est-ssr marker

Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes...

Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C...

The present investigation was conducted to assess the nutritional diverseness and identify novel genetic resources to be utilized in chickpea breeding for macro and micro nutrients. The plants were grown in randomized block design. Nutritional and phytochemical properties of nine chickpea genotypes were estimated. The EST sequences from NCBI database were downloaded in FASTA format, clustered into contigs using CAP3, mined for novel SSRs using TROLL analysis and primer pairs were designed using Primer 3 software...

Curcuma aeruginosa Roxb. is an Indonesian traditional medicinal plant of the Zingiberaceae family. C. aeruginosa is known to have anticancer activity, especially in the rhizomes. Despite many studies on the phytochemical content of this plant with antioxidant and anticancer activity, transcriptomic studies are still limited in terms of genetic information. We ran transcriptome of Curcuma aeruginosa using a paired-end Illumina NextSeq 550 with PE150 mode and generating 12.8 GB of raw data. Raw reads have been filed with NCBI under project number PRJNA918644...

INTRODUCTION: Sclerotium rolfsii Sacc . is a globally dispersed pathogenic fungus that causes southern blight disease in many crops and Chinese herbal medicine. The high degree of variation and diversity in the fungi altered population genetic structure. Therefore, the important factors of variation within the pathogen population should be considered during the development of management strategies for the disease. METHODS: In this study, S. rolfsii isolates from 13 hosts in 7 provinces of China were collected and analyzed to identify their morphological features and perform molecular characterization...

BACKGROUND: Anopheles darlingi is a monotypic species in terms of its morphological, genetic, and behavioral aspects and is the primary transmitter of human malaria (99%) in Brazil, especially in the Brazilian Amazon. In this pioneering study, 15 expressed sequence tag (EST)-simple sequence repeat (SSR) markers were obtained and characterized in samples from the municipality of São Gabriel da Cachoeira, Amazonas state, Brazil, with polymorphisms that can be used for further genetic research...

UNLABELLED: Radish ( Raphanus sativus L.), an important annual or biennial root vegetable crop, is widely cultivated in the world for its high nutritive value. Isolated microspore culture (IMC) is one of the most effective methods for rapid development of homozygous lines. Due to imperfection of the IMC technology system, it is particularly important to establish an efficient IMC system in radish. In this study, the effects of different factors on radish microspore embryogenesis were investigated with 23 genotypes...

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A...

Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2...

In this study, the genetic diversity and population structure of 4 wild ancient tea tree (Camellia taliensis) populations at different altitudes (2,050, 2,200, 2,350, and 2,500 m) in Qianjiazhai Nature Reserve, Zhenyuan country, Yunnan province, were investigated using EST-SSR molecular markers to compare their genetic variation against altitude. In total, 182 alleles were detected across all loci, ranging from 6 to 25. The top one informative SSR was CsEMS4 with polymorphism information content (PIC) of 0...

BACKGROUND: The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state...

Evaluating the contributions of geographic distance and environmental heterogeneity to the genetic divergence can inform the demographic history and responses to environmental change of natural populations. The isolation-by-distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation-by-environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations. Here, we sampled and genotyped 330 individuals from 18 natural populations of Cephalotaxus oliveri throughout the species' distribution...

Wheat stripe rust is a destructive disease in many cool and temperate regions around the world. Exploiting novel sources of resistance can provide wheat cultivars with robust and durable resistance to stripe rust. The wheat- Thinopyrum intermedium addition line TAI-14 was proven to carry a stripe rust resistance gene (named as YrT14 ) on the alien Th. intermedium chromosome. In order to transfer the resistance gene to wheat, wheat- Th. intermedium translocation lines were created by irradiating the pollen of the line TAI-14...

Tropical lotus ( Nelumbo ) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively...

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano ( Origanum vulgare L. ssp. hirtum ), common oregano ( O. vulgare L. ssp. vulgare ), and sweet marjoram ( O. majorana L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0...

BACKGROUND: Elymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures. RESULTS: We obtained 9...

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum . SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species...

The development of high-throughput sequencing technology has made it possible to develop molecular markers such as EST-SSR from transcriptome sequences in non-model plants such as bulbous flowers. However, the EST-SSR markers that have been developed are weakly validated and low polymorphic due to the short read size and poor quality of the assembled sequences. This study therefore used the CandiSSR pipeline to identify 550 potential polymorphic SSR loci among 487 homologous unigenes based on the transcriptomic sequences of three varieties of colored calla lily, and 460 of these loci with appropriate flanking sequences were suitable for primer pairs design...

BACKGROUND: Lilium genus consists of approximately 100 species and numerous varieties, many of which are interspecific hybrids, which result in a complicated genetic background. The germplasm identification, genetic relationship analysis, and breeding of Lilium rely on exploiting genetic information among different accessions. Hence, an attempt was made to develop new EST-SSR markers and study the molecular divergence among 65 genotypes of Lilium. METHODS AND RESULTS: A total of 5509 EST-SSRs were identified from the high-throughput sequencing database of L...

Micro-RNAs (mi-RNAs) are regulatory elements that play a vital role in the growth, development, and metabolic regulation of plants. In current research, the isolation of miRNAs is a tedious and difficult task using in vitro methods. However, recent exploration into the remarkably highly conserved nature of nucleotide sequences of miRNAs assists in the identification of miRNAs in plant species through homologous approaches. Here, we describe the in silico-based method for identification of miRNAs from the EST database which is emerging as a faster and more reliable approach along with the development of miRNA-SSR markers...