Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis

Abstract

One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

“…Variable SSR repeats identified within the LTR part of a pea Ty1/copia retrotransposon Following sequence analysis of 45 pea SSR loci (Loridon et al, 2005) used for pea germplasm characterization (Smý kal et al, 2008), 21 contained similar sequences surrounding the variable SSR motif. The similarity included most of the amplified loci except at the 3 0 end, in which it abruptly terminated at a conserved CCTTCA motif, which preceded a divergent sequence that was different for each locus (Figure 2).…”

“…Using pea derived locus-specific primers from Loridon et al, (2005), all 21 SSR loci were amplifiable from P. sativum, P. abyssinicum, P. fulvum and P. elatius species, but not from other legumes, including the Viceae tribe genera (data not shown). Moreover, the application of four of the 21 SSR loci (A-9, B-14, AD-175, AA-321) for genetic relationship analysis across 800 P. sativum accessions had earlier revealed a high level of length polymorphism and indicated further repeat expansion, even within the cultivated pea genepool (Smý kal et al, 2008).…”

Combining ability, heterosis, genetic distance and their intercorrelations for waterlogging tolerance traits in chrysanthemum

“…Different methods have been used to evaluate the level of genetic distance, including morphological markers, isozymes and molecular techniques (Weeden and Wendel 1989;Ferriol et al 2003;Smýkal et al 2008). Significant time and effort are required to obtain morphological markers, which are frequently influenced by environmental factors.…”

Genetic Diversity and Taxonomic Studies of Allium Akaka and A. Elburzense Native to Iran Using Morphological Characters

“…Their populations have declined drastically during recent years, and will soon be threatened with extinction (Akhavan et al 2015). To prevent the extinction of wild plant genotypes, ex situ conservation of germplasm resources was pioneered by Vavilov (1926) and nowadays, germplasm collections hold over 6 million crop plant accessions world-wide (Smykal et al 2008). The study of genetic diversity for both germplasm management and breeding has received much attention.…”

“…Morphological descriptors are widely used in germplasm groups and remain the only legitimate marker type accepted by the international union for the protection of new cultivars of plants (UPOV). Morphological traits represent the action of numerous genes and thus contain high information value (Smykal et al 2008). For characterization and evaluating morphological diversity of Alliums, it is important to use descriptors with high heritability and stability.…”