Detecting seed purity of wheat varieties using microsatellite markers based on eliminating the influence of non-homozygous loci

Wang, L.X.; Liu, L.H.; Zhang, F.T.; Liu, H.B.; Pang, Bin-Shuang; Zhao, Chang Ping

doi:10.15258/sst.2014.42.3.07

Cited by 8 publications

(9 citation statements)

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“…However, double peaks or double bands for a locus are not only the result of contaminant plants, but also represent non-homozygous loci. That's why we propose isolating individual plant DNA from a varietal sample and to comparing genotypes at 10 or 30 loci among the individuals in order to identify and eliminate contaminants from the sample (Wang et al 2014b). A bulk sample lacking contaminants is suitable for variety testing.…”

Section: Verification Of Procedures Feasibilitymentioning

confidence: 99%

“…The criteria and methods used to distinguish individual contaminant genotypes from non-homozygous SSR loci were previously described in detail (Wang et al 2014b).…”

Section: Distinguishing Contaminant Genotypes From Non-homozygous Ssrmentioning

confidence: 99%

“…In addition, the genotype of contaminants and the non-homozygous loci of the variety tested will reduce the accuracy of the molecular profile on distinctness testing. A locus with two homozygous genotypes (alleles) among individuals of a variety (assuming no contaminants) was regarded as a non-homozygous locus (Wang et al 2014a(Wang et al , 2014b. A non-homozygous locus arises from a residual heterozygote of a self-pollinating plant variety, and causes inter-plant genotypic differences within a variety.…”

Section: Introductionmentioning

confidence: 99%

“…As a wheat variety testing laboratory, we have been working since 2005 to develop a method for testing the distinctness of wheat varieties with SSR markers for a large collection of samples taken from the national winter wheat [键入文字] 4 regional trials. We have established methods to distinguish contaminants and non-homozygous loci as well as to represent each homozygous locus genotype with a pair of two-digit codes and each non-homozygous locus as two different genotypic characters (Wang et al 2014a(Wang et al , 2014b. This paper describes the criteria and technical procedures for the assessment of wheat variety distinctness using SSR markers in detail.…”

Section: Introductionmentioning

confidence: 99%

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Assessment of wheat variety distinctness using SSR markers

Wang

Qiu²,

Chang

et al. 2015

Journal of Integrative Agriculture

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Assessment of variety distinctness is important for both the registration and the protection of particular variety. However, the current testing system, which assesses a range of morphological characters of each pair of varieties grown side-by-side, is time consuming and is not suitable for the assessment of hundreds of samples. The objective of this study was to develop a procedure for the assessment of wheat variety distinctness using simple sequence repeat (SSR) markers. A comparison between the molecular and morphological profile of 797 varieties was made. On the basis of the comparison, pairs of varieties with a genetic similarity value (GSV) ≤ 90% were deemed to be distinct, accounting for ~85% of varieties assessed in wheat regional trials. For the remaining ~15% of varieties, GSVs between different varieties were > 90%, among which ~35% were not distinct and the other ~65% were distinct. Therefore, if given a GSV > 90%, the pairs of varieties should be morphologically assessed in the field. To avoid any errors in the assessments, we proposed the elimination of contaminant plants from the sample before comparing the varietal genotypes, scoring of the genotype at each locus with a pair of allele numbers when constructing a molecular profile, and faithfully recording two alleles at a non-homozygous locus. To reduce the workload and cost, a three-grade markers comparison among varieties is suggested. In addition, 80 SSR markers and a technical procedure for assessment of wheat variety distinctness have been proposed. Based on the procedure, the distinctness assessment of ~85% of all wheat varieties is completed in our laboratory annually. Consequently, total field assessment has been reduced considerably.

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Section: Verification Of Procedures Feasibilitymentioning

confidence: 99%

“…The criteria and methods used to distinguish individual contaminant genotypes from non-homozygous SSR loci were previously described in detail (Wang et al 2014b).…”

Section: Distinguishing Contaminant Genotypes From Non-homozygous Ssrmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Assessment of wheat variety distinctness using SSR markers

Wang

Qiu²,

Chang

et al. 2015

Journal of Integrative Agriculture

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“…Globally there are large number of varieties and such varietal differentiation also requires whole genome scanning of SSRs in order to get polymorphic markers. Molecular markers are also required for wheat seed purity testing and differentiation of hybrids (Wang et al, 2014a ).…”

Section: Introductionmentioning

confidence: 99%

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management

et al. 2017

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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.

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