Read by QxMD icon Read

est-ssr marker

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
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
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
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')...
September 8, 2016: Molecular Genetics and Genomics: MGG
Xin Yin, Yunqiang Yang, Yongping Yang
PREMISE OF THE STUDY: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using Illumina sequencing for further genetic diversity studies of Stipa purpurea (Poaceae). METHODS AND RESULTS: Twenty-nine polymorphic and eight monomorphic EST-SSR loci were developed and characterized in 90 individuals from nine S. purpurea populations. The number of alleles per locus ranged from two to 13, and heterozygosity within populations and total heterozygosity ranged from 0...
August 2016: Applications in Plant Sciences
Shanshan Zhu, Yanqian Ding, Zhaoyan Yap, Yingxiong Qiu
Lindera glauca (Lauraceae) is an economically important East Asian forest tree characterized by a dioecy in China and apomixis in Japan. However, patterns of population genetic diversity and structure of this species remain unknown for this species due to a lack of efficient molecular markers. In this study, we employed Illumina sequencing to analyze the transcriptomes of the female and male flower buds of L. glauca. We retrieved 59,753 and 75,075 unigenes for the female and male buds, respectively. Based on sequence similarity, 44,379 (74...
November 2016: Molecular Biology Reports
A W Gichira, Z C Long, Q F Wang, J M Chen, K Liao
Isoëtes sinensis is a critically endangered quillwort. To facilitate studies on the conservation genetics of this species, we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 50,063 unigenes were predicted by transcriptome sequencing, 5294 (10.6%) of which significantly matched 3011 Gene Ontology annotations and 2363 were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways. Most of these (2297) were involved in metabolism. A total of 1982 SSR motifs were identified, with trinucleotides being the dominant repeat motif, and 1438 (72...
2016: Genetics and Molecular Research: GMR
Marina Arias, Monica Hernandez, Naroa Remondegui, Koen Huvenaars, Peter van Dijk, Enrique Ritter
Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers...
2016: Scientific Reports
Rakesh Singh, Rajesh Kumar, Ajay Kumar Mahato, Ritu Paliwal, Amit Kumar Singh, Sundeep Kumar, Soma S Marla, Ashok Kumar, Nagendra K Singh
Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified...
September 2016: Functional & Integrative Genomics
Haibin Wu, Xiaoli He, Hao Gong, Shaobo Luo, Mingzhu Li, Junqiu Chen, Changyuan Zhang, Ting Yu, Wangping Huang, Jianning Luo
The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L...
2016: Frontiers in Plant Science
Landi Luo, Pin Zhang, Xiaokun Ou, Yupeng Geng
PREMISE OF THE STUDY: Tithonia diversifolia (Asteraceae) is an invasive plant species that can outcompete natives and thus poses a great threat to biodiversity in introduced areas. Here, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized. METHODS AND RESULTS: Sixteen polymorphic microsatellite loci were isolated from T. diversifolia using transcriptome sequencing and bioinformatic screening. The number of alleles per locus varied from two to four alleles in 48 individuals from three populations...
July 2016: Applications in Plant Sciences
Karim Sorkheh, Angela S Prudencio, Azim Ghebinejad, Mehrana Kohei Dehkordi, Deniz Erogul, Manuel Rubio, Pedro Martínez-Gómez
BACKGROUND: Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions. RESULTS: A total of 316 SSRs were identified using MISA software...
2016: BMC Research Notes
Shangguo Feng, Renfeng He, Jiangjie Lu, Mengying Jiang, Xiaoxia Shen, Yan Jiang, Zhi'an Wang, Huizhong Wang
Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12...
2016: Frontiers in Genetics
Naoko Ishikawa, Shota Sakaguchi, Motomi Ito
PREMISE OF THE STUDY: Simple sequence repeat (SSR) markers were developed for Aster savatieri (Asteraceae) and the serpentine variety A. savatieri var. pygmaeus to re-evaluate their taxonomic status. METHODS AND RESULTS: Using RNA-Seq data, 22 expressed sequence tag (EST)-SSR markers were developed. Polymorphisms were assessed in A. savatieri and in A. savatieri var. pygmaeus. The average number of alleles ranged from four to 15, and expected heterozygosity ranged from 0...
June 2016: Applications in Plant Sciences
Shamshad Ul Haq, Pradeep Kumar, R K Singh, Kumar Sambhav Verma, Ritika Bhatt, Meenakshi Sharma, Sumita Kachhwaha, S L Kothari
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA)...
2016: Genetics Research International
Q Z Wang, M Huang, S R Downie, Z X Chen
Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37...
2016: Genetics and Molecular Research: GMR
Weicong Qi, Feng Lin, Yuhe Liu, Bangquan Huang, Jihua Cheng, Wei Zhang, Han Zhao
BACKGROUND: The allohexaploid Crambe abyssinica (crambe) is an oilseed crop that has been recognized for its potential value in the chemical industry, particularly in terms of producing high-erucic acid content vegetable oil. However, as an understudied crop, improvement of crambe has been hampered by the lack of genetic and genomic information to enhance its yield, oil quality and resistance against biotic and abiotic stress. Development of molecular markers is therefore of great significance to facilitate genetic improvement of crambe...
2016: BMC Plant Biology
Li Huang, Bei Wu, Jiaojiao Zhao, Haitao Li, Weigang Chen, Yanli Zheng, Xiaoping Ren, Yuning Chen, Xiaojing Zhou, Yong Lei, Boshou Liao, Huifang Jiang
Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data...
2016: PloS One
Sathaporn Chotechung, Prakit Somta, Jinbing Chen, Tarika Yimram, Xin Chen, Peerasak Srinives
The Br locus confers bruchid resistance in mungbean; VrPGIP2 (encoding a polygalacturonase inhibitor) is a strong candidate gene for this resistance. The VrPGIP2 sequence differs between resistant and susceptible lines. Azuki bean weevil (Callosobruchus chinensis) and cowpea weevil (Callosobruchus maculatus) are serious insect pests of mungbean during storage. Bruchid resistance in mungbean is controlled by a single dominant locus, Br. Although the Br locus has been located on a genetic map, molecular basis and function of the gene remain unknown...
September 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
G F Pena, A T do Amaral, R M Ribeiro, H C C Ramos, M S B Boechat, J S Santos, G S Mafra, S H Kamphorst, V J de Lima, M Vivas, G A de Souza Filho
Molecular markers are a useful tool for identification of complementary heterotic groups in breeding programs aimed at the production of superior hybrids, particularly for crops such as popcorn in which heterotic groups are not well-defined. The objective of the present study was to analyze the genetic diversity of 47 genotypes of tropical popcorn to identify possible heterotic groups for the development of superior hybrids. Four genotypes of high genetic value were studied: hybrid IAC 125, strain P2, and varieties UENF 14 and BRS Angela...
2016: Genetics and Molecular Research: GMR
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"