Petra Hlásná Čepková

Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2–9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, FST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (ΦPT = 0.252–0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.

Sorghum and Foxtail Millet—Promising Crops for the Changing Climate in Central Europe

Climate change is connected to many undesirable aspects which may strongly affect agricultural production in the future, not only in the Czech Republic but also in other countries in Central Europe. The most serious risks with the main impacts on agricultur‐ al production are the frequency and intensity of occurrence of extreme events. Prob‐ lems caused by drought and its impact on agricultural production are starting to be serious and urgent. One of the solutions is using the drought-tolerant/resistant species and/or varieties more adaptable to water stress. Sorghum and foxtail millet might be the solution for Czech conditions. They can provide good yields even in dry periods. This study discusses grain quality of foxtail millet and biomass quality in the case of sorghum. In addition, the benefits of cultivation of these two species and current knowledge from a scientific point of view are summarised here.

Genetic diversity in Guazuma crinita from eleven provenances in the Peruvian Amazon revealed by ISSR markers

Guazuma crinita es una importante especie maderable de rapido crecimiento ampliamente usada en sistemas agroforestales en la Amazonia Peruana. Los objetivos de nuestra investigacion fueron; (i) evaluar la diversidad genetica de G. crinita revelada por marcadores de intersecuencias simples repetidas (ISSR) ademas de (ii) estimar la correlacion entre las distancias geneticas y geograficas entre procedencias. La muestra incluyo 44 genotipos de 11 procedencias en las cuencas de Aguaytia y Pachitea en la Amazonia Peruana. Diez cebadores ISSR amplificaron un total de 65 bandas de las cuales 61 fueron polimorficas (93,8 %). El rango de amplificaciones de ADN vario desde 260 hasta 2.200 bp. Entre las procedencias, Macuya exhibio el mayor porcentaje de bandas polimorficas (PPB) con 67,7 %, 0,21 diversidad genetica de Nei (He) y 0,33 de indice de Shannon (I). La diferenciacion genetica general (Gst) fue 0,03, indicando 97 % de la variacion genetica dentro de las procedencias. El flujo genetico (Nm) fue 12,9 alelos por generacion. El analisis de agrupamiento no estuvo relacionado con el origen geografico sugiriendo una fuente genetica en comun. Sin embargo, se encontro una correlacion positiva debil (r = 0,27, P < 0,05) entre las distancias geneticas y geograficas. Este es el primer estudio sobre la diversidad y estructura genetica de G. crinita. Se recomiendan estrategias de conservacion in situ para las poblaciones con altos niveles de diversidad genetica

Genetic diversity of eight millet genera assessed by using molecular and morphological markers

Abstract. In this study, the genetic diversity and relationships among eight millet genera were investigated by molecular and morphological data analyses. Sixty-nine millet accessions were analysed by using amplified fragment length polymorphism (AFLP) markers, and evaluated for morphological traits. Eight AFLP primer pairs were amplified successfully and 779 bands were scored for all accessions, with a high level of polymorphism detected. Nei’s genetic distance among all accessions varied from 0.0123 to 0.4246 and the Shannon’s index was estimated at 0.9708. The neighbour joining tree, using the unweighted neighbour-joining method and Dice’s dissimilarity coefficient, was constructed. The AFLP markers revealed the close relatedness between the Eragrostis and Panicum genera, whereas the greatest distance was found the Pennisetum and Echinochloa genera. Cluster analysis based on the AFLP profiles revealed that the majority of accessions of a given millet genus tend to group together. Clustering from morphological data allocated individuals into three main clusters with high variation. The genetic variability found between the analysed accessions was weakly negatively correlated (r = –0.074) with their morphological attributes. However, high molecular and morphological variability indicated that this collection includes rich and valuable plant materials for millet breeding.

Characterisation of the Amaranth Genetic Resources in the Czech Gene Bank

The human species depends on plants. These constitute the basis for food, supply most of our needs (including clothes and shelter) and are used in industry for manufacturing fuels, medicines, fibres, rubber and other products. However, the number of plants that humans use for food is minimal, compared to the number of species existing in nature. Only 30 crops, the most outstanding of which are rice, wheat and maize, provide 95% of the calories needed in the human diet (Jaramillo & Baena, 2002). However, agricultural biodiversity is in sharp decline due to the effects of modernisation, such as concentration on a few competitive species and changes in diets. Since the beginning of agriculture, the world’s farmers have developed roughly 10 000 plant species for use in food and fodder production. Today, only 150 crops feed most of the world’s population, and just 12 crops provide 80% of dietary energy from plants, with rice, wheat, maize and potato providing 60%. It is estimated that about three quarters of the genetic diversity found in agricultural crops have been lost over the past century, and this genetic erosion continues (EC, 2007).

Preliminary Study of Diversity of Plukenetia volubilis Based on the Morphological and Genetic Characteristics

Abstract The aim of this study was to make an initial step in clarification of morphological diversity of sacha inchi (Plukenetia volubilis L.), a traditional oilseed crop, together with use of ISSR primers for a preliminary assessment of genetic variability in the species. Quantitave and qualitative morphological data together with leaf samples for twenty plant individuals of sacha inchi from five distinct populations were gathered in three different communities neighbouring the city of Pucallpa in Peru. Morphological data were processed into PCA analysis graph while for DNA analysis the method of fingerprinting processed into PCO graph and dendrogram was used. Visible morphological dissimilarities in the plant appearance were confirmed and observable differences in phenotypical characteristics among different types of associated cultivations were recorded. For genetic variability twelve from eighteen ISSR primers used and tested in the study could be used directly for further molecular pursuit on this species. Dendrogram with six main clusters was created and thus confirmed polymorphism as allogamy plants shows. Obtained results contributed to the identification of suitable method for further assessment of genetic variability within this species. New horizons for the focus of further research and improvements in onward development and genetic conservation of sacha inchi cultivation were identified, thus linking the observation of morphological features with DNA analysis proved as effective.