- PE&RC (6)
- WIAS (5)
- Animal Breeding and Genetics (3)
- Animal Breeding and Genomics (3)
- PRI Biodiversity and Breeding (3)
- M. Bosse (2)
- C. Boëte (1)
- M.P.L. Calus (1)
- S.C. Cheah (1)
- R.P.M.A. Crooijmans (3)
- Armanda D.S. Bastos (2)
- R.P. Dirks (1)
- O. Dolstra (1)
- C. Drakeley (1)
- Dewald F. Keet (1)
- M. Forlenza (1)
- D.J. Goedbloed (1)
- G. Goff le (1)
- M. Groenen (2)
- P. Guo (1)
- P. Gélin (1)
- C.S. Haley (1)
- C.V. Henkel (1)
- J. Herrero-Medrano (2)
- G. Hoarau (1)
- W.F. Hooft van (3)
- K. Howe (1)
- Barend J. Greyling (1)
- J. Jansen (1)
- H.J. Jansen (1)
- P.W. Jong de (1)
- Diana K. Brebner (1)
- D.J. Koning, de (1)
- K. Langenbeck (1)
- V. Loeschcke (1)
- E.T.L. Low (1)
- W.Z. Lu (1)
- W. Lutz (1)
- Wayne M. Getz (1)
- H. Magalon (1)
- S. Magesa (1)
- A. Martin (1)
- C. Maxwell (1)
- H.J.W.C. Megens (3)
- G. Muskens (1)
- J.L. Olsen (1)
- L.C.L. Ooi (1)
- L.M. Panandam (1)
- C. Pertoldi (1)
- K.K. Petersen (1)
- H.H.T. Prins (1)
- M. Pérez-Enciso (1)
- Eric R. Dougherty (1)
- R.A. Rahman (1)
- G. Ramis (1)
- L. Ren (1)
- A.D. Rijnsdorp (1)
- V. Robert (1)
- Z. Satovic (1)
- O.E. Scholten (1)
- M. Sharma (1)
- R. Singh (1)
- T. Sluis van der (1)
- M.J.M. Smulders (1)
- H.P. Spaink (1)
- W.T. Stam (1)
- W. Takken (2)
- S.G. Tan (1)
- G.E. Thillart van den (1)
- H.W. Veer van der (1)
- M. Vliet van de (1)
- C.C. Vos (1)
- B. Vosman (1)
- W.P.C. Westende van 't (1)
- G.F. Wiegertjes (1)
- S.E. Wieren van (1)
- R.C. Ydenberg (1)
- L. Zande van de (1)
- X. Zhang (1)
- M.P. Zhou (1)
- B.J. Zwaan (1)
Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa
Hooft, W.F. van; Keet, Dewald F. ; Brebner, Diana K. ; Bastos, Armanda D.S. - \ 2018
lion - Panthera leo - microsatellite - mitochondrial DNA - RS-3 - Kruger National Park - gene flow - dispersal - disease spread - management
Background Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National Park, a bush-like ecosystem in South Africa where bovine tuberculosis prevalence ranges from low to high across a north-south gradient. Results A total of 109 individuals sampled from 1998 to 2004 were typed using 11 microsatellite markers, and mitochondrial RS-3 gene sequences were generated for 28 of these individuals. Considerable north-south genetic differentiation was observed in both datasets. Dispersal was male-biased and generally further than 25 km, with long-distance male gene flow (75–200 km, detected for two individuals) confirming that male lions can travel large distances, even in bush-like ecosystems. In contrast, females generally did not disperse further than 20 km, with two distinctive RS-3 gene clusters for northern and southern females indicating no or rare long-distance female dispersal. However, dispersal rate for the predominantly non-territorial females from southern Kruger (fraction dispersers ≥0.68) was higher than previously reported. Of relevance was the below-average body condition of dispersers and their low presence in prides, suggesting low fitness. Conclusions Large genetic differences between the two sampling localities, and low relatedness among males and high dispersal rates among females in the south, suggestive of unstable territory structure and high pride turnover, have potential implications for spread of diseases and the management of the Kruger lion population.
Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?
Hooft, W.F. van; Dougherty, Eric R. ; Getz, Wayne M. ; Greyling, Barend J. ; Zwaan, B.J. ; Bastos, Armanda D.S. - \ 2018
sex-ratio distorter - sex-ratio suppressor - sex-ratio adjustment - microsatellite - deleterious allele - sexually-antagonistic allele - African buffalo - Syncerus caffer - Kruger National Park - epigenetics - epigenetic modification - Y chromosome - frequency-dependent selection - bovine tuberculosis - body condition
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
The fine-scale genetic structure of the malaria vectors Anopheles funestus and Anopheles gambiae (Diptera: Culicidae) in the north-eastern part of Tanzania
Gélin, P. ; Magalon, H. ; Drakeley, C. ; Maxwell, C. ; Magesa, S. ; Takken, W. ; Boëte, C. - \ 2016
International Journal of Tropical Insect Science 36 (2016)4. - ISSN 1742-7584 - p. 161 - 170.
altitude - Anopheles funestus - Anopheles gambiae - malaria - microsatellite - population genetics - Tanzania - 016-3966
Understanding the impact of altitude and ecological heterogeneity at a fine scale on the populations of malaria vectors is essential to better understand and anticipate eventual epidemiological changes. It could help to evaluate the spread of alleles conferring resistance to insecticides and also determine any increased entomological risk of transmission in highlands due to global warming. We used microsatellite markers to measure the effect of altitude and distance on the population genetic structure of Anopheles funestus and Anopheles gambiae s.s. in the Muheza area in the north-eastern part of Tanzania (seven loci for each species). Our analysis reveals strong gene flow between the different populations of An. funestus from lowland and highland areas, as well as between populations of An. gambiae sampled in the lowland area. These results highlight for An. funestus the absence of a significant spatial subpopulation structuring at small-scale, despite a steep ecological and altitudinal cline. Our findings are important in the understanding of the possible spread of alleles conferring insecticide resistance through mosquito populations. Such information is essential for vector control programmes to avoid the rapid spread and fixation of resistance in mosquito populations.
Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.
Herrero-Medrano, J. ; Megens, H.J.W.C. ; Groenen, M. ; Bosse, M. ; Pérez-Enciso, M. ; Crooijmans, R.P.M.A. - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 12 p.
quantitative trait loci - il-12 receptor beta-2 - genetic diversity - domestic pig - conservation - variants - scan - zinc-alpha-2-glycoprotein - microsatellite - association
Background - A major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds. Results - Our results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r¿=¿0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig. Conclusions - The high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.
Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula
Herrero-Medrano, J. ; Megens, H.J.W.C. ; Groenen, M. ; Ramis, G. ; Bosse, M. ; Crooijmans, R.P.M.A. - \ 2013
BMC Genetics 14 (2013). - ISSN 1471-2156
linkage disequilibrium - genetic diversity - wide association - genotype data - ancient dna - breeds - size - cattle - microsatellite - homozygosity
Background Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations. A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history. Results The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian - including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo -, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds. Conclusions High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.
Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar
Goedbloed, D.J. ; Hooft, W.F. van; Megens, H.J.W.C. ; Langenbeck, K. ; Lutz, W. ; Crooijmans, R.P.M.A. ; Wieren, S.E. van; Ydenberg, R.C. ; Prins, H.H.T. - \ 2013
BMC Genetics 14 (2013). - ISSN 1471-2156
deer cervus-elaphus - sus-scrofa - hybridization - ecology - microsatellite - conservation - association - management - diversity - package
Background: Population genetic studies focus on natural dispersal and isolation by landscape barriers as the main drivers of genetic population structure. However, anthropogenic factors such as reintroductions, translocations and wild x domestic hybridization may also have strong effects on genetic population structure. In this study we genotyped 351 Single Nucleotide Polymorphism markers evenly spread across the genome in 645 wild boar (Sus scrofa) from Northwest Europe to evaluate determinants of genetic population structure. Results: We show that wild boar genetic population structure is influenced by historical reintroductions and by genetic introgression from domestic pigs. Six genetically distinct and geographically coherent wild boar clusters were identified in the Netherlands and Western Germany. The Dutch Veluwe cluster is known to be reintroduced, and three adjacent Dutch and German clusters are suspected to be a result of reintroduction, based on clustering results, low levels of heterozygosity and relatively high genetic distances to nearby populations. Recent wild x domestic hybrids were found geographically widespread across clusters and at low frequencies (average 3.9%). The relationship between pairwise kinship coefficients and geographic distance showed male-biased dispersal at the population genetic level. Conclusions: Our results demonstrate that wildlife and landscape management by humans are shaping the genetic diversity of an iconic wildlife species. Historical reintroductions, translocation and recent restocking activities with farmed wild boar have all influenced wild boar genetic population structure. The current trend of wild boar population growth and range expansion has recently led to a number of contact zones between clusters, and further admixture between the different wild boar clusters is to be expected.
Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio)
Henkel, C.V. ; Dirks, R.P. ; Jansen, H.J. ; Forlenza, M. ; Wiegertjes, G.F. ; Howe, K. ; Thillart, G.E. van den; Spaink, H.P. - \ 2012
Zebrafish 9 (2012)2. - ISSN 1545-8547 - p. 59 - 67.
transcriptome analysis - genetic-variability - antibody-production - nitrosative stress - dna-sequences - genome - fish - macrophages - lines - microsatellite
Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability of sufficient organ material for transcriptomics, proteomics, and metabolomics. Here we describe the shot gun sequencing of a clonal double-haploid common carp line. The assembly consists of 511891 scaffolds with an N50 of 17¿kb, predicting a total genome size of 1.4–1.5¿Gb. A detailed analysis of the ten largest scaffolds indicates that the carp genome has a considerably lower repeat coverage than zebrafish, whilst the average intron size is significantly smaller, making it comparable to the fugu genome. The quality of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters. In the ten largest scaffolds analyzed, the synteny of genes is almost complete. Comparisons of predicted exons of common carp with those of the zebrafish revealed only few genes specific for either zebrafish or carp, most of these being of unknown function. This supports the hypothesis of an additional genome duplication event in the carp evolutionary history, which—due to a higher degree of compactness—did not result in a genome larger than that of zebrafish.
Including copy number variation in association studies to predict genotypic values
Calus, M.P.L. ; Koning, de, D.J. ; Haley, C.S. - \ 2010
Genetics Research 92 (2010)2. - ISSN 0016-6723 - p. 115 - 125.
wide linkage disequilibrium - human genome - mutation-rates - genetic risk - disease - polymorphism - markers - cattle - snps - microsatellite
The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus.
Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm
Singh, R. ; Tan, S.G. ; Panandam, L.M. ; Rahman, R.A. ; Ooi, L.C.L. ; Low, E.T.L. ; Sharma, M. ; Jansen, J. ; Cheah, S.C. - \ 2009
BMC Plant Biology 9 (2009). - ISSN 1471-2229
elaeis-guineensis jacq. - genetic-linkage map - marker-assisted selection - brassica-napus - rapd markers - eucalyptus-grandis - pseudo-testcross - seed oil - microsatellite - identification
Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Result: A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E.guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2. CONCLUSION: This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes
Genetic structure within and among regional populations of the Eurasian badger (Meles meles) from Denmark and the Netherlands
Zande, L. van de; Vliet, M. van de; Pertoldi, C. ; Loeschcke, V. ; Muskens, G. ; Bijlsma, R. - \ 2007
Journal of Zoology 271 (2007)3. - ISSN 0952-8369 - p. 302 - 309.
microsatellite - extinction - differentiation - europe - flow
The Eurasian badger Meles meles has a wide distribution area ranging from Japan to Ireland. In western Europe badger habitats are severely disturbed by anthropogenic factors, leading to fragmentation into subpopulations and formation of a metapopulation substructuring of once continuous panmictic populations. We have examined the genetic structure of Dutch and Danish badger populations on a relatively small scale (within countries) and a larger scale (between countries). The levels of genetic variation of populations were moderate and did not differ significantly among populations (overall HO=0.30, overall HE=0.34). Considerable genetic differentiation between the Dutch and Danish populations was found (overall FST=0.32, mean pairwise Dutch–Danish FST=0.42), indicating a large-scale substructuring of these western European badger populations. Further analysis showed that the Danish badger population can be substructured into three clusters [P(k=3)=0.99], but the Dutch populations cluster into one more or less panmictic population [P(k=1)=0.99] with little or no substructuring. The presence of migration barriers, such as roads, together with the peninsular geography of Denmark, may have led to this structuring of badger populations. In contrast, measures that improve migration and connection to other populations from neighboring countries may have prevented substructuring of the Dutch badger population.
Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands
Arens, P.F.P. ; Sluis, T. van der; Westende, W.P.C. van 't; Vosman, B. ; Vos, C.C. ; Smulders, M.J.M. - \ 2007
Landscape Ecology 22 (2007)10. - ISSN 0921-2973 - p. 1489 - 1500.
landscape genetics - flow - microsatellite - conservation - diversity - distance - markers - toad
We studied the effects of landscape structure, habitat loss and fragmentation on genetic differentiation of Moor frog populations in two landscapes in The Netherlands (Drenthe and Noord-Brabant). Microsatellite data of eight loci showed small to moderate genetic differentiation among populations in both landscapes (F ST values 0.022 and 0.060, respectively). Both heterozygosity and population differentiation indicate a lower level of gene flow among populations in Noord-Brabant, where populations were further apart and have experienced a higher degree of fragmentation for a longer period of time as compared to populations in Drenthe. A significant isolation-by-distance pattern was found in Drenthe, indicating a limitation in dispersal among populations due to geographic distance. In Noord-Brabant a similar positive correlation was obtained only after the exclusion of a single long-time isolated population. After randomised exclusion of populations a significant additional negative effect of roads was found but not of other landscape elements. These results are discussed in view of improving methodology of assessing the effects of landscape elements on connectivity.
Population structure of the malaria vector Anopheles funestus (Diptera: Culicidae) in Madagascar and Comoros
Ayala, D. ; Goff, G. le; Robert, V. ; Jong, P.W. de; Takken, W. - \ 2006
Acta Tropica 97 (2006)3. - ISSN 0001-706X - p. 292 - 300.
genetic differentiation - west-africa - microsatellite - gambiae - east - disease - kenya - assay - loci
Microsatellites were used as markers for a study of the population structure of Anopheles funestus on Madagascar and Comoros. Mosquitoes were collected in four different localities on Madagascar and one on Comoros. There was a significant genetic differentiation between all samples from Madagascar and that from Comoros (P <0.05). With respect to the Madagascar mosquito samples, it was found that there were no significant genetic differences between samples that were collected at the east coast, and in the highlands, respectively. By contrast, the west coast sample exhibited significant genetic differences (with regard to all Madagascar samples). The results are discussed with respect to population distribution and migration of A. funestus from mainland Africa and the islands east of the mainland
Molecular characterization of Fusarium head blight resistance from wheat variety Wangshuibai
Zhang, X. ; Zhou, M.P. ; Ren, L. ; Bai, G. ; Scholten, O.E. ; Guo, P. ; Lu, W.Z. - \ 2004
Euphytica 139 (2004)1. - ISSN 0014-2336 - p. 59 - 64.
spring wheat - scab resistance - markers - qtls - microsatellite - spread - barley - genes - aflp
Fusarium head blight (FHB) is a destructive disease of wheat worldwide. FHB resistance genes from Sumai 3 and its derivatives such as Ning 7840 have been well characterized through molecular mapping. In this study, resistance genes in Wangshuibai, a Chinese landrace with high and stable FHB resistance, were analyzed through molecular mapping. A population of 104 F-2 -derived F-7 recombinant inbred lines (RILs) was developed from the cross between resistant landrace Wangshuibai and susceptible variety Alondra's'. A total of 32 informative amplified fragment length polymorphism (AFLP) primer pairs (EcoRI/MseI) amplified 410 AFLP markers segregating among the RILs. Among them, 250 markers were mapped in 23 linkage groups covering a genetic distance of 2,430 cM. In addition, 90 simple sequence repeat (SSR) markers were integrated into the AFLP map. Fifteen markers associated with three quantitative trait loci (QTL) for FHB resistance (P <0.01) were located on two chromosomes. One QTL was mapped on 113 and two others were mapped on 3B. One QTL on 3BS showed a major effect and explained up to 23.8% of the phenotypic variation for type II FHB resistance.
Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers
Atienza, S.G. ; Satovic, Z. ; Petersen, K.K. ; Dolstra, O. ; Martin, A. - \ 2002
Theoretical and Applied Genetics 105 (2002)6-7. - ISSN 0040-5752 - p. 946 - 952.
eucalyptus-urophylla - arbitrary primers - isozyme markers - aflp - rflp - dna - microsatellite - genomes - polymorphisms - construction
We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2n = 2x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between two genotypes from a previously designed cross. Consequently, both parents are fullsibs. The same proportion of bi-parental markers (heterozygotic in both parents) and pseudo-testcross markers (heterozygotic in one parent and null in the other), mono-parental markers, have been obtained. A total of 383 RAPD markers were analysed within the 89 F1 plants. Out of these markers, 257 were mapped into 28 linkage groups which spanned a total map length of around 1,074.5 cM with an average density of 4.2 cM per marker. Out of 257 mapped markers, 62 were inherited from F1.1 (P1), 63 from F1.7 (P7) and 132 were bi-parental markers. The contribution to the map was equal from both parents. This map provides a useful tool for genetic analyses of agronomically interesting characters in M. sinensis such as flowering, yield, plant height, stem diameter and mineral constitution. The offspring cross mapping strategy is proposed to obtain a higher efficiency in developing integrated maps including both parents
Population structure of plaice (Pleuronectes platessa L.) in orthern Europe: microsatellites revealed large-scale spatial and temporal homogeneity
Hoarau, G. ; Rijnsdorp, A.D. ; Veer, H.W. van der; Stam, W.T. ; Olsen, J.L. - \ 2002
Molecular Ecology 11 (2002). - ISSN 0962-1083 - p. 1165 - 1176.
flatfish - genetic structure - microsatellite - Pleuronectes platessa
Philopatry to spawning grounds combined with well-known migratory patterns in the flatfish Pleuronectes platessa (plaice) has led to the hypothesis that regional populations may reflect relatively discrete, genetic stocks. Using six microsatellite loci we genotyped 240 adult individuals collected from locations in Norway, the Faeroe plateau, the Irish Sea, the Femer Baelt, Denmark, and the southern North Sea, and 240 0-class juveniles collected from five nursery-ground locations in Iceland, northwest Scotland, two sites in the Wadden Sea, and the Bay of Vilaine in Southern Brittany. The mean number of alleles/locus ranged from 5.3 to 20.4, with a mean of 13.9. Expected heterozygosity was uniformly high across all locations (multilocus Hexp = 0.744 ± 0.02). Pairwise comparisons of among all 11 locations revealed significant differentiation between Iceland and all other locations ( = 0.0290*** to 0.0456***), which is consistent with the deep-water barrier to dispersal in plaice. In contrast, no significant differentiation was found among any of the remaining continental-shelf sampling locations. This suggests that regional stocks are themselves composed of several genetic stocks under a model of panmixia which persists even to the spawning grounds. The presence of significant heterozygote deficiencies at all locations (not due to null alleles) suggests a temporal Wahlund effect yet the absence of significant population differentiation among continental shelf localities makes this explanation alone, difficult to reconcile. Sampling of eggs at the spawning grounds will be required to resolve this issue. Causes of the mismatch between genetic and geographical stocks is discussed in the context of high gene flow.