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KASP<sup>TM</sup> genotyping technology and its use in genetic-breeding programs (a study of maize)
2017
Н. Е. Волкова | В. М. Соколов
Purpose. To review publications relating to the key point of the genotyping technology that is competitive allele-specific polymerase chain reaction (which is called now Kompetitive Allele Specific PCR, KASPTM) and its use in various genetic-breeding researching (a study of maize).Results. The essence of KASP-genotyping, its advantages are highlighted. The requirements for matrix DNA are presented, since the success of the KASP-analysis depends on its quality and quantity. Examples of global projects of plant breeding for increasing crop yields using the KASP genotyping technology are given. The results of KASP genotyping and their introduction into breeding and seed production, in particular, for determining genetic identity, genetic purity, origin check, marker-assisted selection, etc. are presented using maize as an example. It is demonstrated how genomic selection according to KASP genotyping technology can lead to rapid genetic enhancement of drought resistance in maize. Comparison of the effectiveness of creating lines with certain traits (for example, combination of high grain yield and drought resistance) using traditional breeding approaches (phenotype selection) and molecular genetic methods (selection by markers) was proved that it takes four seasons (two years in case of greenhouses) in order to unlock the potential of the plant genotype using traditional self-pollination, test-crossing and definitions), while using markers, the population was enriched with target alleles during one season. At the same time, there was no need for a stress factor.Conclusions. KASP genotyping technology is a high-precision and effective tool for modern genetics and breeding, which is successfully used to study genetic diversity, genetic relationship, population structure, genetic identity, genetic purity, origin check, quantitative locus mapping, allele mapping, marker-assisted selection, marker-assisted breeding. It is expedient and timely to introduce KASP genotyping technology in our country to solve a wide range of modern genetics, breeding, seed production tasks.
Показать больше [+] Меньше [-]Rice (<em>Oryza sativa</em> L.) blast resistance genes bioinformatic analysis
2017
К. В. Бондаренко | Г. І. Сліщук | Н. Е. Волкова
Purpose. To investigate rice blast resistance genes polymorphism by using bioinformatic methods. Methods. Global and local nucleotide alignment, phylogenetic analysis, HyPhy test. Results. For Pib gene, numerous single nucleotide substitutions and deletions of 1–3 bp were established. The phylogeny of this gene has been studied and homologues have been found both in various rice species and in other cereals. These sequences can encode proteins that «recognize» the phytopathogens effectors, and can also be associated with resistance to phytopathogens. The Pi4 gene is characterized by single nucleotide substitutions, insertions and deletions; the number of non-synonymous substitutions exceeds the number of synonymous ones. The Pi54 gene variability is significantly lower than that of the Pi4 and Pib genes. The predominant types of polymorphism were single nucleotide substitutions and small-sized indels. It was found that non-synonymous substitutions in Pi54, Pi4 and Pib genes were in close proximity, sometimes forming clusters, while some coding regions were either superconservative or contained predominantly synonymous substitutions. On philodendrograms, cultivated rice samples were clustered with samples of ancestral wild-growing species. Conclusions. Evolution of the rice blast resistance genes Pi4, Pib and Pi54 is characterized by diversification selection. Considering that tense coevolution and significant rate of adaptation and creation of new pathogen races are typical for a plant and a parasite, these genes are subjected to intensive selection aimed at increasing diversity for obtaining the resistance to new races of the pathogen.
Показать больше [+] Меньше [-]KASP<sup>TM</sup> genotyping technology and its use in genetic-breeding programs (a study of maize)
2017
Волкова, Н. Е | Sokolov, V. M.
Purpose. To review publications relating to the key point of the genotyping technology that is competitive allele-specific polymerase chain reaction (which is called now Kompetitive Allele Specific PCR, KASPTM) and its use in various genetic-breeding researching (a study of maize). Results. The essence of KASP-genotyping, its advantages are highlighted. The requirements for matrix DNA are presented, since the success of the KASP-analysis depends on its quality and quantity. Examples of global projects of plant breeding for increasing crop yields using the KASP genotyping technology are given. The results of KASP genotyping and their introduction into breeding and seed production, in particular, for determining genetic identity, genetic purity, origin check, marker-assisted selection, etc. are presented using maize as an example. It is demonstrated how genomic selection according to KASP genotyping technology can lead to rapid genetic enhancement of drought resistance in maize. Comparison of the effectiveness of creating lines with certain traits (for example, combination of high grain yield and drought resistance) using traditional breeding approaches (phenotype selection) and molecular genetic methods (selection by markers) was proved that it takes four seasons (two years in case of greenhouses) in order to unlock the potential of the plant genotype using traditional self-pollination, test-crossing and definitions), while using markers, the population was enriched with target alleles during one season. At the same time, there was no need for a stress factor. Conclusions. KASP genotyping technology is a high-precision and effective tool for modern genetics and breeding, which is successfully used to study genetic diversity, genetic relationship, population structure, genetic identity, genetic purity, origin check, quantitative locus mapping, allele mapping, marker-assisted selection, marker-assisted breeding. It is expedient and timely to introduce KASP genotyping technology in our country to solve a wide range of modern genetics, breeding, seed production tasks.
Показать больше [+] Меньше [-]Rice (<em>Oryza sativa</em> L.) blast resistance genes bioinformatic analysis
2017
Бондаренко, К. В | Сліщук, Г. І | Волкова, Н. Е
Purpose. To investigate rice blast resistance genes polymorphism by using bioinformatic methods. Methods. Global and local nucleotide alignment, phylogenetic analysis, HyPhy test. Results. For Pib gene, numerous single nucleotide substitutions and deletions of 1–3 bp were established. The phylogeny of this gene has been studied and homologues have been found both in various rice species and in other cereals. These sequences can encode proteins that «recognize» the phytopathogens effectors, and can also be associated with resistance to phytopathogens. The Pi4 gene is characterized by single nucleotide substitutions, insertions and deletions; the number of non-synonymous substitutions exceeds the number of synonymous ones. The Pi54 gene variability is significantly lower than that of the Pi4 and Pib genes. The predominant types of polymorphism were single nucleotide substitutions and small-sized indels. It was found that non-synonymous substitutions in Pi54, Pi4 and Pib genes were in close proximity, sometimes forming clusters, while some coding regions were either superconservative or contained predominantly synonymous substitutions. On philodendrograms, cultivated rice samples were clustered with samples of ancestral wild-growing species. Conclusions. Evolution of the rice blast resistance genes Pi4, Pib and Pi54 is characterized by diversification selection. Considering that tense coevolution and significant rate of adaptation and creation of new pathogen races are typical for a plant and a parasite, these genes are subjected to intensive selection aimed at increasing diversity for obtaining the resistance to new races of the pathogen.
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