Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management
نویسندگان
چکیده
Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.
منابع مشابه
Assessing genetic diversity of promising wheat (Triticum aestivum L.) lines using microsatellite markers linked with salinity tolerance
Narrow genetic variability may lead to genetic vulnerability of field crops against biotic and abiotic stresses which can cause yield reduction. In this study a set of 37 wheat microsatellite markers linked with identified QTLs for salinity tolerance were used for the assessment of genetic diversity for salinity in 30 promising lines of hexaploid bread wheat (Triticum aestivum L.). A total of 4...
متن کاملAssessment of genetic diversity and identification of SSR markers associated with grain iron content in Iranian prevalent wheat genotypes
Iron is one of the most important nutrients in the human diet. According to the high consumption of staple foods such as wheat, the deficiency of iron in these crops would lead to nutritional disorders and related complications. To identify microsatellite markers associated with wheat grain iron content,38Iranian prevalent wheat genotypes were assessed using 30 pairs of genomic and EST microsat...
متن کاملApplication of Random Amplified Microsatellite Polymorphism (RAMP) in Prunus Characterization and Mapping
Random amplified microsatellite polymorphism (RAMP) is a PCR-based marker which uses a combination of two classes of markers: Simple sequence repeat (SSR) and Random amplified DNA polymorphism (RAPD) markers. RAMP has been demonstrated to be a potentially valuable molecular marker for the study of genetic relationships in cultivated plant species. The objective of this study was to optimize the...
متن کاملGenotyping common SNP and a microsatellite sequence closely linked to waxy gene in rice by DNA based markers
The potential of different DNA based molecular markers was examined for the detection of single nucleotide polymorphism (SNP) in the waxy gene and a microsatellite (SSR) sequence closely linked to it in a collection of rice varieties. DNA was extracted from leaf samples of 68 different rice cultivars by the CTAB method and specific primers were designed for the amplification of waxy gene and SS...
متن کاملWheat and barley seed system in Syria: farmers, varietal perceptions, seed sources and seed management
A total of 206 wheat and 200 barley farmers were interviewed in northeastern Syria to understand farmer perceptions and practice relating to modern varieties, seed sources and seed quality. Wheat farmers had better awareness and grew modern varieties (87%), applied fertilizers (99.5%), herbicides (93%), seed treatment (90%) or insecticides (41%). In contrast barley growers had low awareness (36...
متن کامل