High Degree of Multiple Paternity and Reproductive Skew in the Highly Fecund Live-Bearing Fish Poecilia gillii (Family Poeciliidae)
Dekker, Myrthe L. ; Hagmayer, Andres ; Leon-Kloosterziel, Karen M. ; Furness, Andrew I. ; Pollux, Bart J.A. - \ 2020
Frontiers in Ecology and Evolution 8 (2020). - ISSN 2296-701X
brood size - COLONY - female size - GERUD - microsatellites - polyandry - viviparity
Multiple paternity is a common phenomenon within the live-bearing fish family Poeciliidae. There is a great variety in brood sizes of at least two orders-of-magnitude across the family. However, little is known about the ramifications of this remarkable variation for the incidence and degree of multiple paternity and reproductive skew. Mollies (subgenus Mollienesia, genus Poecilia) produce some of the largest broods in the family Poeciliidae, making them an excellent model to study the effects of intra-specific variation in brood size on patterns of multiple paternity. We collected samples of the live-bearing fish Poecilia gillii from 9 locations in Costa Rica. We measured body size of 159 adult females, of which 72 were pregnant. These samples had a mean brood size of 47.2 ± 3.0 embryos, ranging from 4 to 130 embryos. We genotyped 196 field-collected specimens with 5 microsatellite markers to obtain location-specific allele frequencies. In addition, we randomly selected 31 pregnant females, genotyped all their embryos (N = 1346) and calculated two different parameters of multiple paternity: i.e., the minimum number of sires per litter using an exclusion-based method (GERUD) and the estimated number of sires per litter using a maximum likelihood approach (COLONY). Based on these two approaches, multiple paternity was detected in 22 and 27 (out of the 31) females, respectively, with the minimum number of sires ranging from 1 to 4 (mean ± SE: 2.1 ± 0.16 sires per female) and the estimated number of fathers ranging from 1 to 9 (mean ± SE: 4.2 ± 0.35 sires per female). The number of fathers per brood was positively correlated with brood size, but not with female size. Next, we calculated the reproductive skew per brood using the estimated number of sires, and found that in 21 out of the 27 multiply sired broods sires did not contribute equally to the offspring. Skew was not correlated with either female size, brood size or the number of sires per brood. Finally, we discuss several biological mechanisms that may influence multiple paternity and reproductive skew in P. gillii as well as in the Poeciliidae in general.
Data from: Distinguishing migration events of different timing for wild boar in the Balkans
Alexandri, Panoraia ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Goedbloed, D.J. ; Herrero Medrano, J.M. ; Rund, L.A. ; Schook, Lawrence B. ; Chatzinikos, Evangelos ; Triantaphyllidis, Costas ; Triantafyllidis, Alexander - \ 2016
Wageningen University & Research
SNPs - population genetics - recent migration - genetic diversity - mammal - microsatellites - Sus scrofa
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimation analysis. Results: Both microsatellite and SNP data analyses detected genetic structure caused by historic events and support the existence of three groups in the studied area. A hybrid zone between two of the groups was also detected. We also showed that genome-wide SNP data analysis can identify recent events in bottlenecked populations. Main conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp when populations contracted to different refugia. Our findings strengthened the evidence that the southern Balkan area was a glacial refugium including further local smaller refugia. Genome-wide genotyping inferred a recent population expansion that can mimic a ‘refugium within refugium’ scenario. It seems that microsatellite data tend to overestimate genetic structure when genetic drift happens in bottlenecked populations over a short distance. Therefore, genome-wide SNPs are more powerful at inferring phylogeography in natural populations, resolving inconsistencies from mitochondrial and microsatellite data sets.
Data from: Molecular biogeography of prickly lettuce (Lactuca serriola L.) shows traces of recent range expansion
Andrea, L. D'; Meirmans, Patrick ; Wiel, C.C.M. van de; Guadagnuolo, Roberto ; Treuren, R. van; Kozlowski, Gregor ; Nijs, Hans den; Felber, F. - \ 2016
Wageningen University & Research
biogeography - microsatellites - chloroplast PCR-RFLP - population genetics - global change - population structure - phylogeography
Microsatellite data in GenePop format for Lactuca serriola in Europe
The allo-octoploid strawberry: simply complex
Dijk, Thijs van - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Eric van de Weg. - Wageningen : Wageningen University - ISBN 9789462579637 - 185
fragaria ananassa - strawberries - polyploidy - microsatellites - linkage mapping - genome analysis - quantitative trait loci - genetic mapping - flowering - plant breeding - fragaria ananassa - aardbeien - polyploïdie - microsatellieten - koppelingskartering - genoomanalyse - loci voor kwantitatief kenmerk - genetische kartering - bloei - plantenveredeling
The garden strawberry (Fragaria x ananassa) is a fruit species that was developed through human intervention less than 300 years ago. Currently, it is the most important soft fruit in both production as well as value and renowned for its deliciousness. There are many challenges in growing such a delicate fruit, many of which have been overcome through improved cultivation techniques and breeding. The perishability of the product is, however, not the only challenge faced by strawberry breeders. In terms of genome composition, strawberry appears to have accumulated a wonderful array of obstacles to genetic studies. It is a vegetatively propagated allo-octoploid outbreeder, and only few crop species are worse of in this respect. Many of the molecular genetic ground work is therefore performed in its diploid ancestor, the woodland strawberry Fragaria vesca, which was sequenced in 2011. However, since nearly all strawberries that are eaten are octoploid, genetic research can’t linger at the wild diploids forever. In this thesis we developed new tools and analysis methods for genetic studies in the allo-octoploid strawberry and subsequently applied these methods in the detection of marker-trait associations.
The purpose of Chapter 2 was to develop a method to interpret the complex peak patterns generated by microsatellites in octoploid strawberry in such a way that we ended up with as much information as one would expect to retrieve from a microsatellite in a diploid system. This information could then be used to generate high quality linkage maps for the different sub-genomes and allow for easy alignment and comparison. We named the method MADCE, which stands for Microsatellite Allele Dose & Configuration Establishment. In the MADCE methodology, we first need to determine the dose of each allele present in an individual. For this we used the signal of fluorescent microsatellite peaks in relation to the total fluorescent signal generated by all peaks for that microsatellite. We then used the disomic inheritance of strawberry to establish the allelic configuration of each different homoeologue (subgenome). The repulsion of alleles from the same subgenome in offspring allowed us to form subgenomic pairs of alleles. We found that in single cross mapping populations, the deployment of our method was fairly easy due to the high number of offspring that can be used to establish repulsion between alleles. However, for pedigreed breeding germplasm this was another matter, as generally only few offspring were available. For this we added some additional tricks to the MADCE method, although some uncertainty about the configuration would remain for problematic lines and alleles.
In Chapter 3 we used the MADCE method from Chapter 2 to generate a genome wide linkage map for the Holiday x Korona (HxK) mapping population. This linkage map was to be used in subsequent experiments for QTL discovery as well as provide the strawberry community with a highly detailed map consisting not only of marker distances, but allele and haplotype configuration of the parents Holiday and Korona as well. The haplotype information revealed that inbreeding (homozygosity) levels in Holiday were similar to the levels expected from its pedigree, but that inbreeding levels of Korona were more than three times higher than expected, which could be resultant from selection pressure enacted by breeders. Selection pressure could also be causal to our discovery that the kinship between the two cultivars was twice as high as expected from their shared ancestry. Another discovery was a large inversion on one of the subgenomes of linkage group 2 (D). Up until the publication of our linkage map this inversion had not been reported in other linkage maps. Another innovation was our attempt at giving a biological or evolutionary meaning to the denomination of the linkage groups by arranging them according to similarity to the diploid ancestor F. vesca, based on F. vesca derived primer amplification efficiencies. The HxK map has been used in several (ongoing) research projects outside of our research group and has contributed to the development of the 90k Axiom SNP array for cultivated strawberry.
In Chapter 4 we performed a QTL mapping study for disease resistance against the problematic pathogen Phytophthora cactorum, which causes crown rot in strawberry plants. In this study we used two different mapping populations: the Holiday x Korona (HxK) population from the previous chapter as well as E1998-142 x Elsanta (ExEls), developed more specifically for the purpose of finding resistance against P. cactorum. The HxK and ExEls populations were phenotyped over three years (2008, 2010 and 2011) under different seasons and conditions. The correlation between years for was quite low for both populations (ranging from 0.18 to 0.47), indicating a large environmental effect on disease pressure. Results from the QTL analysis showed that most QTLs were small in effect and only just above the statistical significance threshold. Only for ExEls we uncovered two QTLs with relatively high significance levels, but none were significant in all three years. Because of the high environmental influence, and the desire to have QTLs that are robust over environments, we used the average of all three years (AOTY) as an additional phenotype. When we used the AOTY trait, the QTL on LG7D became stronger than for any of the individual years. Whereas for the LG7C QTL the significance dropped to just below threshold levels. These results indicated that removing environmental noise through averaging over experiments is a good way to uncover the most reliable and therefore more valuable to a breeding program.
In Chapter 5 we investigated the genetics behind two different flowering habits that are grown commercially worldwide: seasonal flowering habit (SF) and perpetual flowering (PF) These varieties initiate flowering under long days, and can therefore produce fruit for a much longer period: throughout the summer and early fall. Evidence from literature and practical breeding suggested that PF is under dominant control. We decided to treat PF as a qualitative trait and divided two small mapping populations into PF and SF individuals. After screening several microsatellites, we found one locus that completely cosegregated with the PF trait at the bottom of LG4D. At the moment of mapping, a paper was published which mapped the same trait to the same location. We found that there were two very clear candidate genes within our QTL interval, FaCDF2 and FaFT2, which were homologous to genes that are major factors in the flowering pathway of Arabidopsis and many other plant species. We then sequenced the FaCDF2 gene from a number of distinct PF and SF cultivars. This resulted in the discovery of two quite distinct allelic variants, one of which was present in all PF cultivars. However this variant was also present in some of the SF cultivars, indicating that either FaCDF2 is not the causal gene, or that other loci can have a qualitative effect on the switch from SF to PF. We then performed microsatellite haplotyping on hundreds of cultivars and this revealed that all PF varieties of all origins carry the same haplotype in the PF QTL region, and that there weren’t any recombinations between the candidate genes FaCDF2 and FaFT2, which are 250kb apart on the physical genome. This makes it still undecided which of these two candidate genes are causal to the PF trait. Another interesting result from the haplotyping was that the complete PF haplotype was present with moderate frequency in SF varieties as well. Not only does this suggest a common origin, it also complicates the establishment of a theory for the mechanisms behind perpetual flowering in cultivated strawberry. So far we have not been able to establish whether the PF haplotype that is present in SF cultivars is functionally distinct from the PF haplotype in PF cultivars. All we know is that it does not confer perpetual flowering in these SF cultivars, and further experiments would be needed to find out the exact mechanism behind perpetual flowering.
In the general discussion (Chapter 6), the results of this thesis were placed in the broader context of science in general and plant breeding in particular.
Data from: Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits
Lemoine, Mélissa ; Lucek, Kay ; Perrier, Charles ; Saladin, Verena ; Adriaensen, Frank ; Barba, Emilio ; Belda, Eduardo ; Charmantier, Anne ; Cichoń, Mariusz ; Eeva, Tapio ; Grégoire, Arnaud ; Hinde, C.A. ; Oers, Kees van; Visser, M.E. - \ 2015
Wageningen University & Research
microsatellites - F-statistics - isolation-by-distance - latitude - winter severity - Population genetic structure
This file contains the combined dataset collected on great tits (Parus major) from 30 sites in Europe. Provided are individual data for microsatellites (GenData) and environmental data by site (EnvData)
Natural loss-of-function mutation of EDR1 conferring resistance to tomato powdery mildew in Arabidopsis thaliana accession C24
Gao, D. ; Appiano, M. ; Huibers, R.P. ; Loonen, A.E.H.M. ; Visser, R.G.F. ; Wolters, A.M.A. ; Bai, Y. - \ 2015
Molecular Plant Pathology 16 (2015)1. - ISSN 1464-6722 - p. 71 - 82.
salicylic-acid - downy mildew - gene - defense - plants - microsatellites - mechanism - evolution - cloning - kinase
To screen for potentially novel types of resistance to tomato powdery mildew Oidium neolycopersici, a disease assay was performed on 123 Arabidopsis thaliana accessions. Forty accessions were fully resistant, and one, C24, was analysed in detail. By quantitative trait locus (QTL) analysis of an F2 population derived from C24 × Sha (susceptible accession), two QTLs associated with resistance were identified in C24. Fine mapping of QTL-1 on chromosome 1 delimited the region to an interval of 58¿kb encompassing 15 candidate genes. One of these was Enhanced Disease Resistance 1 (EDR1). Evaluation of the previously obtained edr1 mutant of Arabidopsis accession Col-0, which was identified because of its resistance to powdery mildew Golovinomyces cichoracearum, showed that it also displayed resistance to O.¿neolycopersici. Sequencing of EDR1 in our C24 germplasm (referred to as C24-W) revealed two missing nucleotides in the second exon of EDR1 resulting in a premature stop codon. Remarkably, C24 obtained from other laboratories does not contain the EDR1 mutation. To verify the identity of C24-W, a DNA region containing a single nucleotide polymorphism (SNP) unique to C24 was sequenced showing that C24-W contains the C24-specific nucleotide. C24-W showed enhanced resistance to O.¿neolycopersici compared with C24 not containing the edr1 mutation. Furthermore, C24-W displayed a dwarf phenotype, which was not associated with the mutation in EDR1 and was not caused by the differential accumulation of pathogenesis-related genes. In conclusion, we identified a natural edr1 mutant in the background of C24.
Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms
The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.
Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies
Pham, H.T.M. ; Berthouly-Salazar, C. ; Crooijmans, R.P.M.A. - \ 2013
Animal Genetics 44 (2013)5. - ISSN 0268-9146 - p. 509 - 521.
multilocus genotype data - breeds - program - microsatellites - construction - resources - inference - software - ecotypes - alleles
The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within- and between-populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high-priority breeds, within-breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.
Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps
Sharma, S.K. ; Bolser, D. ; Boer, J.M. de; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
G3 : Genes Genomes Genetics 3 (2013)11. - ISSN 2160-1836 - p. 2031 - 2047.
tomato genome - sequence - dna - microsatellites - identification - centromeres - solanaceae - evolution
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new STS marker based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished using a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2,469 marker loci. In silico anchoring approaches employed genetic and physical maps from the diploid potato genotype RH and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules is closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal 'pseudomolecules'.
Variability and connectivity of plaice populations from the Eastern North Sea to the Western Baltic Sea, and implications for assessment and management
Ulrich, C. ; Boje, J. ; Cardinale, M. ; Hintzen, N.T. ; Miller, D.C.M. ; Rijnsdorp, A.D. - \ 2013
Journal of Sea Research 84 (2013). - ISSN 1385-1101 - p. 40 - 48.
pleuronectes-platessa l. - marine fishes - skagerrak - kattegat - atlantic - flatfish - stocks - size - microsatellites - recruitment
An essential prerequisite of sustainable fisheries is the match between biologically relevant processes and management action. Various populations may however co-occur on fishing grounds, although they might not belong to the same stock, leading to poor performance of stock assessment and management. Plaice in Kattegat and Skagerrak have traditionally been considered as one stock unit. Current understanding indicates that several plaice components may exist in the transition area between the North Sea and the Baltic Sea. A comprehensive review of all available biological knowledge on plaice in this area is performed, including published and unpublished literature together with the analyses of commercial and survey data and historical tagging data. The results suggest that plaice in Skagerrak is closely associated with plaice in the North Sea, although local populations are present in the area. Plaice in Kattegat, the Belts Sea and the Sound can be considered a stock unit, as is plaice in the Baltic Sea. The analyses revealed great heterogeneity in the dynamics and productivity of the various local components, and suggested for specific action to maintain biodiversity.
Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus
Foulongne-Oriol, M. ; Murat, C. ; Castanera, R. ; Ramírez, L. ; Sonnenberg, A.S.M. - \ 2013
Fungal Genetics and Biology 55 (2013). - ISSN 1087-1845 - p. 6 - 21.
simple sequence repeats - rice blast fungus - magnaporthe-oryzae - neurospora-crassa - chromosome ends - transposable elements - molecular markers - variable-number - evolution - microsatellites
Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of the genome- wide distribution of these elements and provide insights into potential mechanisms of genome plasticity. The present study uses in silico approaches to describe tandem repeats and transposable elements distribution in the genome of the button mushroom, Agaricus bisporus. Transposable elements comprised 12.43% of the assembled genome, and 66% of them were found clustered in the centromeric or telomeric regions. Methylation of retrotransposon has been demonstrated. A total of 1996 mini-, 4062 micro-, and 37 satellites motifs were identified. The microsatellites appeared widely and evenly spread over the whole genome sequence, whereas the minisatellites were not randomly distributed. Indeed, minisatellites were found to be associated with transposable elements clusters. Telomeres exhibited a specific sequence with a TnAGn signature. A comparison between the two available genome sequences of A. bisporus was also performed and sheds light on the genetic divergence between the two varieties. Beyond their role in genome structure, repeats provide a virtually endless source of molecular markers useful for genetic studies in this cultivated species.
The design and cross-population application of a genome-wide SNP chip for the great tit Parus major
Bers, N.E.M. van; Santure, A.W. ; Oers, K. van; Cauwer, I. de; Dibbits, B.W. ; Mateman, A.C. ; Crooijmans, R.P.M.A. ; Visser, M.E. ; Groenen, M.A.M. - \ 2012
Molecular Ecology Resources 12 (2012)4. - ISSN 1755-098X - p. 753 - 770.
generation sequencing technology - linkage disequilibrium - genotyping assay - climate-change - wild - chicken - microsatellites - adaptation - evolution - selection
The vast amount of phenotypic information collected in some wild animal populations makes them extremely valuable for unravelling the genetics of ecologically important traits and understanding how populations adapt to changes in their environment. Next generation sequencing has revolutionized the development of large marker panels in species previously lacking genomic resources. In this study, a unique genomics toolkit was developed for the great tit (Parus major), a model species in ecology and behavioural biology. This toolkit consists of nearly 100 000 SNPs, over 250 million nucleotides of assembled genomic DNA and more than 80 million nucleotides of assembled expressed sequences. A SNP chip with 9193 SNP markers expected to be spaced evenly along the great tit genome was used to genotype 4702 birds from two of the most intensively studied natural vertebrate populations [Wytham Woods/Bagley Woods (United Kingdom) and de Hoge Veluwe/Westerheide (The Netherlands)]. We show that (i) SNPs identified in either of the two populations have a high genotyping success in the other population, (ii) the minor allele frequencies of the SNPs are highly correlated between the two populations and (iii) despite this high correlation, a large number of SNPs display significant differentiation (FST) between the populations, with an overrepresentation of genes involved in cardiovascular development close to these SNPs. The developed resources provide the basis for unravelling the genetics of important traits in many long-term studies of great tits. More generally, the protocols and pitfalls encountered will be of use for those developing similar resources.
Convergent adaptations: bitter manioc cultivation systems in fertile anthropogenic dark earths and floodplain soils in central Amazonia
Fraser, J.A. ; Alves-Pereira, A. ; Braga Junqueira, A. ; Peroni, N. ; Clement, C.R. - \ 2012
PLoS ONE 7 (2012)8. - ISSN 1932-6203 - 13 p.
manihot-esculenta crantz - genetic diversity - traditional agroecosystems - cassava - management - dynamics - ecology - brazil - seed - microsatellites
Shifting cultivation in the humid tropics is incredibly diverse, yet research tends to focus on one type: long-fallow shifting cultivation. While it is a typical adaptation to the highly-weathered nutrient-poor soils of the Amazonian terra firme, fertile environments in the region offer opportunities for agricultural intensification. We hypothesized that Amazonian people have developed divergent bitter manioc cultivation systems as adaptations to the properties of different soils. We compared bitter manioc cultivation in two nutrient-rich and two nutrient-poor soils, along the middle Madeira River in Central Amazonia. We interviewed 249 farmers in 6 localities, sampled their manioc fields, and carried out genetic analysis of bitter manioc landraces. While cultivation in the two richer soils at different localities was characterized by fast-maturing, low-starch manioc landraces, with shorter cropping periods and shorter fallows, the predominant manioc landraces in these soils were generally not genetically similar. Rather, predominant landraces in each of these two fertile soils have emerged from separate selective trajectories which produced landraces that converged for fast-maturing low-starch traits adapted to intensified swidden systems in fertile soils. This contrasts with the more extensive cultivation systems found in the two poorer soils at different localities, characterized by the prevalence of slow-maturing high-starch landraces, longer cropping periods and longer fallows, typical of previous studies. Farmers plant different assemblages of bitter manioc landraces in different soils and the most popular landraces were shown to exhibit significantly different yields when planted in different soils. Farmers have selected different sets of landraces with different perceived agronomic characteristics, along with different fallow lengths, as adaptations to the specific properties of each agroecological micro-environment. These findings open up new avenues for research and debate concerning the origins, evolution, history and contemporary cultivation of bitter manioc in Amazonia and beyond.
Multiplex SSR analysis of Phytophthora infestans in different countries and the importance for potato breeding
Li, Y. - \ 2012
Wageningen University. Promotor(en): Evert Jacobsen, co-promotor(en): Theo van der Lee; D.E.L. Cooke. - S.l. : s.n. - ISBN 9789461732798 - 206
solanum tuberosum - aardappelen - plantenveredeling - plantenziekteverwekkende schimmels - phytophthora infestans - microsatellieten - populaties - ziekteresistentie - genetische merkers - moleculaire merkers - bio-informatica - genomica - plant-microbe interacties - solanum tuberosum - potatoes - plant breeding - plant pathogenic fungi - phytophthora infestans - microsatellites - populations - disease resistance - genetic markers - molecular markers - bioinformatics - genomics - plant-microbe interactions
Potato is the most important non-cereal crop in the world. Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease of potato. In the mid-19th century, P. infestans attacked the European potato fields and this resulted in a widespread famine in Ireland and other parts of Europe. Late blight remains the most important pathogen to potato and causes a yearly multi-billion US dollar loss globally. In Europe and North America, late blight control heavily relies on the use of chemicals, which is hardly affordable to farmers in developing countries and also raises considerable environmental concerns in the developed countries.
No evident spatial genetic structuring in the rapidly declining Black-tailed Godwit Limosa limosa in the Netherlands
Trimbos, K.B. ; Kentie, R. ; Verkuil, Y. ; Musters, C.J.M. ; Piersma, Th. ; Snoo, G.R. de - \ 2011
Conservation Genetics 12 (2011)3. - ISSN 1566-0621 - p. 629 - 636.
population-genetics - software - markers - microsatellites - management - regression - diversity - program - tests - dna
With 40% of the European Black-tailed Godwit population breeding in The Netherlands, this country harbours internationally significant numbers of this species. However, ongoing agricultural intensification has resulted in the fragmentation of the population and drastic population declines since 1967. By establishing genetic diversity, genetic differentiation and gene flow on the basis of 12 microsatellites, we investigated whether the population genetic structure of the Dutch Black-tailed Godwit bears the marks of these changes. Genetic diversity appeared to be moderate, and Bayesian model-based analysis of individual genotypes revealed no clustering in the Dutch populations. This was supported by pairwise FST values and AMOVA, which indicated no differentiation among the nine breeding areas. Gene flow estimates were larger than “one migrant per generation” between sample locations, and no isolation by distance was demonstrated. Our results indicate the maintenance of moderate levels of genetic diversity and genetic connectivity between breeding sites throughout the Dutch Black-tailed Godwit breeding population. We suggest that the Dutch Black-tailed Godwit breeding areas should be managed as a single panmictic unit, much as it is presently done
High resolution mapping of a novel late blight resistance gene Rpi-avll, from the wild Bolivian species Solanum avilesii
Verzaux, E.C. ; Budding, D.J. ; Vetten, N. de; Niks, R.E. ; Vleeshouwers, V.G.A.A. ; Vossen, E.A.G. van der; Jacobsen, E. ; Visser, R.G.F. - \ 2011
American Journal of Potato Research 88 (2011)6. - ISSN 1099-209X - p. 511 - 519.
marker-assisted selection - potato-virus-y - phytophthora-infestans - disease-resistance - quantitative resistance - cultivated potato - bulbocastanum - rflp - qtl - microsatellites
Both Mexico and South America are rich in Solanum species that might be valuable sources of resistance (R) genes to late blight (Phytophthora infestans). Here, we focus on an R gene present in the diploid Bolivian species S. avilesii. The genotype carrying the R gene was resistant to eight out of 10 Phytophthora isolates of various provenances. The identification of a resistant phenotype and the generation of a segregating population allowed the mapping of a single dominant R gene, Rpi-avl1, which is located in an R gene cluster on chromosome 11. This R gene cluster is considered as an R gene “hot spot”, containing R genes to at least five different pathogens. High resolution mapping of the Rpi-avl1 gene revealed a marker co-segregating in 3890 F1 individuals, which may be used for marker assisted selection in breeding programs and for further cloning of Rpi-avl1
The patterns of population differentiation in a Brassica rapa core collection
Pino del Carpio, D. ; Basnet, R.K. ; Vos, R.C.H. de; Maliepaard, C.A. ; Visser, R.G.F. ; Bonnema, A.B. - \ 2011
Theoretical and Applied Genetics 122 (2011)6. - ISSN 0040-5752 - p. 1105 - 1118.
genetic diversity - morphological traits - l. - association - aflp - microsatellites - spectroscopy - metabolomics - frequencies - landraces
With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC–MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa
Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification
Treuren, R. van; Kemp, H. ; Ernsting, G. ; Jongejans, B. ; Houtman, H. ; Visser, L. - \ 2010
Genetic Resources and Crop Evolution 57 (2010)6. - ISSN 0925-9864 - p. 853 - 865.
appels - genenbanken - genotypen - genetische merkers - microsatellieten - genetische diversiteit - fenotypen - apples - gene banks - genotypes - genetic markers - microsatellites - genetic diversity - phenotypes - molecular characterization - ssr markers - construction - polymorphism - database - tomato - plants - dna
A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varieties
Association mapping in tetraploid potato
hoop, B.B. D' - \ 2009
Wageningen University. Promotor(en): Richard Visser; Fred van Eeuwijk, co-promotor(en): Herman van Eck. - [S.l.] : S.n. - ISBN 9789085853336 - 161
solanum tuberosum - genetische kartering - microsatellieten - loci voor kwantitatief kenmerk - verstoord koppelingsevenwicht - genetische analyse - genetische merkers - cultivars - marker assisted breeding - aflp - solanum tuberosum - genetic mapping - microsatellites - quantitative trait loci - linkage disequilibrium - genetic analysis - genetic markers - cultivars - marker assisted breeding - amplified fragment length polymorphism
The results of a four year project within the Centre for BioSystems Genomics (www.cbsg.nl), entitled “Association mapping and family genotyping in potato” are described in this thesis. This project was intended to investigate whether a recently emerged methodology, association mapping, could provide the means to improve potato breeding efficiency.
In an attempt to answer this research question a set of potato cultivars representative for the commercial potato germplasm was selected. In total 240 cultivars and progenitor clones were chosen. In a later stage this set was expanded with 190 recent breeds contributed by five participating breeding companies which resulted in a total of 430 genotypes.
In a pilot experiment, the results of which are reported in Chapter 2, a subset of 220 of the abovementioned 240 cultivars and progenitor clones was used. Phenotypic data was retrieved through contributions of the participating breeding companies and represented summary statistics of recent observations for a number of traits across years and locations, calculated following company specific procedures. With AFLP marker data, in the form of normalised log-transformed band intensities, obtained from five well-known primer combinations, the extent of linkage disequilibrium (LD), using the r2 statistic, was estimated. Population structure within the set of 220 cultivars was analysed by deploying a clustering approach. No apparent, nor statistically supported population structure was revealed and the LD seemed to decay below the threshold of 0.1 at a genetic distance of about 3cM with this set of marker data. Furthermore, marker-trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with and without correction for population structure. Population structure correction was performed in a straightforward way by incorporating a design matrix into the model assuming that each breeding company represented a different breeding germplasm pool. The potential of association mapping in tetraploid potato has been demonstrated in this pilot experiment, because existing phenotypic data, a modest number of AFLP markers, and a relatively straightforward statistical analysis allowed identification of interesting associations for a number of agro-morphological and quality traits.
These promising results encouraged us to engage into an encompassing genome-wide association mapping study in potato. Two association mapping panels were compiled. One panel comprising 205 genotypes, all of which were also present in the set used for the pilot experiment, and another panel containing in total 299 genotypes including the entire set of 190 recent breeds together with a series of standard cultivars, about 100 of which are in common with the first panel. Phenotypic data for the association panel with 205 genotypes were obtained in a field trial performed in 2006 in Wageningen at two locations with two replicates. We will refer to this set as the “2006 field trial”. Phenotypic data for the other panel with 299 genotypes was contributed by the five participating breeding companies and consisted of multi-year-multi-location data obtained during generations of clonal selection. The 2006 data were nicely balanced, because the trial was designed in that way. The historical breeding dataset was highly unbalanced. Analysis of these two differing phenotypic datasets was performed to deliver insight in variance components for the genotypic main effects and the genotype by environment interaction (GEI), besides estimated genotype main effects across environments. Both phenotypic datasets were analysed separately within a mixed model framework including terms for GEI. In Chapter 3 we describe both phenotypic datasets by comparing variance components, heritabilities (=repeatabilities), intra-dataset relationships and inter-dataset relationships. Broader aspects related to phenotypic datasets and their analysis are discussed as well.
To retrieve information about hidden population structure and genetic relatedness, and to estimate the extent of LD in potato germplasm, we used marker information generated with 41 AFLP primer combinations and 53 microsatellite loci on a collection of 430 genotypes. These 430 genotypes contain all genotypes present in the two association mapping panels introduced before plus a few extra genotypes to increase potato germplasm coverage. Two methods were used: a Bayesian approach and a distance-based clustering approach. Chapter 4 describes the results of this exercise. Both strategies revealed a weak level of structure in our material. Groups were detected which complied with criteria such as their intended market segment, as well as groups differing in their year of first registration on a national list. Linkage disequilibrium, using the r2 statistic, appeared to decay below the threshold of 0.1 across linkage groups at a genetic distance of about 5cM on average. The results described in Chapter 4 are promising for association mapping research in potato. The odds are reasonable that useful marker-trait associations can be detected and that the potential mapping resolution will suffice for detection of QTL in an association mapping context.
In Chapter 5 a comprehensive genome-wide association mapping study is presented. The adjusted genotypic means obtained from two association mapping panels as a result of phenotypic analysis performed in Chapter 3 were combined with marker information in two association mapping models. Marker information consisted of normalised log-transformed band intensities of 41 AFLP primer combinations and allele dosage information from 53 microsatellites. A baseline model without correction for population structure and a more advanced model with correction for population structure and genetic relatedness were applied. Population structure and genetic relatedness were estimated using available marker information. Interesting QTL could be identified for 19 agro-morphological and quality traits. The observed QTL partly confirm previous studies e.g. for tuber shape and frying colour, but also new QTL have been detected e.g. for after baking darkening and enzymatic browning.
In the final chapter, the general discussion, results of preceding chapters are evaluated and their implications for research as well as breeding are discussed.
Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.
Marle-Koster, E. van; Hefer, C.A. ; Nel, L.H. ; Groenen, M.A.M. - \ 2008
South African Journal of Animal Science = Suid-Afrikaanse Tydskrif Vir Veekun 38 (2008)4. - ISSN 0375-1589 - p. 271 - 281.
kippen - inheems vee - rassen (dieren) - differentiatie - genetische variatie - genetische diversiteit - microsatellieten - merkers - bevolkingsstructuur - conservering - zuid-afrika - fowls - native livestock - breeds - differentiation - genetic variation - genetic diversity - microsatellites - markers - population structure - conservation - south africa - domestic-animal diversity - microsatellite markers - linkage map - naked neck - polymorphisms - biodiversity - genome
In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program.