Theo van Hintum

Genetic erosion in crops: concept, research results and challenges.

The loss of variation in crops due to the modernization of agriculture has been described as genetic erosion. The current paper discusses the different views that exist on the concept of genetic erosion in crops. Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop. Two stages in this bottleneck are recognized: the initial replacement of landraces by modern cultivars; and further trends in diversity as a consequence of modern breeding practices. Genetic erosion may occur at three levels of integration: crop, variety and allele. The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level. According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following: a reduction in diversity due to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed.

Genetic diversity trends in twentieth century crop cultivars: a meta analysis

In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.

Duplication within and between germplasm collections

SummaryThe extent of duplication within and between barley genebank collections has been determined from a comparative analysis of four European barley collections. These collections were those of the Centre for Genetic Resources, the Netherlands, the Institute of Plant Genetics and Crop Plant Research and the Braunschweig Genetic Resources Centre, both in Germany, and finally that of the John Innes Institute in the United Kingdom. These collections comprise over thirty thousand accessions.A random set of 100 accessions from the CGN barley collections was matched with all four collections to identify probable duplication, resulting in 61% of the accessions being matched. Passport data were used to identify probable duplicates. This was hindered by the low quality of these data; simple perfect matches were rare.The probable duplication, excluding parental duplication, involved 144 other accessions.Using seed traits, field observations and electrophoretic markers, it could be shown that more than three quarters of the matched accessions in the random set, excluding parental duplication, were completely duplicated in the others and one fifth were more or less duplicated in other matched accessions.If individual comparisons between accessions from the random set and the matched accessions were made, about one fifth of the probable duplicates were shown not to be duplicates at all. One half were identical duplicates, and the rest were common or partial duplicates.

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

Dominant and co-dominant molecular markers are routinely used in plant genetic research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A set of 54 diploid sugar beet (Beta vulgaris L. ssp. vulgaris) hybrid varieties from five seed companies was genotyped with 702 Diversity Array-Technology (DArT), 34 Single Nucleotide Polymorphisms (SNP), and 30 Simple Sequence Repeats (SSR) markers. Analysis of the population structure revealed three well-defined populations and clustering of varieties that generally correlates with their seed company origin. Two populations each contained varieties from two different seed companies indicating genetic similarity of this material. The third population was comprised only of varieties from a single seed company. Analysis of the SSR and SNP datasets indicates that some of the hybrid varieties likely have a common (or very closely related) parent. Comparison of the three marker-systems revealed substantial differences in the number of loci needed for analyses. Varietal clustering required approximately 1.8-2×more SSR, 3-4.5×more SNP, and 4.8×more DArT markers than were required for detection of genotypic diversity. When marker-systems were compared across different types of analyses per locus success-rate was the highest for the SSR and the lowest for the DArT markers. Generally, about 1.4-3×more SNPs, and 4.9-13.3×more DArTs then SSRs were needed to achieve the 100% success-rate. However, using only DArT markers with a high level of polymorphism decreased the number of DArT loci needed for analyses by 38-61%. Results from the present work provide a premise to selecting the type(s) and number of markers that are needed for genetic diversity analysis of sugar beet hybrid varieties.

Duplication within and between germplasm collections: I. Identifying duplication on the basis of passport data

SummaryPrinciples of duplication within and between genebank collections have been explored, terminology is proposed and the difficulties in identifying probable duplication are discussed.Identical duplication concerns genetically identical accessions, whereas common duplication refers to accessions derived from the same original population that are mixtures of lines with differing genotype frequencies, or random mating populations with the same alleles but differing allele frequencies. Partial and compound duplication are types of incomplete duplication. An additional type of duplication is the relation between the parents in a cross and their offspring, i.e. parental duplication.Identifying probable duplication on the basis of passport data is often hindered by their incompleteness or poor quality. The genetic identity of accessions is also subject to changes during maintenance in genebanks. Therefore, probable duplicates will often not be true duplicates.Examples from the European Barley Database illustrate the problems.

Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be clearly distinguished into spring and winter types and was classified into five subgroups based on 253 DArT or 22 SSR markers. Despite the fact, that the same number of groups was revealed by both marker types, it could be shown that this grouping was more distinct for the SSRs than the DArTs, when assigned to a Q-matrix by STRUCTURE. This was supported by the findings from principal coordinate analysis, where the SSRs showed a better resolution according to seasonal habit and row number than the DArTs. A considerable influence on the rate of significant associations with malting and kernel quality parameters was revealed by different marker types in this genome-wide association study using general and mixed linear models considering population structure. Fewer spurious associations were observed when population structure was based on SSR rather than on DArT markers. We therefore conclude that it is advisable to use independent marker datasets for calculating population structure and for performing the association analysis.

Identification of intra-accession genetic diversity in selfing crops using AFLP markers: implications for collection management

Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.

The Dynamics of on-farm Management of Sorghum in Ethiopia: Implication for the Conservation and Improvement of Plant Genetic Resources

On-farm conservation of plant genetic resources for food and agriculture has received strong support worldwide in recent years. It has been justified on appealing assumptions: it complements ex situ conservation, allows co-evolutionary interaction of host–pathogens and crop–weed complexes, and involves local knowledge systems. This article illustrates how on-farm conservation being set for its sake is extremely difficult under farmers’ dynamic management of plant genetic resources based on sorghum. The dynamics of their management could be explained by continued introduction, displacement, loss and maintenance of aboriginal landraces that have distinct functional attributes, patch-occupancy and relative abundance profiles. Such management and hence the dynamic landrace demography has largely been triggered by co-evolving biophysical stresses, spatial and seasonal variations. The best viable alternative to support farmers’ management of genetic resources is to link conservation to crop improvement both to enhance on-farm genetic diversity and make the biophysical environment a comfortable home for the plant genotypes.

Duplication within and between germplasm collections. III. A quantitative model

Estimating the level of duplication of germpIasm accessions within and between genebanks is of high importance for judging the coverage as well as the efficiency of ex situ conservation efforts. Therefore, a method was developed to quantify probable duplication within and between genebanks. To estimate total internal duplication, the fraction of distinct accessions was determined in a sample from the collection. To estimate the duplication between collections, set theory was used. Again based on samples from the collections involved, the size of any intersection between these collections can be estimated. Standard errors of all estimates were calculated as well. To illustrate the feasibility of the method, an example involving four lettuce collections is given.Estimating the level of duplication of germpIasm accessions within and between genebanks is of high importance for judging the coverage as well as the efficiency of ex situ conservation efforts. Therefore, a method was developed to quantify probable duplication within and between genebanks. To estimate total internal duplication, the fraction of distinct accessions was determined in a sample from the collection. To estimate the duplication between collections, set theory was used. Again based on samples from the collections involved, the size of any intersection between these collections can be estimated. Standard errors of all estimates were calculated as well. To illustrate the feasibility of the method, an example involving four lettuce collections is given.

Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce.