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https://www.readbyqxmd.com/read/28791211/development-and-characterization-of-polymorphic-est-based-ssr-markers-in-barley-hordeum-vulgare
#1
Won-Sam Jo, Hye-Yeong Kim, Kyung-Min Kim
In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28791205/development-of-est-derived-microsatellite-markers-in-the-aquatic-macrophyte-ranunculus-bungei-ranunculaceae
#2
Zhigang Wu, Jinwei Wu, Yalin Wang, Hongwei Hou
PREMISE OF THE STUDY: Microsatellite or simple sequence repeat (SSR) markers were developed to investigate the influence of ecological factors on gene flow and spatial genetic structuring of the submerged plant Ranunculus bungei (Ranunculaceae), which is regarded as an important species for understanding how plants adapt to an aquatic environment. METHODS AND RESULTS: Twenty-two microsatellite loci were identified from an expressed sequence tag (EST) library. The number of alleles per locus ranged from one to five, and the expected heterozygosity varied from 0...
July 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28769972/the-first-molecular-identification-of-an-olive-collection-applying-standard-simple-sequence-repeats-and-novel-expressed-sequence-tag-markers
#3
Soraya Mousavi, Roberto Mariotti, Luca Regni, Luigi Nasini, Marina Bufacchi, Saverio Pandolfi, Luciana Baldoni, Primo Proietti
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...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28755229/characterization-and-amplification-of-gene-based-simple-sequence-repeat-ssr-markers-in-date-palm
#4
Yongli Zhao, Manjunath Keremane, Channapatna S Prakash, Guohao He
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...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28686183/development-and-evaluation-of-a-novel-set-of-est-ssr-markers-based-on-transcriptome-sequences-of-black-locust-robinia-pseudoacacia-l
#5
Qi Guo, Jin-Xing Wang, Li-Zhuo Su, Wei Lv, Yu-Han Sun, Yun Li
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification...
July 7, 2017: Genes
https://www.readbyqxmd.com/read/28683768/extrapolative-microrna-precursor-based-ssr-mining-from-tea-est-database-in-respect-to-agronomic-traits
#6
Anjan Hazra, Nirjhar Dasgupta, Chandan Sengupta, Sauren Das
Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified...
July 6, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#7
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28630801/characterization-of-the-transcriptome-and-est-ssr-development-in-boea-clarkeana-a-desiccation-tolerant-plant-endemic-to-china
#8
Ying Wang, Kun Liu, De Bi, Shoubiao Zhou, Jianwen Shao
BACKGROUND: Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28545396/transcriptomic-resources-for-the-medicinal-legume-mucuna-pruriens-de-novo-transcriptome-assembly-annotation-identification-and-validation-of-est-ssr-markers
#9
N Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J Doyle, Ashley N Egan
BACKGROUND: The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28529834/development-and-characterization-of-est-ssr-markers-for-begonia-luzhaiensis-begoniaceae
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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...
August 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
#18
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...
August 15, 2017: Gene
https://www.readbyqxmd.com/read/28457942/identification-and-characterization-of-simple-sequence-repeats-ssrs-for-population-studies-of-puccinia-novopanici
#19
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
#20
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
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