Single nucleotide substitutions (SNPs) account for the largest share of DNA polymorphism in virtually any organism, including humans, and have a significant impact on their life status. Detection of already known polymorphic nucleotides (SNP typing) is of great importance, which explains the extremely wide variety of existing methods for SNP analysis. One of the most widely used approaches is allele-specific PCR (AS-PCR) with primers characterized by differences in structure and the resulting ability to discriminate polymorphic nucleotides in DNA. AS-PCR is implemented in a variety of variants (about fifty), which are briefly considered in this review.
Due to the fact that single nucleotide substitutions account for the largest share of DNA polymorphism in almost any organisms and have a noticeable effect on their vital status, the detection of already known such polymorphic nucleotides is extremely important. This explains the huge variety of methods of such genotyping. Among the old approaches to the detection of polymorphic nucleotides, allele-specific hybridization with oligonucleotides stands out, which later received a new life in the form of fluorescently labeled probes. Also, such a method as PCR-RFLP, based on the cleavage of amplicons by suitable restriction endonucleases, whose sites contain polymorphic nucleotides or primers are designed in such a way that such sites arise during PCR, is not completely forgotten. The methods used relatively less frequently for detecting mutations in heteroduplexes using some chemical reagents, as well as using some endonucleases, are also briefly considered in this review.
As confirmation of the huge diversity of DNA content in the nuclei of plant cells, the boundary values of minimum and maximum parameters such as the number of chromosomes, varying in plants per haploid genome from two chromosomes to 480 (or even up to 720) chromosomes, as well as the "weight" sizes of genomes in picograms in the form of 1C-value with a range from 0.065 to 152.23 pg per haploid set of chromosomes. The importance of knowledge of the amount of DNA and the number of chromosomes for the implementation of projects for sequencing complete yet unknown plant genomes was noted. Examples of sequenced complete genomes of plants with very different sizes (less than 100 million bp and more than 30 billion bp) are also given. Attention is paid to the need to give the century-old term "genome" a new meaning, according to which it should already mean the entire amount of DNA in all chromosomes, regardless of ploidy, but not a haploid set, as before, since only the totality of all DNA (all alleles, both homologous and homeologous chromosomes) determines the vital status of a plant, and of any other eukaryotic organism. Attention is drawn to the fact that the concept of a "complete genome" includes various levels of their completeness from contigs and other draft quasi-haploid genomes to the so-called T2T genomes, which represent established nucleotide sequences chromosomally from "telomere to telomere". The most complete information about the organism can be given by the diploid genome, which is determined by the so-called phased assembly by haplotypes. At the same time, for plants and especially for cultivars of agricultural plants, as the reference genome should serve a pangenome that carries maximum information about the differences in nucleotide sequences characteristic of the sample under study. The use of plant pangenomic data in breeding will mark the transition to a new level of such work. Perhaps in the future, when the mass sequencing of truly complete diploid genomes in the T2T format begins, a new term will be needed for them, which could become "digenome" or briefly “dinome”.
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