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https://www.readbyqxmd.com/read/28529834/development-and-characterization-of-est-ssr-markers-for-begonia-luzhaiensis-begoniaceae
#1
Yu-Hsin Tseng, Han-Yau Huang, Wei-Bin Xu, Hsun-An Yang, Yan Liu, Ching-I Peng, Kuo-Fang Chung
PREMISE OF THE STUDY: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. METHODS AND RESULTS: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28526937/molecular-confirmation-of-intraspecific-tomato-solanum-lycopersicum-hybrids-and-their-evaluation-against-late-blight-and-cucumber-mosaic-virus
#2
Amjad Hameed, Muhammad Yussouf Saleem, Khalid Pervaiz Akhtar, Muhammad Shoaib, Qumer Iqbal, Muhammad Asghar
Tomato is one of the most consumed vegetables in the world. Diseases are the number one concern in the development of high-yield and disease-resistant tomato hybrids which is the foremost priority of breeders. Present study was conducted (1) to develop DNA-based markers for genetic confirmation of tomato F1 hybrids, (2) to utilize sequenced characterized amplified region (SCAR) marker linked to the Ph-3 gene for Phytophthora infestans resistance in tomato and (3) to evaluate male and female parental genotypes and their F1 hybrids against late blight (LB) and cucumber mosaic virus (CMV)...
May 19, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28510247/characterization-and-development-of-56-est-ssr-markers-derived-from-the-transcriptome-of-odontobutis-potamophila
#3
P P Wang, M Ren, S Q Chen, S W Yin, C Zhao, H Y Zhang, X R Li, Q Q Cao, G Q Zhou
Expressed sequence tags (ETSs) are the sources of microsatellite development. In this study, we isolated and characterized microsatellite markers for Odontobutis potamophila by using Illumina RNA-sequencing. We sequenced a large number of ESTs and screened 200 potential microsatellites. Consequently, a total of 56 novel polymorphic microsatellite repeat markers were identified in thirty-two individuals from a wild population area (Jiande, Zhejiang Province, China). The number of alleles per locus varied from two to eight, the observed heterozygosity (HO) ranged from 0...
May 10, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28500405/est-ssr-marker-revealed-effective-over-biochemical-and-morphological-scepticism-towards-identification-of-specific-turmeric-curcuma-longa-l-cultivars
#4
Ambika Sahoo, Sudipta Jena, Basudeba Kar, Suprava Sahoo, Asit Ray, Subhashree Singh, Raj Kumar Joshi, Laxmikanta Acharya, Sanghamitra Nayak
Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28493955/molecular-diversity-analysis-drought-related-marker-traits-association-mapping-and-discovery-of-excellent-alleles-for-100-day-old-plants-by-est-ssrs-in-cassava-germplasms-manihot-esculenta-cranz
#5
Bin Wang, Xin Guo, Pingjuan Zhao, Mengbin Ruan, Xiaoling Yu, Liangping Zou, Yiling Yang, Xiao Li, Deli Deng, Jixiang Xiao, Yiwei Xiao, Chunji Hu, Xue Wang, Xiaolin Wang, Wenquan Wang, Ming Peng
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2...
2017: PloS One
https://www.readbyqxmd.com/read/28489870/new-gssr-and-est-ssr-markers-reveal-high-genetic-diversity-in-the-invasive-plant-ambrosia-artemisiifolia-l-and-can-be-transferred-to-other-invasive-ambrosia-species
#6
Lucie Meyer, Romain Causse, Fanny Pernin, Romain Scalone, Géraldine Bailly, Bruno Chauvel, Christophe Délye, Valérie Le Corre
Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species...
2017: PloS One
https://www.readbyqxmd.com/read/28481399/analysis-of-genetic-diversity-of-leuciscus-leuciscus-baicalensis-using-novel-microsatellite-markers-with-cross-species-transferability
#7
D J Lei, G Zhao, P Xie, Y Li, H Yuan, M Zou, J G Niu, X F Ma
We used next-generation sequencing technology to characterize 19 genomic simple sequence repeat (SSR) markers and 11 expressed sequence tag (EST) SSR markers from Leuciscus leuciscus baicalensis, a small freshwater fish that is widely distributed in Xinjiang, China. Primers were used to test for polymorphisms in three L. leuciscus baicalensis populations in Xinjiang. There were 4-27 (average 11.3) alleles (NA), the expected heterozygosity (HE) was 0.36-0.94 (average 0.75 ± 0.14), the observed heterozygosity (HO) was 0...
May 4, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28477044/bayesian-qtl-mapping-using-genome-wide-ssr-markers-and-segregating-population-derived-from-a-cross-of-two-commercial-f1-hybrids-of-tomato
#8
Akio Ohyama, Kenta Shirasawa, Hiroshi Matsunaga, Satomi Negoro, Koji Miyatake, Hirotaka Yamaguchi, Tsukasa Nunome, Hiroyoshi Iwata, Hiroyuki Fukuoka, Takeshi Hayashi
Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations...
May 5, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28465169/genetic-diversity-and-population-structure-of-indigofera-szechuensis-complex-fabaceae-based-on-est-ssr-markers
#9
Li-Na Guo, Xin-Fen Gao
Indigofera, the third largest genus of Fabaceae, comprises approximately 750 species worldwide with a pantropical distribution. Eight Indigofera species, namely I. calcicola, I. delavayi, I. franchetii, I. hancockii, I. lenticellata, I. pendula, I. rigioclada, and I. szechuensis, are considered a species complex because of their morphological similarities and the phylogenetic analysis based on Internal Transcribed Spacer (ITS). Small populations of these species are allopatrically distributed in Hengduan Mountains in China...
April 29, 2017: Gene
https://www.readbyqxmd.com/read/28457942/identification-and-characterization-of-simple-sequence-repeats-ssrs-for-population-studies-of-puccinia-novopanici
#10
Gabriela K Orquera-Tornakian, Patricia Garrido, Brent Kronmiller, Robert Hunger, Brett M Tyler, Carla D Garzon, Stephen M Marek
Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P...
April 27, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28439477/development-and-characterization-of-est-ssr-markers-in-stipa-breviflora-poaceae
#11
Jing Ren, Zhi-Zhen Su, Zhen-Hua Dang, Yu Ding, Pei-Xuan Wang, Jian-Ming Niu
PREMISE OF THE STUDY: Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. METHODS AND RESULTS: A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism...
April 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28435133/de-novo-comparative-transcriptome-analysis-of-genes-involved-in-fruit-morphology-of-pumpkin-cultivars-with-extreme-size-difference-and-development-of-est-ssr-markers
#12
Aliki Xanthopoulou, Ioannis Ganopoulos, Fotis Psomopoulos, Maria Manioudaki, Theodoros Moysiadis, Aliki Kapazoglou, Maslin Osathanunkul, Sofia Michailidou, Apostolos Kalivas, Athanasios Tsaftaris, Irini Nianiou-Obeidat, Panagiotis Madesis
The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28337393/development-and-validation-of-est-ssr-markers-for-fokienia-hodginsii-cupressaceae
#13
Mingyan Ding, Kaikai Meng, Qiang Fan, Weizheng Tan, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Fokienia hodginsii (Cupressaceae) is a Tertiary relict evergreen conifer of the monotypic genus Fokienia. Polymorphic microsatellite markers were developed to investigate its genetic diversity and population structure. METHODS AND RESULTS: RNA transcripts of F. hodginsii were sequenced and de novo assembled into 85,818 unigenes, and 1892 simple sequence repeat (SSR) markers were detected from the unigenes. A total of 273 expressed sequence tag-SSR primer pairs were designed and tested, and 129 successfully amplified...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#14
Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jeong-Gwan Ham, Il Kyung Chung, Kyung-Min Kim
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28289556/molecular-characterization-and-genetic-diversity-of-jatropha-curcas-l-in-costa-rica
#15
Marcela Vásquez-Mayorga, Eric J Fuchs, Eduardo J Hernández, Franklin Herrera, Jesús Hernández, Ileana Moreira, Elizabeth Arnáez, Natalia M Barboza
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...
2017: PeerJ
https://www.readbyqxmd.com/read/28231525/construction-of-new-est-ssrs-for-fusarium-resistant-wheat-breeding
#16
Aysen Yumurtaci, Hulya Sipahi, Ayed Al-Abdallat, Abdulqader Jighly, Michael Baum
Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#17
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28188068/ssr-and-morphological-trait-based-population-structure-analysis-of-130-diverse-flax-linum-usitatissimum-l-accessions
#18
Shashi Bhushan Choudhary, Hariom Kumar Sharma, Arroju Anil Kumar, Rangappa Thimmaiah Maruthi, Jiban Mitra, Isholeena Chowdhury, Binay Kumar Singh, Pran Gobinda Karmakar
A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous...
February 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28187131/genome-size-cytogenetic-data-and-transferability-of-est-ssrs-markers-in-wild-and-cultivated-species-of-the-genus-theobroma-l-byttnerioideae-malvaceae
#19
Rangeline Azevedo da Silva, Gustavo Souza, Lívia Santos Lima Lemos, Uilson Vanderlei Lopes, Nara Geórgia Ribeiro Braz Patrocínio, Rafael Moysés Alves, Lucília Helena Marcellino, Didier Clement, Fabienne Micheli, Karina Peres Gramacho
The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized...
2017: PloS One
https://www.readbyqxmd.com/read/28155670/esap-plus-a-web-based-server-for-est-ssr-marker-development
#20
Piyarat Ponyared, Jiradej Ponsawat, Sissades Tongsima, Pusadee Seresangtakul, Chutipong Akkasaeng, Nathpapat Tantisuwichwong
BACKGROUND: Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases...
December 22, 2016: BMC Genomics
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