Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Crop wild relatives of pigeonpea [Cajanus cajan (L.) Millsp.]: Distributions, ex situ conservation status, and potential genetic resources for abiotic stress tolerance
Khoury, C.K. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Bernau, V. ; Kassa, M.T. ; Norton, S.L. ; Maesen, L. ; Upadhyaya, H.D. ; Ramirez-Villegas, J. ; Jarvis, A. ; Struik, P.C. - \ 2015
Biological Conservation 184 (2015). - ISSN 0006-3207 - p. 259 - 270.
species distribution models - global food security - male-sterility - climate-change - osmotic adjustment - diversity - bias - biodiversity - adaptation - accessions
Pigeonpea [Cajanus cajan (L.) Millsp.] is a versatile, stress-tolerant, and nutritious grain legume, possessing traits of value for enhancing the sustainability of dry sub-tropical and tropical agricultural systems. The use of crop wild relatives (CWR) in pigeonpea breeding has been successful in providing important resistance, quality, and breeding efficiency traits to the crop. Current breeding objectives for pigeonpea include increasing its tolerance to abiotic stresses, including heat, cold, drought, and waterlogging. Here we assess the potential for pigeonpea CWR to be further employed in crop improvement by compiling wild species occurrence and ex situ conservation information, producing geographic distribution models for the species, identifying gaps in the omprehensiveness of current germplasm collections, and using ecogeographic information to identify CWR populations with the potential to contribute agronomic traits of priority to breeders. The fifteen prioritized relatives of pigeonpea generally occur in South and Southeast Asia to Australia, with the highest concentrations of species in southern India and northern Australia. These taxa differ considerably among themselves and in comparison to the crop in their adaptations to temperature, precipitation and edaphic conditions. We find that these wild genetic resources are broadly under-represented in ex situ conservation systems, with 80% of species assessed as high priority for further collecting, thus their availability to plant breeders is insufficient. We identify species and highlight geographic locations for further collecting in order to improve the completeness of pigeonpea CWR germplasm collections, with particular emphasis on potential traits for abiotic stress tolerance.
Morphological Characterization of African Bush Mango trees (Irvingia species) in the Dahomey Gap (West Africa)
Vihotogbe, R. ; Berg, R.G. van den; Sosef, M.S.M. - \ 2013
Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1597 - 1614.
phenotypic variation - indigenous fruits - domestication - gabonensis - cameroon - selection - nigeria - accessions - kernels - farmers
The variation of the morphological characters of bitter and sweet African bush mango trees (Irvingia species) was investigated in the Dahomey Gap which is the West African savannah woodland area separating the Upper and the Lower Guinean rain forest blocks. African bush mangoes have been rated as the highest priority multi-purpose food trees species that need improvement research in West and Central Africa. A total of 128 trees from seven populations were characterized for their bark, fruits, mesocarp and seeds to assess the morphological differences between bitter and sweet trees and among populations. Multivariate analysis revealed that none of the variables: type of bark, mature fruit exocarp colour, fruit roughness and fresh mesocarp colour, could consistently distinguish bitter from sweet trees in the field. The analysis of the measurements of fruits, mesocarps and seeds demonstrated that bitter fruits have the heaviest seeds and this consistently distinguishes them from sweet fruits. However, the measurements of the fruit, mesocarp and seed did not have a joint effect in grouping types and populations of ABMTs. This indicates high diversity with a potential for selection existing across all phytogeographical regions investigated. The sweet trees of Couffo and those of Dassa in Benin are clearly different from all other populations. This can be attributed to traditional domestication (bringing into cultivation) and climate, respectively. The large fruits and the heavy seeds of the cultivated populations are evidence of successful on-going traditional selection of sweet trees in the Dahomey Gap.
The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat
Zhang, J. ; Esselink, G. ; Che, D. ; Fougère-Danezan, M. ; Arens, P. ; Smulders, M.J.M. - \ 2013
Journal of Horticultural Science and Biotechnology 88 (2013)1. - ISSN 1462-0316 - p. 85 - 92.
genetic diversity - genus rosa - phylogenetic analysis - dna-sequences - matk - aflp - lycopersicon - accessions - cultivars - varieties
The taxonomy of the genus Rosa is complex, not least because of hybridisations between species.We aimed to develop a method to connect the diploid Rosa taxa to the allopolyploid taxa to which they contributed, based on the sharing of haplotypes. For this we used an SNPSTR marker, which combines a short tandem repeat (STR; microsatellite) marker with single nucleotide polymorphisms (SNPs) in the flanking sequences. In total, 53 different sequences (haplotypes) were obtained for the SNPSTR marker, Rc06, from 20 diploid and 35 polyploid accessions from various species of Rosa. Most accessions of the diploid species had only one allele, while accessions of the polyploid species each contained two-to-five different alleles.Twelve SNPs were detected in the flanking sequences, which alone formed a total of 18 different haplotypes. A maximum likelihood dendrogram revealed five groups of haplotypes. Diploid species in the same Section of the genus Rosa contained SNP haplotypes from only one haplotype group. In contrast, polyploid species contained haplotypes from different haplotype groups. Identical SNP haplotypes were shared between polyploid species and diploid species from more than one Section of the genus Rosa. There were three different polymorphic repeat regions in the STR region. The STR repeat contained eight additional SNPs, but these contributed little to the resolution of the haplotype groups. Our results support hypotheses on diploid Rosa species that contributed to polyploid taxa. Finding different sets of haplotypes in different groups of species within the Sections Synstylae and Pimpinellifoliae supports the hypothesis that these may be paraphyletic.
Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data
Heerwaarden, J. van; Odong, T.L. ; Eeuwijk, F.A. van - \ 2013
Theoretical and Applied Genetics 126 (2013)3. - ISSN 0040-5752 - p. 763 - 772.
population-structure - germplasm collections - model - distance - conservation - accessions - algorithms - management - diversity - richness
Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups.
Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation
Odong, T.L. ; Jansen, J. ; Eeuwijk, F.A. van; Hintum, T.J.L. van - \ 2013
Theoretical and Applied Genetics 126 (2013)2. - ISSN 0040-5752 - p. 289 - 305.
morphological descriptors - germplasm collection - sampling strategies - diversity - algorithm - establishment - accessions - selection - markers - sorghum
Definition of clear criteria for evaluation of the quality of core collections is a prerequisite for selecting high-quality cores. However, a critical examination of the different methods used in literature, for evaluating the quality of core collections, shows that there are no clear guidelines on the choices of quality evaluation criteria and as a result, inappropriate analyses are sometimes made leading to false conclusions being drawn regarding the quality of core collections and the methods to select such core collections. The choice of criteria for evaluating core collections appears to be based mainly on the fact that those criteria have been used in earlier publications rather than on the actual objectives of the core collection. In this study, we provide insight into different criteria used for evaluating core collections. We also discussed different types of core collections and related each type of core collection to their respective evaluation criteria. Two new criteria based on genetic distance are introduced. The consequences of the different evaluation criteria are illustrated using simulated and experimental data. We strongly recommend the use of the distance-based criteria since they not only allow the simultaneous evaluation of all variables describing the accessions, but they also provide intuitive and interpretable criteria, as compared with the univariate criteria generally used for the evaluation of core collections. Our findings will provide genebank curators and researchers with possibilities to make informed choices when creating, comparing and using core collections
Authenticity of old cultivars in genebank collections: a case study on lettuce
Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van - \ 2011
Crop Science 51 (2011)2. - ISSN 0011-183X - p. 736 - 746.
genenbanken - slasoorten - aflp - oude plantenrassen - ex-situ conservering - cultivarauthenticiteit - lactuca sativa - rassen (planten) - cultivars - gene banks - lettuces - amplified fragment length polymorphism - old varieties - ex situ conservation - cultivar authenticity - varieties - genetic diversity - maintenance - accessions - longevity - level - l.
Ex situ collections in genebanks conserve many old cultivars that had disappeared from mainstream agriculture before modern genebanks were established. The collections incorporated cultivars from many sources, such as botanical gardens and working collections, sometimes with little further information on their origin. Many old cultivars with identical or synonymous names are maintained in multiple collections and often more than once within collections. This research investigates the authenticity of old cultivars in genebanks using a large lettuce (Lactuca sativa L.) collection as a case study. Accessions presumed to be identical, based on the cultivar names accompanying the accessions, were compared for their DNA marker profiles, based on amplified fragment length polymorphisms (AFLPs). Using the genetic similarity of these accessions, the probability of authenticity of the old cultivars maintained in the collection was estimated. Separate analyses were done for different classes of cultivars, on the basis of the year of release or the donor history of the cultivar. The two largest cultivar groups within the collection, Sans Rivale à Graine Blanche and Maikönig, were analyzed in detail. Nonauthenticity of the investigated cultivars appeared to be high. This was especially true for the oldest cultivars, but even for the cultivars released from the 1960s to 1990 it was estimated that approximately 10% was not authentic. Recommendations to improve authenticity of cultivars in ex situ collections were presented
Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection
Treuren, R. van; Hintum, T.J.L. van; Wiel, C.C.M. van de - \ 2008
Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 319 - 330.
genetic-variation - bremia-lactucae - accessions - construction - resistance - database - tomato - aflps - rapd
To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationists
Diversity and linkage disequilibrium analysis wihtin a selected set of cultivated tomatoes
Berloo, R. van; Zhu, A. ; Ursem, R.A. ; Verbakel, H. ; Gort, G. ; Eeuwijk, F.A. van - \ 2008
Theoretical and Applied Genetics 117 (2008). - ISSN 0040-5752 - p. 89 - 101.
fragment-length-polymorphism - lycopersicon-esculentum - genetic diversity - rapd markers - aflp markers - software - accessions - stability - inference - map
Within the Dutch genomics initiative the ¿Centre for Biosystems Genomics¿ (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies
The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects on diversity of regeneration, as measured with AFLPs
Hintum, T.J.L. van; Wiel, C.C.M. van de; Visser, D.L. ; Treuren, R. van; Vosman, B.J. - \ 2007
Theoretical and Applied Genetics 114 (2007)5. - ISSN 0040-5752 - p. 777 - 786.
molecular characterization - germplasm - maintenance - accessions - integrity - dna - l.
The ex situ conservation of plant genetic resources in gene banks involves the selection of accessions to be conserved and the maintenance of these accessions for current and future users. Decisions concerning both these issues require knowledge about the distribution of genetic diversity within and between accessions sampled from the gene pool, but also about the changes in variation of these samples as a result of regenerations. These issues were studied in an existing gene bank collection of a cross-pollinating crop using a selection of groups of very similar Dutch white cabbage accessions, and additional groups of reference material representing the Dutch, and the global white cabbage gene pool. Six accessions were sampled both before and after a standard regeneration. 30 plants of each of 50 accessions plus 6 regeneration populations included in the study were characterised with AFLPs, using scores for 103 polymorphic bands. It was shown that the genetic changes as a result of standard gene bank regenerations, as measured by AFLPs, are of a comparable magnitude as the differences between some of the more similar accessions. The observed changes are mainly due to highly significant changes in allele frequencies for a few fragments, whereas for the majority of fragments the alleles occur in similar frequencies before and after regeneration. It is argued that, given the changes of accessions over generations, accessions that display similar levels of differentiation may be combined safely.
New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci.
El-Lithy, M.E.M. ; Bentsink, L. ; Hanhart, C.J. ; Ruys, G.J. ; Rovito, D. ; Broekhof, J.L.M. ; Poel, H.J. van der; Eijk, M.J. ; Vreugdenhil, D. ; Koornneef, M. - \ 2006
Genetics 172 (2006)3. - ISSN 0016-6731 - p. 1867 - 1876.
natural allelic variation - landsberg erecta - qtl analysis - thaliana - accessions - polymorphism - expression - ecotypes - mutants - markers
The SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Ler as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Ler has an allele different from one, two, or three of the other accessions
The economic value of coffee (Coffea arabica) genetic resources
Hein, L.G. ; Gatzweiler, F. - \ 2006
Ecological Economics 60 (2006)1. - ISSN 0921-8009 - p. 176 - 185.
resistance - diversity - rust - accessions - benefits - seeds
Whereas the economic value of genetic diversity is widely recognized there are, to date, relatively few experiences with the actual valuation of genetic resources. This paper presents an analysis of the economic value of Coffea arabica genetic resources contained in Ethiopian highland forests. The valuation is based on an assessment of the potential benefits and costs of the use of C. arabica genetic information in breeding programs for enhanced coffee cultivars. The study considers the breeding for three types of enhanced cultivars: increased pest and disease resistance, low caffeine contents and increased yields. Costs and benefits are compared for a 30 years discounting period, and result in a net present value of coffee genetic resources of 1458 and 420 million US$, at discount rates of 5% respectively 10%. The value estimate is prone to considerable uncertainty, with major sources of uncertainty being the length of breeding programs required to transfer valuable genetic information into new coffee cultivars, and the potential adoption rate of such enhanced cultivars. Nevertheless, the study demonstrates the high economic value of genetic resources, and it underlines the need for urgent action to halt the currently ongoing, rapid deforestation of Ethiopian highland forests.
The heavy metal hyperaccumulator Thlaspi caerulescens expresses many species-specific genes, as identified by comparative expressed sequence tag analysis
Rigola, D. ; Fiers, M.W.E.J. ; Vurro, E. ; Aarts, M.G.M. - \ 2006
New Phytologist 170 (2006)4. - ISSN 0028-646X - p. 753 - 765.
arabidopsis genome - zn hyperaccumulator - tolerance - plants - accumulation - model - brassicaceae - transporter - populations - accessions
¿ Thlaspi caerulescens is a natural zinc (Zn), cadmium (Cd) and nickel (Ni) hyperaccumulator and an emerging plant model species to study heavy metal hyperaccumulation and tolerance. This paper describes the analysis of the first expressed sequence tag (EST) collection from T. caerulescens. This collection is a new resource to unravel the molecular basis of plant metal homeostasis, tolerance and hyperaccumulation. ¿ In total, 4289 ESTs were generated originating from Zn-exposed root and shoot tissues, leading to 3709 T. caerulescens assembled partial cDNA sequences (unigenes). ¿ In comparison to Arabidopsis or other publicly available plant sequences, a fraction of c. 8% of the T. caerulescens unigenes (TcUGs) had no significant similarity with any known DNA sequence and, so far, these sequences are T. caerulescens specific. Three per cent of the TcUGs correspond to Arabidopsis thaliana orthologues that, as yet, have not been found to be expressed. ¿ The T. caerulescens transcriptome generally relates very well to the A. thaliana transcriptome, although, compared with other closely related species, a relatively large number of T. caerulescens-specific transcripts were found. T. caerulescens also expresses a relatively large number of genes which are expressed at a very low level in A. thaliana.
Evaluation of the Simultaneous Effects of Processing Parameters on the Iron and Zinc Solubility of Infant Sorghum Porridge by Response Surface Methodology
Kayodé, A.P.P. ; Nout, M.J.R. ; Bakker, E.J. ; Boekel, M.A.J.S. van - \ 2006
Journal of Agricultural and Food Chemistry 54 (2006)12. - ISSN 0021-8561 - p. 4253 - 4259.
plant foods - fermentation - varieties - grains - maize - seeds - supplementation - availability - accessions - components
The purpose of this study was to improve the micronutrient quality of indigenous African infant flour using traditional techniques available in the region. Response surface methodology was used to study the effect of duration of soaking, germination, and fermentation on phytate and phenolic compounds (PC), pH, viscosity, and the in vitro solubility (IVS) of iron and zinc in infant sorghum flour. The phytate and the PC concentrations of the flour were significantly modified as a result of the duration of germination and fermentation and their mutual interaction. These modifications were accompanied by a significant increase in % IVS Zn after 24 h of sprouting. Except for the interaction of soaking and fermentation, none of the processing parameters exerted a significant effect on the % IVS Fe. The viscosity of the porridge prepared with the flour decreased significantly with the duration of germination, making it possible to produce a porridge with high energy and nutrient density. The use of germination in combination with fermentation is recommended in the processing of cereals for infant feeding in developing countries.
Diversity and food quality properties of farmers' varieties of sorghum from Bénin
Kayodé, A.P.P. ; Linnemann, A.R. ; Nout, M.J.R. ; Hounhouigan, J.D. ; Stomph, T.J. ; Smulders, M.J.M. - \ 2006
Journal of the Science of Food and Agriculture 86 (2006)7. - ISSN 0022-5142 - p. 1032 - 1039.
genetic diversity - aflp analysis - dna - markers - accessions - cultivars - ethiopia - barley - rapds
Farmers' varieties of sorghum from three communities in different regions of northern Bénin were analysed for their food quality and agro-morphological properties, and also for their genetic diversity using amplified fragment length polymorphism (AFLP). Farmers' varieties of sorghum differed greatly with respect to their morphology and agronomic and food traits. Most of the varieties had long (>200 cm) stems (87%), loose panicles (79%) and a red or pink colour (52%). Most were susceptible to drought (54%) and to attacks by striga (79%), insects (99%) and birds (77%). Farmers evaluated the quality of the seeds for preparing porridges as being high for 60% of the varieties and 26% of the varieties were regarded as suitable for making beverages. Late-maturing, large-seeded, red or pink varieties are preferred by farmers for porridges and beverages. Gene diversity among varieties within regions, as measured by neutral markers, was similar for the three regions (0.211-0.240). However, across regions the short (
Characterization of host tolerance to Striga hermonthica
Rodenburg, J. ; Bastiaans, L. ; Kropff, M.J. - \ 2006
Euphytica 147 (2006)3. - ISSN 0014-2336 - p. 353 - 365.
pennisetum-glaucum - maize cultivars - resistance - sorghum - yield - infestation - accessions - infection - asiatica - seedbank
One of the most promising control options against the parasitic weed Striga hermonthica is the use of crop varieties that combine resistance with high levels of tolerance. The aim of this study was to clarify the relation between Striga infestation level, Striga infection level and relative yield loss of sorghum and to use this insight for exploring the options for a proper screening procedure for tolerance. In three pot experiments, conducted in Mali (2003) and The Netherlands (2003, 2004), four sorghum genotypes were exposed to a range of Striga infestation levels, ranging from 0.0625 to 16 seeds cm¿3. Observations included regular Striga emergence counts and sorghum grain yield at maturity. There were significant genotype, infestation and genotype × infestation effects on sorghum yield. The relation between infestation level and infection level was density dependent. Furthermore, the relation between Striga infection level and relative yield loss was non-linear, though for the most resistant genotype Framida only the linear part of the relation was obtained, as even at high infestation levels only moderate infection levels were achieved. The results suggest that for resistant genotypes, tolerance can best be quantified as a reduced relative yield loss per aboveground Striga plant, whereas for less resistant genotypes the maximum relative yield loss can best be used. Whether both expressions of tolerance are interrelated could not be resolved. Complications of screening for tolerance under field conditions are discussed
Genetic and Environmental Impact on Iron, Zinc, and Phytate in Food Sorghum Grown in Benin
Kayodé, A.P.P. ; Linnemann, A.R. ; Hounhouigan, J.D. ; Nout, M.J.R. ; Boekel, M.A.J.S. van - \ 2006
Journal of Agricultural and Food Chemistry 54 (2006)1. - ISSN 0021-8561 - p. 256 - 262.
nutrient composition - aflp analysis - dna - bioavailability - accessions - availability - fermentation - cultivars - diversity - nutrition
Seventy-six farmers' varieties of sorghum from Benin were distinguished by amplified fragment length polymorphism (AFLP) and clustered into 45 distinct genotypes. The genotype clusters were evaluated for their Fe, Zn, and phytate concentrations to assess the impact of genetic and environmental effects on the composition of the grains and to identify farmers' varieties with high potential Fe and Zn availability. The Fe concentration of the grains ranged from 30 to 113 mg/kg with an average of 58 mg/kg. The Zn concentration ranged from 11 to 44 mg/kg with an average of 25 mg/kg. The phytate concentration of the grain ranged from 0.4 to 3.5% with a mean of 1.2%. The grain-Fe and grain-Zn did not show consistent linkage to genetic variation, but varied significantly across field locations, suggesting a predominant environmental impact. The phytate concentration of the grains appeared to be environmentally as well as genetically determined. No varieties provide adequate Zn to meet nutritional requirements of sorghum consumers. The most promising varieties for Fe supply were tokogbessenou, mahi swan, biodahu, saï maï, mare dobi, sakarabokuru, and chabicouma, as they showed a [phytate]/[Fe] ratio of
How can field selection for Striga resistance and tolerance in sorghum be improved?
Rodenburg, J. ; Bastiaans, L. ; Weltzien, E. ; Hess, D.E. - \ 2005
Field Crops Research 93 (2005)1. - ISSN 0378-4290 - p. 34 - 50.
hermonthica del benth - pennisetum-glaucum - yield losses - maize - cultivars - infestation - accessions - expression - infection - varieties
Breeding for high yielding Sorghum bicolor varieties with effective resistance and tolerance against the hemi-parasitic weed Striga hermonthica requires suitable selection measures for both characteristics. The objective of this research was to constitute a set of practical selection measures that contain independent, reliable and discriminative criteria for resistance and tolerance. Ten sorghum genotypes were grown in the field with and without Striga infestation in a split-plot design in 3 successive years (2001-2003) using different Striga infestation levels (low, high and intermediate). Resistance against Striga in the below-ground stages was determined separately in an agar-gel assay and a pot trial. The addition of Striga-free control plots facilitated the calculation of the relative yield loss, which represents the result of resistance and tolerance combined. Correlation analysis indirectly demonstrated that both resistance and tolerance are important yield determining traits under Striga infestation. Tolerance was relatively more important under low Striga infestation levels, whereas resistance was relatively more important at high infestation levels. With respect to resistance, both the area under the Striga number progress curve (ASNPC) and maximum above-ground Striga number (NSmax) turned out to be discriminative and consistent selection measures. Both measures also corresponded well with the expression of resistance during below-ground stages of the parasite. It proved more difficult to arrive at a satisfactory measure for tolerance. Inclusion of Striga-free plots is an essential step for the determination of tolerance, but in itself not sufficient. It provides a basis for the determination of the relative yield loss, which then needs to be corrected for differences in infection level resulting from genotypic differences in resistance. A linear correction for infection level disregards the density dependency of the relative yield loss function. It is expected that clarification of the relation between Striga infection level and yield loss, provides a solid basis for the development of unambiguous tolerance measures in the field. This will enable the breeder to select for resistance and tolerance separately, which is likely to result in the optimum combination of both defence mechanisms.
Genetic and economic aspects of marker-assisted reduction of redundancy from a wild potato germplasm collection
Treuren, R. van; Magda, A. ; Hoekstra, R. ; Hintum, T.J.L. van - \ 2004
Genetic Resources and Crop Evolution 51 (2004)3. - ISSN 0925-9864 - p. 277 - 290.
rapd analysis - aflp markers - dna - accessions - conservation - identification - management - diversity - resources - rflp
The wild potato germplasm collection of the series Acaulia, maintained at the Centre for Genetic Resources, The Netherlands, consists of 314 accessions. In previous investigations, 15 potential duplication groups with a total of 36 accessions were identified based on AFLP analysis of a limited sample per accession. In the present study, the potential redundancies, plus one additional accession, were studied with increased sample sizes to examine intra- and inter-accession variation more accurately, with the aim to reduce the size of the collection. No variation was observed within two potential duplication groups, whereas only limited differentiation among accessions was detected within seven groups, resulting in a total of 15 redundant accessions (nearly 5% of the collection). A cluster analysis of all the accessions of the collection showed that these nine groups each had a distinct identity. It was decided to maintain the accessions of the remaining six groups as separate entries based on the large differentiation observed among accessions and the absence of a clear identity. An analysis of molecular variance in the set of 37 accessions showed that 91% of the observed variation could be found among accessions. This variance component appeared unaffected when the set was analysed without the 15 redundant accessions. The invested costs to identify redundancies in the series Acaulia by AFLP analysis are estimated at k 57.3, whereas the savings achieved by reduction of the collection are estimated at k 21.0 per generation. However, a cost-benefit analysis should not only focus on the short-term return of investments, but should also consider the value of newly obtained data and information. These include taxonomic information about accessions, optimised sampling strategies, optimised regeneration procedures, additional data for core collection formation and more efficient utilisation of germplasm.
Quantitative trait local analysis of growth-related traits in a new Arabidopsis recombinant inbred population
El-Lithy, M.E.M. ; Clerkx, E.J.M. ; Ruijs, G.J. ; Koornneef, M. ; Vreugdenhil, D. - \ 2004
Plant Physiology 135 (2004)1. - ISSN 0032-0889 - p. 444 - 458.
natural allelic variation - late-flowering mutants - plant-growth - image-analysis - landsberg erecta - thaliana - time - accessions - gene - qtl
Arabidopsis natural variation was used to analyze the genetics of plant growth rate. Screening of 22 accessions revealed a large variation for seed weight, plant dry weight and relative growth rate but not for water content. A positive correlation was observed between seed weight and plant area 10 d after planting, suggesting that seed weight affects plant growth during early phases of development. During later stages of plant growth this correlation was not significant, indicating that other factors determine growth rate during this phase. Quantitative trait locus (QTL) analysis, using 114 (F9 generation) recombinant inbred lines derived from the cross between Landsberg erecta (Ler, from Poland) and Shakdara (Sha, from Tadjikistan), revealed QTLs for seed weight, plant area, dry weight, relative growth rate, chlorophyll fluorescence, flowering time, and flowering-related traits. Growth traits (plant area, dry weight, and relative growth rate) colocated at five genomic regions. At the bottom of chromosome 5, colocation was found of QTLs for leaf area, leaf initiation speed, specific leaf area, and chlorophyll fluorescence but not for dry weight, indicating that this locus might be involved in leaf development. No consistent relation between growth traits and flowering time was observed despite some colocations. Some of the QTLs detected for flowering time overlapped with loci detected in other recombinant inbred line populations, but also new loci were identified. This study shows that Arabidopsis can successfully be used to study the genetic basis of complex traits like plant growth rate.
Marker-assisted rationalisation of genetic resources collections: a case study in flax using AFLPs
Treuren, R. van; Soest, L.J.M. van; Hintum, T.J.L. van - \ 2001
Theoretical and Applied Genetics 103 (2001)1. - ISSN 0040-5752 - p. 144 - 152.
germplasm collections - rapd analysis - accessions - dna - duplication - l. - diversity - spain
Removing redundant germplasm from collections is one of the options for genebanks to increase the efficiency of their genetic resource management. Molecular characterisation of germplasm is thereby becoming more and more important to verify suspected duplication. AFLPs were used to characterise 29 flax accessions of material derived from research activities (hereafter termed breeder's line). Based on similar accession names, the breeder's lines could be classified into three series ('M 25', 'Ru' and 'Rm') that were expected to contain redundancies. In addition, 12 reference cultivars were analysed. A total number of 144 polymorphic bands (59.8%) were scored among the 164 individuals investigated. In general, relatively high levels of intra-accession variation were found, even for the cultivars examined. This finding was not in line with the low outcrossing rates reported for flax. A cluster analysis grouped the Ru' and 'Rm' series together, indicating their close genetic relationship. An analysis of molecular variance (AMOVA) showed a significant group effect (fibre/oil flax) only for M 25', explaining 34% of the variation observed within this series. For the cultivars 40.5% of the variation was distributed among accessions within groups and all pairwise comparisons were significantly different, except for one case. Both for the series of breeder's lines and the cultivars the major part of the variation was distributed among individuals within accessions. This component constituted 80.7% and 83.6% of the total variation for the 'Ru' and 'Rm' series, respectively. Pairwise comparisons of accessions were performed by AMOVA in order to identify redundant germplasm. Stepwise bulking of accessions until all remaining accessions were significantly different showed that the 29 accessions of breeder's lines could be reduced to 14. Only a small negative effect of this bulking approach on the among-population component of variance was observed, showing a reduction of 2.6%. Results are discussed in relation to improving the efficiency of collection management
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