Articles
MOLECULAR MARKERS FOR GERMPLASM IDENTIFICATION AND CHARACTERIZATION
Article number
859_5
Pages
59 – 72
Language
English
Abstract
Markers based on DNA polymorphism have become a common tool for genotyping individuals and inferring information on the genetic structure of germplasm collections, discovery of synonymy, and kinship.
Among the numerous DNA markers (RFLP, RAPD, AFLP, SSR, ISSR, SAMPL, S-SAP, SNP, and others) proposed in the literature of the past two decades, microsatellites (or SSRs) and SNPs are the markers that are best suited for this scope, providing the robust data necessary in forensic disputes, as well as for intellectual property and patent rights.
This paper is divided into three parts.
The first part deals with the choice of SSR markers and protocols, with particular focus on the issues that can affect the accuracy of the analyses, such as the core repeat length, fragment binning and sizing, and allele calling.
The protocols adopted for humans are used as a reference.
The second part deals with the statistical analysis of identity and parentage, using once again the procedures adopted in humans as a reference, for the aspects that are common to both fields.
The third part discusses several issues that are more typical of plant genotyping, such as the occurrence of chimeric tri-allelic patterns, polyploidy, and clonal variants.
The last aspect, in particular, which deals with essentially derived varieties, is discussed considering the opportunity offered by the recent evolution of sequencing and genotyping platforms, and the importance of sport variants in fruit crops.
Among the numerous DNA markers (RFLP, RAPD, AFLP, SSR, ISSR, SAMPL, S-SAP, SNP, and others) proposed in the literature of the past two decades, microsatellites (or SSRs) and SNPs are the markers that are best suited for this scope, providing the robust data necessary in forensic disputes, as well as for intellectual property and patent rights.
This paper is divided into three parts.
The first part deals with the choice of SSR markers and protocols, with particular focus on the issues that can affect the accuracy of the analyses, such as the core repeat length, fragment binning and sizing, and allele calling.
The protocols adopted for humans are used as a reference.
The second part deals with the statistical analysis of identity and parentage, using once again the procedures adopted in humans as a reference, for the aspects that are common to both fields.
The third part discusses several issues that are more typical of plant genotyping, such as the occurrence of chimeric tri-allelic patterns, polyploidy, and clonal variants.
The last aspect, in particular, which deals with essentially derived varieties, is discussed considering the opportunity offered by the recent evolution of sequencing and genotyping platforms, and the importance of sport variants in fruit crops.
Authors
R. Testolin, G. Cipriani
Keywords
SSR, simple sequence repeat, SNP, single nucleotide polymorphisms, fingerprinting, pedigree
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