An informational view of accession rarity and allele specificity in germplasm banks for management and conservation

Abstract

Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of diploid, inbred or outbred species.

Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

“…Results of the present study showed a similar number of alleles (56) and average number of alleles (3.29) to results of Choi et al [28] (number of alleles = 51; average number of alleles = 3.0), while genetic diversity (0.490) in the present study was higher than (0.398) in the previous study. Reunova et al [12] have reported similar results (average number of alleles: 2.49; expected heterozygosity (He): 0.453) in 139 individual ginseng plants using 11 SSR primers.…”

“…Such uniqueness makes them prone to be absent in whole collections and their subsets, albeit their potential importance as a source of important traits for plant breeding. Novel strategies in germplasm management are needed to preserve those alleles, prone to be lost, which can be potentially useful for plant breeding, especially in a scenario of rapid climate change that represents serious threats to worldwide food production [56].…”

Development of a Multipurpose Core Collection of Bread Wheat Based on High-Throughput Genotyping Data

“…Some studies reported that this type of allele, likely to be maintained by deleterious mutation-selection balance, would be of less interest; they seldom contribute to the improvement of elite varieties and, therefore, their inclusion in the CC might not be worthwhile [7,56,57]. In contrast, other authors have more recently proposed core subsets focused on preserving rare accessions and uncommon alleles, which may have unique genetic potentials for plant breeding [58]. In our case, the high number of accessions possessing specific rare alleles makes it difficult to retain a greater number of very rare alleles without increasing the sample size.…”

Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

“…Germplasm banks play an important role in the conservation, management and utilization of germplasm resources that is critical for the development of plant breeding [42]. Molecular genetic markers are widely used in germplasm identification and they are important in the construction and management of germplasm banks [43]. For example, the single nucleotide polymorphism (SNP) markers were used to identify Dimocarpus longan L. germplasm [44] and Discorea alata L. germplasm [45].…”

“…For example, the single nucleotide polymorphism (SNP) markers were used to identify Dimocarpus longan L. germplasm [44] and Discorea alata L. germplasm [45]. Reyes-Valdés et al offered an integrated view of accession rarity and allele specificity in germplasm banks for management and conservation [43]. Storme et al [46] analyzed 675 P. nigra L. accessions from nine European gene banks using SSR markers, amplified fragment length polymorphism (AFLP) markers and isozyme systems to estimate the extent of duplication and the genetic diversity within and between banks.…”