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https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#1
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
#2
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 7, 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
#3
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
#4
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
https://www.readbyqxmd.com/read/28101438/development-and-characterization-of-est-ssr-markers-for-artocarpus-hypargyreus-moraceae
#5
Haijun Liu, Weizheng Tan, Hongbin Sun, Yu Liu, Kaikai Meng, Wenbo Liao
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. METHODS AND RESULTS: Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28094539/genetic-diversity-and-population-structure-of-castor-ricinus-communis-l-germplasm-within-the-us-collection-assessed-with-est-ssr-markers
#6
M L Wang, M Dzievit, Z Chen, J B Morris, J E Norris, N A Barkley, B Tonnis, G A Pederson, J Yu
Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations...
October 14, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27995985/de-novo-transcriptome-assembly-development-of-est-ssr-markers-and-population-genetic-analyses-for-the-desert-biomass-willow-salix-psammophila
#7
Huixia Jia, Haifeng Yang, Pei Sun, Jianbo Li, Jin Zhang, Yinghua Guo, Xiaojiao Han, Guosheng Zhang, Mengzhu Lu, Jianjun Hu
Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S...
December 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27966761/genetic-divergence-and-admixture-of-ancestral-genome-groups-in-the-sugarcane-variety-rb867515-saccharum-spp
#8
G B Maranho, R C Maranho, R Desordi, A F das Neves, C A Mangolin, M F P S Machado
We analyzed 80 plants of the sugarcane (Saccharum spp) variety 'RB867515' in order to investigate its diversity and genetic structure at the molecular level. Four simple sequence repeat (SSR) loci (UGSM51, SMC1237, SEGMS1069, and UGSM38) and five expressed sequence tag (EST)-SSR loci (ESTA68, ESTB92, ESTB145, ESTC66, and ESTC84) were used as molecular markers. The polymorphic loci rate was 66.6%. A total of 17 alleles and an average of 1.88 alleles/locus were detected. The number of alleles in the EST-SSR loci was lower than the number of alleles in the SSRs of non-expressed loci...
December 2, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27924126/utilization-of-in-silico-est-ssr-markers-for-diversity-studies-in-castor-ricinus-communis-l
#9
Ramesh Thatikunta, A Siva Sankar, J Sreelakshmi, Gouthami Palle, C Leela, Ch V Durga Rani, V Gouri Shankar, B Lavanya, P Narayana Reddy, M Y Dudhe
Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences...
October 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/27866228/fine-mapping-of-the-chromosome-5b-region-carrying-closely-linked-rust-resistance-genes-yr47-and-lr52-in-wheat
#10
Naeela Qureshi, Harbans Bariana, Kerrie Forrest, Matthew Hayden, Beat Keller, Thomas Wicker, Justin Faris, Elena Salina, Urmil Bansal
Fine mapping of Yr47 and Lr52 in chromosome arm 5BS of wheat identified close linkage of the marker sun180 to both genes and its robustness for marker-assisted selection was demonstrated. The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population to identify markers closely linked with Yr47 and Lr52...
November 19, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27833630/de-novo-transcriptome-analysis-revealed-genes-involved-in-flavonoid-and-vitamin-c-biosynthesis-in-phyllanthus-emblica-l
#11
Avneesh Kumar, Sunil Kumar, Savita Bains, Vanya Vaidya, Baljinder Singh, Ravneet Kaur, Jagdeep Kaur, Kashmir Singh
Phyllanthus emblica is an affluent source of various therapeutic components. A few of them like vitamin C and flavonoids are predominant bioactive compounds that are being used in immense pharmacological applications. In-spite of numerous applications, the genomic information of this plant was limited to a few expressed sequence tags (ESTs) in DNA databases. Herein, we developed in-depth transcriptome information of P. emblica using Illumina Hiseq 2000 platform and characterized. A total of 31,285,965 high-quality reads were assembled into 91,288 contigs with the N50 value 358...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27827007/genomic-and-transcriptomic-resources-for-marker-development-in-synchytrium-endobioticum-an-elusive-but-severe-potato-pathogen
#12
Friederike Busse, Annette Bartkiewicz, Diro Terefe-Ayana, Frank Niepold, Yvonne Schleusner, Kerstin Flath, Nicole Sommerfeldt-Impe, Jens Lübeck, Josef Strahwald, Eckhard Tacke, Hans-Reinhard Hofferbert, Marcus Linde, Jarosław Przetakiewicz, Thomas Debener
Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S...
March 2017: Phytopathology
https://www.readbyqxmd.com/read/27813587/development-and-characterization-of-novel-est-ssr-markers-and-their-application-for-genetic-diversity-analysis-of-jerusalem-artichoke-helianthus-tuberosus-l
#13
T Mornkham, P P Wangsomnuk, X C Mo, F O Francisco, L Z Gao, H Kurzweil
Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences...
October 24, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27813565/development-of-est-ssr-markers-in-the-relict-tree-davidia-involucrata-davidiaceae-using-transcriptome-sequencing
#14
Z C Long, A W Gichira, J M Chen, Q F Wang, K Liao
Davidia involucrata, reputed to be a "living fossil" in the plant kingdom, is a relict tree endemic to China. Extant natural populations are diminishing due to anthropogenic disturbance. In order to understand its ability to survive in a range of climatic conditions and to design conservation strategies for this endangered species, we developed genic simple sequence repeats (SSRs) from mRNA transcripts. In total, 142,950 contigs were assembled. Of these, 30,411 genic SSR loci were discovered and 12,208 primer pairs were designed...
October 17, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27785384/development-and-characterization-of-novel-est-ssr-markers-for-speranskia-tuberculata-euphorbiaceae
#15
Yi Fu, Miao-Miao Ju, Huan-Cheng Ma, Pei-Yao Xin, Cheng-Zhong He, Dong-Rui Jia, Bin Tian
PREMISE OF THE STUDY: The first set of expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species. METHODS AND RESULTS: In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27785382/isolation-and-identification-of-est-ssr-markers-in-chunia-bucklandioides-hamamelidaceae
#16
Kaikai Meng, Mingwan Li, Qiang Fan, Weizheng Tan, Jian Sun, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Chunia bucklandioides (Hamamelidaceae), endemic to Hainan, China, is listed as threatened in the IUCN Red List and is now only found on Mt. Diaoluo and Mt. Jianfeng. Thus, microsatellite markers were developed for future conservation genetic studies of this species. METHODS AND RESULTS: A total of 115 primers were designed on the basis of the transcriptome data of C. bucklandioides. Of them, 59 successfully amplified in C. bucklandioides and polymorphisms were detected in 11; the number of alleles per locus varied from two to five, the observed heterozygosity ranged from 0...
October 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27669004/development-and-characterization-of-genic-ssr-markers-from-indian-mulberry-transcriptome-and-their-transferability-to-related-species-of-moraceae
#17
B Mathi Thumilan, R S Sajeevan, Jyoti Biradar, T Madhuri, Karaba N Nataraja, Sheshshayee M Sreeman
Improving mulberry leaf production with enhanced leaf quality holds the key to sustain the ever increasing demand for silk. Adoption of modern genomic approaches for crop improvement is severely constrained by the lack of sufficient molecular markers in mulberry. Here, we report development and validation of 206 EST derived SSR markers using transcriptome data generated from leaf tissue of a drought tolerant mulberry genotype, Dudia white. Analysis of transcriptome data containing 10169 EST sequences, revealed 1469 sequences with microsatellite repeat motifs...
2016: PloS One
https://www.readbyqxmd.com/read/27659323/a-deep-sequencing-analysis-of-transcriptomes-and-the-development-of-est-ssr-markers-in-mungbean-vigna-radiata
#18
Changyou Liu, Baojie Fan, Zhimin Cao, Qiuzhu Su, Yan Wang, Zhixiao Zhang, Jing Wu, Jing Tian
Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3-39.8 million pairedend reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80...
September 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27635342/transcriptome-analysis-of-colored-calla-lily-zantedeschia-rehmannii-engl-by-illumina-sequencing-de-novo-assembly-annotation-and-est-ssr-marker-development
#19
Zunzheng Wei, Zhenzhen Sun, Binbin Cui, Qixiang Zhang, Min Xiong, Xian Wang, Di Zhou
Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. 'Rehmannii' using an Illumina HiSeq 2000 instrument. More than 59...
2016: PeerJ
https://www.readbyqxmd.com/read/27631966/de-novo-transcriptomic-analysis-and-development-of-est-ssr-markers-in-the-siberian-tiger-panthera-tigris-altaica
#20
Taofeng Lu, Yujiao Sun, Qin Ma, Minghao Zhu, Dan Liu, Jianzhang Ma, Yuehui Ma, Hongyan Chen, Weijun Guan
The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA')...
December 2016: Molecular Genetics and Genomics: MGG
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