Data analysis for molecular characterization of plant genetic resources

Abstract

Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and nonhierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei's parameters, or Wright's F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.

Simple Sequence Repeat (SSR) Marker Assay-Based Genetic Diversity among Dolichos Bean (Lablab purpureus L. Sweet) Advanced Breeding Lines Differing for Productivity per se Traits

“…Therefore, large differences between observed and the effective number of alleles indicate low frequencies of a few alleles because they are present in only one or a few genotypes. For this reason, estimate of effective number of alleles could be useful in indicating rare alleles (Laurentin, 2009). In the present study, large differences between the estimates of observed and the effective number of alleles indicate relatively low frequency of a few alleles, which could be considered as rare alleles.…”

“…While investigating the diversity of related genotypes in predominately self-pollinated crops such as dolichos bean where only homozygous genotypes were used in the study, Simple Matching Coefficient (SMC) is the most appropriate diversity measure as it takes care of absence of the amplicons in addition to presence of the amplicons in both the compared genotypes as causes of similarity (Laurentin, 2009 (Tanksley and McCouch, 1997).…”

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

“…Relevant applications include the identification of diverse parental combinations to create segregating progeny with maximum genetic variability, introgression of desirable genes from diverse germplasm into the available genetic base, identification of adaptation patterns by linking genetic variability to environmental data, understanding the genetic relationships between major groups of inbred lines used in crosses, assigning inbred lines to specific heterotic groups, and plant varietal protection (Mohammadi and Prasanna, 2003;Reif et al, 2005;Jombart et al, 2009;Laurentin, 2009). The observed genetic diversity is affected by the data (morphological, biochemical, and molecular marker data), the sample size of markers and individuals genotyped, the criterion for defining the optimal number of groups, and the amount of data lost (Mohammadi and Prasanna, 2003).…”

Biodiversity Measures in Agriculture Using DNA

“…Monitoring forest maintenance by satellites has been criticized because it would not be enough to measure the size of the preserved forest area, but real diversity is not perceived. Species identification must be done in situ (Fonseca et al, 2008), and molecular markers distributed along the genome and not linked to the special selected traits may provide general diversity measures as the number of alleles per locus, as well as the population structure (Laurentin, 2009). …”