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.

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QTL analysis for stomatal functioning in tetraploid Rosa x hybrida grown at high relative air humidity and its implications on postharvest longevity
Carvalho, D.R.A. ; Koning, C.F.S. ; Fanourakis, D. ; Vasconcelos, M.W. ; Carvalho, S.M.P. ; Heuvelink, E. ; Krens, F.A. ; Maliepaard, C.A. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 11 p.
marker-assisted selection - water relations - cut roses - in-vitro - traits - environments - conductance - sensitivity - improvement - resistance
High relative air humidity (RH = 85 %) during leaf development disturbs stomatal functioning leading to excessive water loss in conditions of high evaporative demand, resulting in severe reduction in postharvest longevity. In roses, this effect depends on the genotype, opening the possibility for breeding cultivars with more responsive stomata. In this study, we aim at identifying genomic regions associated with the control of water loss following growth at high RH. The F1 generation (108 offspring) and the two parents (P540 and P867) of a tetraploid cut rose population grown at high (85 %) RH were phenotyped for stomatal control to water loss by assessing the relative water content after 4 h of leaflet desiccation (RWC_4 h). The RWC_4 h varied between 7 and 62 % across the 110 studied individuals, with parents P540 and P867 showing 51 and 20 % RWC_4 h, respectively. Based on these data, a quantitative trait locus (QTL) analysis was performed. The impact of the identified QTLs on postharvest longevity of ten selected offspring was further evaluated. Three QTLs were identified: two major [positioned on linkage group 5 of the integrated consensus map (ICM 5) of both parents and on ICM 2 of the parent P867] and one putative minor (mapped to ICM 6 of both parents), explaining 32 % of the variability in the RWC_4 h. Low RWC_4 h was found to be a good proxy for eliminating the offspring with short vase life. This study constitutes a first step toward identifying the most likely regions for genes of interest controlling stomatal functioning in high RH-grown plants.
Genome-wide association mapping for kernel and malting quality traits using hostorical European barley records
Matthies, I.E. ; Malosetti, M. ; Roder, M.S. ; Eeuwijk, F.A. van - \ 2014
PLoS One 9 (2014)11. - ISSN 1932-6203 - 15 p.
marker-assisted selection - grain protein-content - hordeum-vulgare l. - doubled-haploid population - different germplasm groups - backcross-qtl analysis - linkage disequilibrium - spring barley - yield components - 2-row barley
Malting quality is an important trait in breeding barley (Hordeum vulgare L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.
A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry
Peace, C.P. ; Luby, J. ; Weg, W.E. van de; Bink, M.C.A.M. ; Iezzoni, A.F. - \ 2014
Tree Genetics and Genomes 10 (2014)6. - ISSN 1614-2942 - p. 1679 - 1694.
x domestica borkh. - marker-assisted selection - fire blight resistance - breeding program - population-structure - pyrus-communis - fruit firmness - map position - md-acs1 - gene
Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.
Dominant resistance against plant viruses
Ronde, D. de; Butterbach, P.B.E. ; Kormelink, R.J.M. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - p. 307 - 307.
cucumber-mosaic-virus - yellow-dwarf virus - phaseolus-vulgaris l - gene-mediated resistance - potato-leafroll-virus - marker-assisted selection - long-distance movement - tobacco ringspot virus - citrus-tristeza-virus - spotted-wilt-virus
To establish a successful infection plant viruses have to overcome a defense system composed of several layers. This review will overview the various strategies plants employ to combat viral infections with main emphasis on the current status of single dominant resistance (R) genes identified against plant viruses and the corresponding avirulence (Avr) genes identified so far. The most common models to explain the mode of action of dominant R genes will be presented. Finally, in brief the hypersensitive response (HR) and extreme resistance (ER), and the functional and structural similarity of R genes to sensors of innate immunity in mammalian cell systems will be described.
Next-generation genebanking: plant genetic resources management and utilization in the sequencing era
Treuren, R. van; Hintum, T.J.L. van - \ 2014
Plant genetic resources: characterization and utilization 12 (2014)3. - ISSN 1479-2621 - p. 298 - 307.
marker-assisted selection - ex-situ conservation - crop improvement - genomic selection - wild relatives - technologies - association - diversity - collection - lettuce
Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crop's gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.
Whole-genome regression and prediction methods applied to plant and animal breeding
Los Campos, G. De; Hickey, J.M. ; Pong-Wong, R. ; Daetwyler, H.D. ; Calus, M.P.L. - \ 2013
Genetics 193 (2013)2. - ISSN 0016-6731 - p. 327 - 345.
marker-assisted selection - quantitative trait locus - genetic-relationship information - single nucleotide polymorphisms - linear unbiased prediction - dense molecular markers - dairy-cattle - variable selection - reference population - beef-cattle
Genomic-enabled prediction is becoming increasingly important in animal and plant breeding, and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of markers concurrently. Following the groundbreaking contribution of MEUWISSEN et al. (2001) several methods have been proposed and evaluated, and genome-enabled selection (GS) is being implemented in several plant and animal breeding programs. The list of methods is long, and the relationships between the available methods have not been fully addressed. In this article we provide an overview of available methods for implementing parametric WGR models, discuss selected topics which emerge in the application of these methods and present a general discussion of lessons learnt from simulation and empirical data analysis in the last decade
QTL analysis reveals the genetic architecture of domestication traits in Crisphead lettuce
Hartman, Y. ; Hooftman, D.A.P. ; Schranz, M.E. ; Tienderen, P.H. van - \ 2013
Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1487 - 1500.
lactuca-serriola asteraceae - marker-assisted selection - arabidopsis-thaliana - plant domestication - crop domestication - sativa l. - wild - loci - sunflower - evolution
The genetic architecture of crop domestication is generally characterized by three trends: relatively few genomic regions with major QTL effects are involved, QTL are often clustered, and alleles derived from the crop do not always contribute to the crop phenotype. We have investigated the genetic architecture of lettuce using a recombinant inbred line population from a cross between a crop Lactuca sativa (‘Salinas’) and its wild relative L. serriola. Few genomic regions with major QTL, plus various intermediate QTL, largely control the transition from wild to cultivated Crisphead lettuce. Allelic effects of all major QTL were in the expected direction, but there were intermediate QTL where the crop contributed to the wild phenotype and vice versa. We found two main regions with clusters of QTL, one on linkage group 3, where the crop allele induced lower seed output, another on linkage group 7, where the crop allele caused a delay in flowering time. Potentially, knowledge of genetic changes due to the domestication could be relevant for the chance that a transgene inserted in a crop genome will spread to wild relatives due to hitchhiking effects. If a transgene would be inserted in one of these regions, background selection on the crop alleles may lead to a reduced fitness of hybrids with the transgene. QTL research on the effects of domestication genes can thus indicate regions in the crop genome that are less likely to introgress, although these still need to be verified under field conditions.
Bringing the voice of consumers into plant breeding with Bayesian modelling
Tesfaye, L.M. ; Bink, M.C.A.M. ; Lans, I.A. van der; Gremmen, B. ; Trijp, H.C.M. van - \ 2013
Euphytica 189 (2013)3. - ISSN 0014-2336 - p. 365 - 378.
marker-assisted selection - quantitative trait loci - product development - crop improvement - quality guidance - chemical traits - tomatoes - genomics - preferences - tool
Improving flavour quality traits in fruit breeding calls for innovative consumer-oriented product development. This paper explores the potential of marker-assisted breeding from genomics and consumer-based quality-improvement models from marketing, and exploits the progresses at both sides as technology push and market pull. An integrative and cross-disciplinary quality-improvement model is proposed based on Bayesian modelling. This Bayesian modelling allows for the integration of elicited knowledge of breeders and flavour researchers concerning the degree of causal associations of metabolites and flavour quality traits of fruits in the model. We also present the flavour quality improvement challenge as a multi-criteria optimization process and show the potential and current limitations of the proposed model. Insights gained from the model would help flavour researchers determine the optimum concentration of flavour-affecting metabolites which could be used for further DNA marker development. These ideas and concepts will help translate consumer-desired product features into genomic information, ultimately resulting in successful new cultivars
Towards genomic selection in apple (Malus x domestica Borkh.) breeding programmes: Prospects, challenges and strategies
Kumar, S. ; Bink, M.C.A.M. ; Volz, R.K. ; Bus, V.G.M. ; Chagne, D. - \ 2012
Tree Genetics and Genomes 8 (2012)1. - ISSN 1614-2942 - p. 1 - 14.
marker-assisted selection - mildew-resistance gene - linear unbiased prediction - quantitative trait loci - fire blight resistance - fruit-quality traits - linkage group 3 - powdery-mildew - venturia-inaequalis - molecular markers
The apple genome sequence and the availability of high-throughput genotyping technologies have initiated a new era where SNP markers are abundant across the whole genome. Genomic selection (GS) is a statistical approach that utilizes all available genome-wide markers simultaneously to estimate breeding values or total genetic values. For breeding programmes, GS is a promising alternative to the traditional marker-assisted selection for manipulating complex polygenic traits often controlled by many small-effect genes. Various factors, such as genetic architecture of selection traits, population size and structure, genetic evaluation systems, density of SNP markers and extent of linkage disequilibrium, have been shown to be the key drivers of the accuracy of GS. In this paper, we provide an overview of the status of these aspects in current apple-breeding programmes. Strategies for GS for fruit quality and disease resistance are discussed, and an update on an empirical genomic selection study in a New Zealand apple-breeding programme is provided, along with a foresight of expected accuracy from such selection.
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
Effects of genomic selection on genetic improvement, inbreeding, and merit of young versus proven bulls
Roos, A.P.W. de; Schrooten, C. ; Veerkamp, R.F. ; Arendonk, J.A.M. van - \ 2011
Journal of Dairy Science 94 (2011)3. - ISSN 0022-0302 - p. 1559 - 1567.
marker-assisted selection - cattle breeding schemes - dairy-cattle - wide selection - populations - prediction - progress - gain
Genomic selection has the potential to revolutionize dairy cattle breeding because young animals can be accurately selected as parents, leading to a much shorter generation interval and higher rates of genetic gain. The aims of this study were to assess the effects of genomic selection and reduction of the generation interval on the rate of genetic gain and rate of inbreeding. Furthermore, the merit of proven bulls relative to young bulls was studied. This is important for breeding organizations as it determines the relative importance of progeny testing. A closed nucleus breeding scheme was simulated in which 1,000 males and 1,000 females were born annually, 200 bulls were progeny tested, and 20 sires and 200 dams were selected to produce the next generation. In the "proven" (PROV) scenario, only cows with own performance records and progeny-tested bulls were selected as parents. The proportion of the genetic variance that was explained by simulated marker information (M) was varied from 0 to 100%. When M increased from 0 to 100%, the rate of genetic gain increased from 0.238 to 0.309 genetic standard deviations (s) per year (+30%), whereas the rate of inbreeding reduced from 1.00 to 0.42% per generation. Alternatively, when young cows and bulls were selected as parents (YNG scenario), the rate of genetic gain for M=0% was 0.292 s/yr but the corresponding rate of inbreeding increased substantially to 3.15% per generation. A realistic genomic selection scheme (YNG with M=40%) gave 108% higher rate of genetic gain (0.495 s/yr) and approximately the same rate of inbreeding per generation as the conventional system without genomic selection (PROV with M=0%). The rate of inbreeding per year, however, increased from 0.18 to 0.52% because the generation interval in the YNG scheme was much shorter. Progeny-testing fewer bulls reduced the rate of genetic gain and increased the rate of inbreeding for PROV, but had negligible effects for YNG because almost all sires were young bulls. In scenario YNG with M=40%, the best young bulls were superior to the best proven bulls by 1.27 s difference in genomic estimated breeding value. This superiority increased even further when fewer bulls were progeny tested. This stochastic simulation study shows that genomic selection in combination with a severe reduction in the generation interval can double the rate of genetic gain at the same rate of inbreeding per generation, but with a higher rate of inbreeding per year. The number of progeny-tested bulls can be greatly reduced, although this will slightly affect the quality of the proven bull team. Therefore, it is important for breeding organizations to predict the future demand for proven bull semen in light of the increasing superiority of young bulls
Towards a unified genetic map of diploid roses
Spiller, M. ; Hibrand-Saint Oyant, L. ; Tsai, C. ; Byrne, D.H. ; Smulders, M.J.M. ; Foucher, A.L.J.L. ; Debener, T. - \ 2011
Theoretical and Applied Genetics 122 (2011)3. - ISSN 0040-5752 - p. 489 - 500.
marker-assisted selection - linkage maps - mapping populations - disease resistance - tetraploid roses - integrated map - aflp markers - construction - traits - genome
We have constructed the first integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597 markers, 206 of which are sequence-based, distributed over a length of 530 cM on seven LGs. By using a larger effective population size and therefore higher marker density, the marker order in the ICM is more reliable than in the single population maps. This is supported by a more even marker distribution and a decrease in gap sizes in the consensus map as compared to the single population maps. This unified map establishes a standard nomenclature for rose LGs, and presents the location of important ornamental traits, such as self-incompatibility, black spot resistance (Rdr1), scent production and recurrent blooming. In total, the consensus map includes locations for 10 phenotypic single loci, QTLs for 7 different traits and 51 ESTs or gene-based molecular markers. This consensus map combines for the first time the information for traits with high relevance for rose variety development. It will serve as a tool for selective breeding and marker assisted selection. It will benefit future efforts of the rose community to sequence the whole rose genome and will be useful for synteny studies in the Rosaceae family and especially in the section Rosoideae
Transgressive segregation for very low and high levels of basal resistance to powdery mildew in barley
Aghnoum, R. ; Niks, R.E. - \ 2011
Journal of Plant Physiology 168 (2011)1. - ISSN 0176-1617 - p. 45 - 50.
marker-assisted selection - quantitative trait loci - adult-plant resistance - erysiphe-graminis - puccinia-hordei - spring barley - host-resistance - stripe rust - lines - map
Basal resistance of barley to powdery mildew is a quantitatively inherited trait that limits the growth and sporulation of barley powdery mildew pathogen by a non-hypersensitive mechanism of defense. Two experimental barley lines were developed with a very high (ErBgh) and low (EsBgh) level of basal resistance to powdery mildew by cycles of convergent crossing and phenotypic selection between the most resistant and between the most susceptible lines, respectively, from four mapping populations of barley. Phenotypic selection in convergent crossing was highly effective in producing contrasting phenotypes for basal resistance and susceptibility. In ErBgh, almost 90% of infection units failed to form a primary haustorium in the epidermal cells in association with papilla formation, but in EsBgh only 33% of infection units failed to form a primary haustorium. The contrast between ErBgh and EsBgh for successful formation of secondary and subsequent haustoria was much less obvious (69% versus 79% successful secondary haustorium formation). In an earlier investigation, we determined seven QTLs for basal resistance in the four mapping populations. Checking the peak markers of these QTLs indicated that only four out of seven QTLs were confirmed to be present in the selected resistant lines and only four QTLs for susceptibility were confirmed to be present in the selected susceptible lines. Surprisingly, none of the expected QTLs could be detected in the resistant line ErBgh. We discuss some reasons why marker aided selection might be less efficient in raising levels of basal resistance than phenotypic selection. The very resistant and susceptible lines developed here are valuable material to be used in further experiments to characterize the molecular basis of basal resistance to powdery mildew
The effect of pyramiding Phytophthora infestans resistance genes R Pi-mcd1 and R Pi-ber in potato
Tan, M.Y.A. ; Hutten, R.C.B. ; Visser, R.G.F. ; Eck, H.J. van - \ 2010
Theoretical and Applied Genetics 121 (2010)1. - ISSN 0040-5752 - p. 117 - 125.
late blight resistance - marker-assisted selection - broad-spectrum resistance - quantitative trait loci - foliage maturity type - solanum-bulbocastanum - bacterial-blight - disease resistance - rpi-ber - rice
Despite efforts to control late blight in potatoes by introducing R(pi)-genes from wild species into cultivated potato, there are still concerns regarding the durability and level of resistance. Pyramiding R(pi)-genes can be a solution to increase both durability and level of resistance. In this study, two resistance genes, R(Pi-mcd1) and R(Pi-ber), introgressed from the wild tuber-bearing potato species Solanum microdontum and S. berthaultii were combined in a diploid S. tuberosum population. Individual genotypes from this population were classified after four groups, carrying no R(pi)-gene, with only R (Pi-mcd1), with only R(Pi-ber), and a group with the pyramided R(Pi-mcd1) and R (Pi-ber) by means of tightly linked molecular markers. The levels of resistance between the groups were compared in a field experiment in 2007. The group with R(Pi-mcd1) showed a significant delay to reach 50% infection of the leaf area of 3 days. The group with R ( Pi-ber ) showed a delay of 3 weeks. The resistance level in the pyramid group suggested an additive effect of R (Pi-mcd1) with R(Pi-ber). This suggests that potato breeding can benefit from combining individual R(pi)-genes, irrespective of the weak effect of R(Pi-mcd1) or the strong effect of R(Pi-ber)
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)114. - ISSN 1471-2229 - p. 1 - 19.
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
Molecular breeding for resistance to Phytophthora infestans (Mont.) de Bary in potato (Solanum tuberosum L.): a perspective of cisgenesis
Park, T.H. ; Vleeshouwers, V.G.A.A. ; Jacobsen, E. ; Visser, R.G.F. ; Vossen, E.A.G. van der - \ 2009
Plant Breeding 128 (2009)2. - ISSN 0179-9541 - p. 109 - 117.
late-blight resistance - race-specific resistance - marker-assisted selection - broad-spectrum resistance - globodera-pallida stone - disease-resistance - quantitative resistance - gene-cluster - cultivated potato - field-resistance
Late blight caused by Phytophthora infestans is one of the most devastating diseases in potato cultivation and is mostly controlled by the application of chemicals. However, introduction of combinations of resistance (R) genes conferring broad-spectrum resistance from wild Solanum species into cultivated potatoes is considered the most practical and promising approach to achieve durable resistance. This can be realized via classical breeding or genetic modification (GM). Because classical breeding is very time-consuming and is often hampered by linkage drag, a GM approach seems logic in this heterozygous and vegetatively propagated crop. During the last decades, many R genes have been identified in several wild Solanum species. Some have been cloned and more will follow. When these genes are derived from species crossable with cultivated potato (so-called cisgenes), application in resistance breeding using a GM approach is similar to an introgression breeding approach, in that the exploited genes are indigenous to the crop. Pending deregulation or derogation of cisgenesis, the use of cisgenic R genes would be an ideal strategy to accomplish durable resistance in potato.
Inbreeding in genome-wide selection
Daetwyler, H.D. ; Villanueva, B. ; Bijma, P. ; Woolliams, J.A. - \ 2007
Journal of Animal Breeding and Genetics 124 (2007)6. - ISSN 0931-2668 - p. 369 - 376.
marker-assisted selection - complex vertebral malformation - mendelian sampling terms - cattle breeding schemes - dairy-cattle - dynamic selection - genetic-markers - prediction - programs - populations
Traditional selection methods, such as sib and best linear unbiased prediction (BLUP) selection, which increased genetic gain by increasing accuracy of evaluation have also led to an increased rate of inbreeding per generation (¿FG). This is not necessarily the case with genome-wide selection, which also increases genetic gain by increasing accuracy. This paper explains why genome-wide selection reduces ¿FG when compared with sib and BLUP selection. Genome-wide selection achieves high accuracies of estimated breeding values through better prediction of the Mendelian sampling term component of breeding values. This increases differentiation between sibs and reduces coselection of sibs and ¿FG. The high accuracy of genome-wide selection is expected to reduce the between family variance and reweigh the emphasis of estimated breeding values of individuals towards the Mendelian sampling term. Moreover, estimation induced intraclass correlations of sibs are expected to be lower in genome-wide selection leading to a further decrease of coselection of sibs when compared with BLUP. Genome-wide prediction of breeding values, therefore, enables increased genetic gain while at the same time reducing ¿FG when compared with sib and BLUP selection.
QTL-based analysis of genotype-by-environment interaction for grain yield of rice in stress and non-stress environments
Manneh, B. ; Stam, P. ; Struik, P.C. ; Bruce-Oliver, S. ; Eeuwijk, F.A. van - \ 2007
Euphytica 156 (2007)1-2. - ISSN 0014-2336 - p. 213 - 226.
quantitative trait loci - oryza-sativa-l - marker-assisted selection - population - resistance - identification - components - rufipogon - barley - l.
Use of DNA-based markers can accelerate cultivar development in variable cultivation environments since, in contrast to phenotype, DNA markers are environment-independent. In an effort to elucidate the genetic basis of genotype-by-environment interaction (G x E) for yield of rice (Oryza sativa L.), the associations between 139 AFLP markers and grain yield were determined for rice grown in fresh water (EC of 0.65 dS m(-1) and saline conditions (EC of 4-8 dS m(-1)) with 0 kg ha(-1) or 100 kg ha(-1) nitrogen fertilizer in the years 2000 and 2001. A population of recombinant inbred lines of rice, developed from an IR29 x Pokkali cross, was used in the study. Both genotype x salinity and genotype x nitrogen level interactions were significant, with the genotype x salinity interaction being stronger. Through multiple regression analysis using a stepwise procedure for selecting markers, 36 markers were detected for grain yield in the four test conditions and of these 28 were detected in only one test condition implying strong environmental specificity for yield QTL expression. However, the fact that eight QTLs were detected in more than one test condition points to the existence of wide-adaptability genes in this cross. Markers with significant associations with yield explained between 37% and 48% of the yield variation in each test condition. Superior genotypes of rice were identified in all four test conditions based on their marker signatures. Furthermore, across N fertilizer regimes, yield predicted from summed additive effects of QTLs were significantly correlated with observed yield in the same year and across years. Thus marker-assisted selection can help breeders overcome the problem of low selection efficiency encountered during phenotypic selection for yield in stress environments.
A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato
Malosetti, M. ; Linden, C.G. van der; Vosman, B. ; Eeuwijk, F.A. van - \ 2007
Genetics 175 (2007)2. - ISSN 0016-6731 - p. 879 - 889.
marker-assisted selection - quantitative trait loci - late blight resistance - linkage disequilibrium - tetraploid potato - flowering time - pairwise relatedness - disease resistance - molecular markers - solanum-tuberosum
Association or linkage disequilibrium (LD)-based mapping strategies are receiving increased attention for the identification of quantitative trait loci (QTL) in plants as an alternative to more traditional, purely linkage-based approaches. An attractive property of association approaches is that they do not require specially designed crosses between inbred parents, but can be applied to collections of genotypes with arbitrary and often unknown relationships between the genotypes. A less obvious additional attractive property is that association approaches offer possibilities for QTL identification in crops with hard to model segregation patterns. The availability of candidate genes and targeted marker systems facilitates association approaches, as will appropriate methods of analysis. We propose an association mapping approach based on mixed models with attention to the incorporation of the relationships between genotypes, whether induced by pedigree, population substructure, or otherwise. Furthermore, we emphasize the need to pay attention to the environmental features of the data as well, i.e., adequate representation of the relations among multiple observations on the same genotypes. We illustrate our modeling approach using 25 years of Dutch national variety list data on late blight resistance in the genetically complex crop of potato. As markers, we used nucleotide binding-site markers, a specific type of marker that targets resistance or resistance-analog genes. To assess the consistency of QTL identified by our mixed-model approach, a second independent data set was analyzed. Two markers were identified that are potentially useful in selection for late blight resistance in potato.
Mapping QTLs and QTL x environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods
Vargas, M. ; Eeuwijk, F.A. van; Crossa, J. ; Ribaut, J.M. - \ 2006
Theoretical and Applied Genetics 112 (2006)6. - ISSN 0040-5752 - p. 1009 - 1023.
quantitative trait loci - marker-assisted selection - tropical maize - flanking markers - genotype - identification - interval - strategies - components - crosses
The study of QTL x environment interaction (QEI) is important for understanding genotype x environment interaction (GEI) in many quantitative traits. For modeling GEI and QEI, factorial regression (FR) models form a powerful class of models. In FR models, covariables (contrasts) defined on the levels of the genotypic and/or environmental factor(s) are used to describe main effects and interactions. In FR models for QTL expression, considerable numbers of genotypic covariables can occur as for each putative QTL an additional covariable needs to be introduced. For large numbers of genotypic and/or environmental covariables, least square estimation breaks down and partial least squares (PLS) estimation procedures become an attractive alternative. In this paper we develop methodology for analyzing QEI by FR for estimating effects and locations of QTLs and QEI and interpreting QEI in terms of environmental variables. A randomization test for the main effects of QTLs and QEI is presented. A population of F-2 derived F-3 families was evaluated in eight environments differing in drought stress and soil nitrogen content and the traits yield and anthesis silking interval (ASI) were measured. For grain yield, chromosomes 1 and 10 showed significant QEI, whereas in chromosomes 3 and 8 only main effect QTLs were observed. For ASI, QTL main effects were observed on chromosomes 1, 2, 6, 8, and 10, whereas QEI was observed only on chromosome 8. The assessment of the QEI at chromosome 1 for grain yield showed that the QTL main effect explained 35.8% of the QTL + QEI variability, while QEI explained 64.2%. Minimum temperature during flowering time explained 77.6% of the QEI. The QEI analysis at chromosome 10 showed that the QTL main effect explained 59.8% of the QTL + QEI variability, while QEI explained 40.2%. Maximum temperature during flowering time explained 23.8% of the QEI. Results of this study show the possibilities of using FR for mapping QTL and for dissecting QEI in terms of environmental variables. PLS regression is efficient in accounting for background noise produced by other QTLs.
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