DNA markers for genetic analysis of crops.

Sukhareva, Anna; Kuluev, B. R.

doi:10.31301/2221-6197.bmcs.2018-15

Cited by 12 publications

(7 citation statements)

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“…Molecular markers (DNA markers) are genetic markers analysed at the nucleotide level (Khlestkina, 2013). Their use allows to identify genetic diversity of populations, subspecies, species, allowing to effectively determine loci controlling economically valuable plant traits even at the initial stage of breeding (Sukhareva, Kuluev, 2018). Some of the most convenient DNA markers for genetic analysis are SNP markers (Khlestkina, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…Some of the most convenient DNA markers for genetic analysis are SNP markers (Khlestkina, 2013). SNP (Single-Nucleotide Polymorphism) is a single-nucleotide position in genomic DNA for which different sequence variations (alleles) occur in the population (Sukhareva, Kuluev, 2018). SNPs are widely used for allelic polymorphism studies, seed purity testing, haplotype and pedigree analyses, as well as for genotyping and construction of genetic maps.…”

Section: Introductionmentioning

confidence: 99%

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GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing

Pronozin,

Salina,

Afonnikov

2023

Vestn. VOGiS

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The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutio nary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing

Pronozin,

Salina,

Afonnikov

2023

Vestn. VOGiS

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“…Особое значение методы ДНК-типирования приобретают в работе с перекрестноопыляемыми злаковыми культурами, характеризующимися высокои� межсорто-вои� и внутрисортовои� гетерогенностью при значитель-нои� степени сходства по морфологическим признакам (Loera-Sánchez et al, 2019). Однако для успешного выполнения задач исследования необходимо учитывать преимущества и недостатки маркеров различных типов, техническую сторону проведения анализа, финансовые затраты и особенности изучаемои� культуры (Amar et al, 2011;Sukhareva, Kuluev, 2018).…”

Section: Introductionunclassified

Genetic structure of the collection of ryegrass (Lolium) cultivars: a study based on SSR and SCoT markers

Mavlyutov,

Vertikova,

Shamustakimova

et al. 2023

Trudy po prikladnoy botanike, genetike i selektsii

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Background. Current molecular and genetic approaches make it possible to accelerate ryegrass breeding, simplify source material evaluation, and increase its accuracy. The efficiency of PCR-based SSR and SCoT marker techniques was studied in the context of evaluating the genetic structure of annual and perennial ryegrass accessions and defining DNA-identifying markers.Materials and methods. Genomic DNA was isolated from the aggregate sample of 30 seedlings from each of the 15 analyzed cultivars according to the modified SDS DNA extraction protocol. In total, 20 SSR and 22 SCoT markers were used to assess genetic polymorphism. Basic parameters of the markers’ informative efficiency were identified. Genetic relationships among the studied cultivars were analyzed on the basis of the Neighbor-Joining dendrogram and Bayesian model.Results. To assess the genetic polymorphism of ryegrass species and varieties, 7 SSR loci were selected, for which 110 allelic variants were identified (34 alleles were unique for individual cultivars), and 9 SCoT loci, for which 78 polymorphic amplification fragments were identified, with 28 being cultivar-specific. The dendrogram of genetic similarity and modeling in the Structure v2.3.4 program according to the results of SSR and SCoT analyses distributed the cultivars by their traits according to their species, ploidy level, origin, and similarity. Based on PCoA, carried out using summarized data of SSR and SCoT analyses, a multidimensional diagram of genetic relationships among ryegrass cultivars was constructed.Conclusions. The systems of SSR and SCoT markers appeared to be an efficient tool to reveal genetic polymorphism and identify differences among ryegrass species and cultivars. We found unique DNA profiles that can be used for genetic identification. The results of the study have practical significance in cultivar-specific identification and selection of cultivars for various purposes.

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“…Some protein molecules like storage proteins or isozymes, or specific DNA loci can be used as molecular markers (Naeem et al, 2014;Chelyustnikova et al, 2019). Passportization of varieties and hybrids of many agricultural plants and crops was carried out using ISSR and IRAP markers (Sukhareva, Kuluev, 2018), as well as molecular certification of rare and endemic plant species and their natural populations like two species of Adonis, A. vernalis and A. sibirica (Boronnikova, 2009). On the basis of this technique, I.V.…”

Section: Introductionmentioning

confidence: 99%

Specific shoot formation in Miscanthus sacchariflorus (Poaceae) under different environmental factors and DNA passportization using ISSR markers

et al. 2022

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The generic complex Miscanthus Anderss. (Poaceae) is a unique example among herbaceous plants characterized by high values of growth of aboveground vegetative mass and practical use as a valuable source of alternative energy. Miscanthus is one of the most efficient solar energy accumulators, and since phytomeliorative use implies the cultivation of these resource plants in inconvenient and semi-shady areas, the question about the effect of insufficient lighting on the productivity of Miscanthus arises. As a result of a long-lasing introduction effort, the Central Siberian Botanical Garden SB RAS created a population of Miscanthus sacchariflorus (Maxim.) Benth., which has good prospects for growing under the conditions of the forest-steppe area in Western Siberia. The goals of our study were: (1) to determine the peculiarities of shoot formation, (2) to assess the cellulose and lignin accumulation in M. sacchariflorus populations under different lighting conditions and (3) to perform a DNA passportization of the Miscanthus population by ISSR marking. Evaluation of shoot formation and the amount of accumulated cellulose and lignin in plants was carried out under different degrees of illumination: one variant was grown in a sunny area, and the other, in partial shade. As a result of analysis of variance, it was found that the number of shoots does not depend on environmental conditions, but on the age of the plant, while environmental conditions have a significant effect on plant height. Although the samples of both M. sacchariflorus variants were characterized by different rates of creation of a continuous projective cover, plants in semi-shaded areas formed up to 89.34 % of shoots compared to their peers in illuminated areas, which did not affect significantly the size of the aboveground mass and the cellulose content in it. As a result of ISSR-analysis of genomic DNA in the M. sacchariflorus population, unique molecular polymorphic fragments were identified, which can be used for identification and DNA passportization at the inter-population level. Thus, the complex use of M. sacchariflorus as a valuable meliorative and bioenergetic culture is due to the high adaptive potential of this species. It was found that the illumination factor has virtually no effect on the amount of the cellulose content in the shoot, and a reduced content of the technologically undesirable lignin was observed in plants growing in the partial shade conditions.

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DNA markers for genetic analysis of crops.

Cited by 12 publications

References 0 publications

GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing

GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing

Genetic structure of the collection of ryegrass (Lolium) cultivars: a study based on SSR and SCoT markers

Specific shoot formation in Miscanthus sacchariflorus (Poaceae) under different environmental factors and DNA passportization using ISSR markers

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