypic and genetic diversity of doubled haploid bread wheat population and molecular validation for spike characteristics, end-use quality, and biofortification capacity." PeerJ 11 (June 9, 2023): e15485. http://dx.doi.org/10.7717/peerj.15485.

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Increasing grain quality and nutritional value along with yield in bread wheat is one of the leading breeding goals. Selection of genotypes with desired traits using traditional breeding selection methods is very time-consuming and often not possible due to the interaction of environmental factors. By identifying DNA markers that can be used to identify genotypes with desired alleles, high-quality and bio-fortified bread wheat production can be achieved in a short time and cost-effectively. In the present study, 134 doubled haploid (DH) wheat lines and their four parents were phenotypically ev

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Li, Xiaoying, Hongxia Xu, Jianjun Feng, and Junwei Chen. "Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat." Journal of the American Society for Horticultural Science 139, no. 5 (2014): 507–17. http://dx.doi.org/10.21273/jashs.139.5.507.

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Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pa

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Varshney, R. K., U. Hähnel, T. Thiel, et al. "Genetic and Physical Mapping of Genic Microsatellites in Barley (Hordeum vulgare L.)." Czech Journal of Genetics and Plant Breeding 41, No. 4 (2011): 153–59. http://dx.doi.org/10.17221/3661-cjgpb.

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Due to the availability of sequence data from large-scale EST (expressed sequence tag) projects, it has become feasible to develop microsatellite or simple sequence repeat (SSR) markers from genes. A set of 111&nbsp;090 barley ESTs (corresponding to 55.9 Mb of sequence) was employed for the identification of microsatellites with the help of a PERL5 script called MISA. As a result, a total of 9 564 microsatellites were identified in 8 766 ESTs (SSR-ESTs). Cluster analysis revealed the presence of 2 823 non-redundant SSR-ESTs in this set. From these 754&nbsp;primer pairs were designed an

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Khlestkina, Elena K., Rajeev K. Varshney, Marion S. Röder, Andreas Graner, and Andreas Börner. "A comparative assessment of genetic diversity in cultivated barley collected in different decades of the last century in Austria, Albania and India by using genomic and genic simple sequence repeat (SSR) markers." Plant Genetic Resources 4, no. 2 (2006): 125–33. http://dx.doi.org/10.1079/pgr2006109.

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Molecular investigations of qualitative and quantitative changes in the genetic diversity of cultivated crops are useful for plant breeding and the management of crop genetic resources. A genotyping study, based on 28 genomic (g-SSR) and 13 expressed sequence tag-derived (e-SSR) microsatellite markers uniformly distributed across the barley genome, was conducted on samples of cultivated barley (Hordeum vulgare L.) collected at intervals of 40–50 years in three comparable geographical regions in Austria, Albania and India. The analysis indicated an absence of any significant differences either

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Zhao, Meiqi, Guoping Shu, Yanhong Hu, Gangqiang Cao, and Yibo Wang. "Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09156-0.

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Abstract Background Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers. The genome-wide distribution and polymorphism of SSRs are not well studied due to the lack of high-quality genome DNA sequence data. Results In this study, using data from high-quality de novo-sequenced maize genomes of five representative maize inbred lines, we revealed that SSRs were more densely present in telomeric regio

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Karcı, Harun. "Development of Novel Genic SSR Markers and Their Transferability Across the Genus Pistacia Species and Comparison of In Silico Genomic SSRs and Genic SSRs in Pistachio." Plant Molecular Biology Reporter, September 28, 2023. http://dx.doi.org/10.1007/s11105-023-01409-2.

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Singh, Akshay, Ajay Kumar Mahato, Avantika Maurya, et al. "Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics." Frontiers in Plant Science 14 (June 28, 2023). http://dx.doi.org/10.3389/fpls.2023.1203855.

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Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs

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Zhong, Huaming, Xuan Shao, Jing Cao, et al. "Comparison of the Distribution Patterns of Microsatellites Across the Genomes of Reptiles." Ecology and Evolution 14, no. 11 (2024). http://dx.doi.org/10.1002/ece3.70458.

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ABSTRACTMicrosatellites or simple sequence repeats (SSRs) are prevalent across various organisms' genomes. However, their distribution patterns and evolutionary dynamics in reptile genomes are rarely studied systematically. We herein conducted a comprehensive analysis of SSRs in the genomes of 36 reptile species. Our findings revealed that the total number of SSRs ranged from 1,840,965 to 7,664,452, accounting for 2.16%–8.19% of the genomes analyzed. The relative density ranged from 21,567.82 to 81,889.41 bp per megabase (Mbp). The abundance of different SSR categories followed the pattern of

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Pérez-Luna, Adriana Isabel, Guillermo Calderón-Zavala, Martha Hernández-Rodríguez, Ángel Villegas-Monter, and Salvador Pérez-González. "GENETIC DIVERSITY OF Prunus persica (L.) Batsch AND THER SPECIES OF Prunus USING MICROSATELLITES." Agrociencia, December 18, 2024, 1–14. https://doi.org/10.47163/agrociencia.v58i8.3092.

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Mexico has three genetic breeding programs for peaches and nectarines (Prunus persica (L.) Batsch). The diversity of its germplasm at a DNA level is unknown. Therefore, the aims of this work were: 1) to characterize the diversity of three P. persica populations using microsatellites or simple sequence repeats (SSRs); 2) to genetically compare two P. persica populations from the Prunus breeding programs of the College of Postgraduates and the Center for Genetic Resources and Improvement; and 3) to extrapolate the use of these SSRs to other Prunus species. DNA was extracted from leaves of 162 in

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Dhaka, Namrata, Arundhati Mukhopadhyay, Kumar Paritosh, Vibha Gupta, Deepak Pental, and Akshay K. Pradhan. "Identification of genic SSRs and construction of a SSR-based linkage map in Brassica juncea." Euphytica 213, no. 1 (2016). http://dx.doi.org/10.1007/s10681-016-1814-z.

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Sihag, Pooja, Vijeta Sagwal, Anuj Kumar, et al. "Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding." Frontiers in Genetics 12 (July 28, 2021). http://dx.doi.org/10.3389/fgene.2021.699420.

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A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR mark

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Desai, Hiral, Rasmieh Hamid, Zahra Ghorbanzadeh, et al. "Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-00100-4.

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AbstractLittle millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority

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Kapoor, Bhuvnesh, Megha Sharma, Rajnish Sharma, et al. "De novo transcriptome profiling and development of novel secondary metabolites based genic SSRs in medicinal plant Phyllanthus emblica L. (Aonla)." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-44317-x.

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AbstractPhyllanthus emblica (Aonla, Indian Gooseberry) is known to have various medicinal properties, but studies to understand its genetic structure are limited. Among the various secondary metabolites, ascorbic acid, flavonoids, terpenoids, phenols and tannins possess great potential for its pharmacological applications. Keeping this consideration, we assembled the transcriptome using the Illumina RNASeq500 platform, generating 39,933,248 high-quality paired-end reads assembled into 1,26,606 transcripts. A total of 87,771 unigenes were recovered after isoforms and unambiguous sequences delet

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Ahmadi, Ahmad Jawid, and Assadollah Ahmadikhah. "Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues." Frontiers in Plant Science 13 (November 17, 2022). http://dx.doi.org/10.3389/fpls.2022.991107.

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Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional fea

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