Quantitative Trait Loci in Solanaceae species
Kuzniar, Arnold ; Singh, G. - \ 2018
Wageningen University & Research
plant breeding - plant genetics - quantitative trait locus - QTL - genetic marker - trait - Solanaceae - tomato - potato - FAIR data - RDF - SQLite - csv
This tar archive contains experimental data on Quantitative Trait Loci (QTLs) mapped in Solanacea species. In particular, the QTL data were extracted from tomato- and potato-specific literature using the QTL TableMiner++ tool, and the resulting data were made available in machine-readable and semantically-interoperable formats: SQLite database (.db); comma-separated value file (.csv); RDF/Turle file (.ttl).
QTL TableMiner++: a tool for mining tables in scientific articles
Singh, G. ; Kuzniar, Arnold - \ 2018
Wageningen University & Research
table mining - text mining - genotype-phenotype relationship - quantitative trait locus - QTL - breeding - FAIR data
Quantitative trait locus (QTL) mapping experiments are commonly described in scientific literature but the results presented in tables are difficult to re-use. QTL TableMiner++ (QTM) enables to make these results available in machine-readable formats.
DOG1-imposed dormancy mediates germination responses to temperature cues
Murphey, M. ; Kovach, K. ; Elnacash, T. ; He, H. ; Bentsink, L. ; Donohue, K. - \ 2015
Environmental and Experimental Botany 112 (2015). - ISSN 0098-8472 - p. 33 - 43.
seed-maturation environment - quantitative trait locus - recent climate-change - arabidopsis-thaliana - life-history - ectopic expression - niche construction - natural-selection - dog1-like genes - dog1
Seed dormancy and environment-dependent germination requirements interact to determine the timing of germination in natural environments. This study tested the contribution of the dormancy gene Delay Of Germination 1 (DOG1) to primary and secondary dormancy induction in response to environmental cues, and evaluated how DOG1-mediated dormancy influenced germination responses to different temperature cues. We verified that DOG1 is involved in the induction of primary dormancy in response to cool seed-maturation temperature experienced by maternal plants, and we found that it is also involved in secondary dormancy in response to warm and prolonged cold stratification experienced by seeds during imbibition. DOG1-imposed dormancy can also mediate germination responses to environmental conditions, including cold stratification and germination temperatures experienced by imbibing seeds. Specifically, germination responsiveness to temperature cues is most apparent when seeds exhibit an intermediate degree of dormancy. However, DOG1 itself does not seem to directly regulate the response to cold stratification nor does it determine the function of temperature-dependent germination, since DOG1 mutants were capable of exhibiting increased germination after cold stratification as well as temperature-dependent germination. Instead, DOG1 has major effects on germination behavior primarily by exposing or masking underlying environmental sensitivity, and thereby strongly influences how environmentally responsive germination can be, and when during a season, it is likely to exhibit environmental sensitivity.
Systematic differences in the response of genetic variation to pedigree and genome-based selection methods
Heidaritabar, M. ; Vereijken, A. ; Muir, W.M. ; Meuwissen, T.H.E. ; Cheng, H. ; Megens, H.J.W.C. ; Groenen, M. ; Bastiaansen, J.W.M. - \ 2014
Heredity 113 (2014). - ISSN 0018-067X - p. 503 - 513.
quantitative trait locus - positive selection - chicken - hitchhiking - programs - size
Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60¿K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P
Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family.
Hofberger, J.A. ; Lyons, E. ; Edger, P.P. ; Pires, J.C. ; Schranz, M.E. - \ 2013
Genome Biology and Evolution 5 (2013). - ISSN 1759-6653 - p. 2155 - 2173.
quantitative trait locus - arabidopsis-thaliana - gene duplication - secondary metabolism - insect resistance - natural variation - provides insight - biosynthesis - evolution - plants
Plants share a common history of successive whole genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and Tandem Duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the Mustard Family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all Mustard Family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95 and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared to the 22% average for all protein-coding genes in Arabidopsis, 52 and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. While 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of tandem- and whole genome duplication events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.
Plant science: the key to preventing slow cadmium poisoning
Clemens, S. ; Aarts, M.G.M. ; Thomine, S. ; Verbruggen, N. - \ 2013
Trends in Plant Science 18 (2013)2. - ISSN 1360-1385 - p. 92 - 99.
quantitative trait locus - rice oryza-sativa - shoot cd translocation - heavy-metal atpase - grain cadmium - wheat cultivars - accumulating cd - potato-tubers - durum-wheat - arabidopsis
Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops
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
Melanin biosynthesis pathway in Agaricus bisporus mushrooms
Weijn, A. ; Bastiaan-Net, S. ; Wichers, H.J. ; Mes, J.J. - \ 2013
Fungal Genetics and Biology 55 (2013). - ISSN 1087-1845 - p. 42 - 53.
quantitative trait locus - lecanicillium-fungicola - polyphenol oxidase - tyrosinase - expression - resistance - cloning - genes - metabolism
With the full genome sequence of Agaricus bisporus available, it was possible to investigate the genes involved in the melanin biosynthesis pathway of button mushrooms. Based on different BLAST and alignments, genes were identified in the genome which are postulated to be involved in this pathway. Seven housekeeping genes were tested of which 18S rRNA was the only housekeeping gene that was stably expressed in various tissues of different developmental stages. Gene expression was determined for most gene homologs (26 genes) involved in the melanin pathway. Of the analysed genes, those encoding polyphenol oxidase (PPO), the PPO co-factor L-chain (unique for Agaricus bisporus), and a putative transcription factor (photoregulator B) were among the highest expressed in skin tissue. An in depth look was taken at the clustering of several PPO genes and the PPO co-factor gene on chromosome 5, which showed that almost 25% of the protein encoding genes in this cluster have a conserved NACHT and WD40 domain or a P-loop nucleoside triphosphate hydrolase. This article will be the start for an in depth study of the melanin pathway and the role in quality losses of this economically important product.
The molecular mechanism of zinc and cadmium stress response in plants
Lin, Y.F. ; Aarts, M.G.M. - \ 2012
Cellular and Molecular Life Sciences 69 (2012)19. - ISSN 1420-682X - p. 3187 - 3206.
hyperaccumulator thlaspi-caerulescens - heavy-metal detoxification - sedum-alfredii hance - arbuscular mycorrhizal fungi - wrky53 transcription factor - quantitative trait locus - induced oxidative stress - programmed cell-death - arabidopsis-thaliana - nicotianam
When plants are subjected to high metal exposure, different plant species take different strategies in response to metal-induced stress. Largely, plants can be distinguished in four groups: metal-sensitive species, metal-resistant excluder species, metal-tolerant non-hyperaccumulator species, and metal-hypertolerant hyperaccumulator species, each having different molecular mechanisms to accomplish their resistance/tolerance to metal stress or reduce the negative consequences of metal toxicity. Plant responses to heavy metals are molecularly regulated in a process called metal homeostasis, which also includes regulation of the metal-induced reactive oxygen species (ROS) signaling pathway. ROS generation and signaling plays an important duel role in heavy metal detoxification and tolerance. In this review, we will compare the different molecular mechanisms of nutritional (Zn) and non-nutritional (Cd) metal homeostasis between metal-sensitive and metal-adapted species. We will also include the role of metal-induced ROS signal transduction in this comparison, with the aim to provide a comprehensive overview on how plants cope with Zn/Cd stress at the molecular level.
The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods
Mulder, H.A. ; Meuwissen, T.H.E. ; Calus, M.P.L. ; Veerkamp, R.F. - \ 2010
Animal 4 (2010)1. - ISSN 1751-7311 - p. 9 - 19.
quantitative trait locus - dairy-cattle - efficient computation - selection - populations - probabilities - prediction - pedigree - mutation - schemes
In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing geneassisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD–LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD–LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD–LA was larger than when all animals had phenotypes. Missing gene contents were predicted with higher accuracy using multiple-marker iterative peeling than with using mixed model methodology, but the difference in accuracy of total EBV was negligible and mixed model methodology was computationally much faster than multiple iterative peeling. For large livestock populations it can be concluded that gene-assisted breeding value estimation can be practically best performed by regression on gene contents, using mixed model methodology to predict missing marker genotypes, combining phenotypic information of genotyped and ungenotyped animals in one evaluation. This technique would be, in principle, also feasible for genomic selection. It is expected that genomic selection for ungenotyped animals using predicted single nucleotide polymorphism gene contents might be beneficial especially for low heritable traits.
An eQTL analysis of partial resistance to Puccinia hordei in barley
Chen, Xinwei ; Hackett, C.A. ; Niks, R.E. ; Hedley, P.E. ; Booth, C. ; Druka, A. ; Marcel, T.C. ; Vels, S.A. ; Bayer, M. ; Milne, I. ; Morris, J. ; Ramsay, L. ; Marshall, D. ; Cardle, L. ; Waugh, R. - \ 2010
PLoS ONE 5 (2010)1. - ISSN 1932-6203 - 15 p.
quantitative trait locus - density consensus map - false discovery rate - gene-expression - powdery mildew - leaf rust - flowering-time - stem rust - basal defense - arabidopsis
Background - Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes.Methodology/Principal Findings - We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis.Conclusions/Significance - The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population
A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans
Doroszuk, A. ; Snoek, L.B. ; Fradin, E. ; Riksen, J.A.G. ; Kammenga, J.E. - \ 2009
Nucleic acids research 37 (2009)16. - ISSN 0305-1048 - p. e110 - e110.
quantitative trait locus - life-history traits - genotype-environment interactions - natural variation - c-elegans - consomic strains - complex traits - qtl - architecture - polymorphism
Recombinant inbred lines (RILs) derived from Caenorhabditis elegans wild-type N2 and CB4856 are increasingly being used for mapping genes underlying complex traits. To speed up mapping and gene discovery, introgression lines (ILs) offer a powerful tool for more efficient QTL identification. We constructed a library of 90 ILs, each carrying a single homozygous CB4856 genomic segment introgressed into the genetic background of N2. The ILs were genotyped by 123 single-nucleotide polymorphism (SNP) markers. The proportion of the CB4856 segments in most lines does not exceed 3%, and together the introgressions cover 96% of the CB4856 genome. The value of the IL library was demonstrated by identifying novel loci underlying natural variation in two ageing-related traits, i.e. lifespan and pharyngeal pumping rate. Bin mapping of lifespan resulted in six QTLs, which all have a lifespan-shortening effect on the CB4856 allele. We found five QTLs for the decrease in pumping rate, of which four colocated with QTLs found for average lifespan. This suggests pleiotropic or closely linked QTL associated with lifespan and pumping rate. Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans
Mapping and Cloning of Late Blight Resistance Genes from Solanum venturii Using an Interspecific Candidate Gene Approach
Pel, M. ; Foster, S.J. ; Park, T.H. ; Rietman, H. ; Arkel, G. van; Jones, J.D.G. ; Eck, H.J. van; Jacobsen, E. ; Visser, R.G.F. ; Vossen, E.A.G. van der - \ 2009
Molecular Plant-Microbe Interactions 22 (2009)5. - ISSN 0894-0282 - p. 601 - 615.
quantitative trait locus - race-specific resistance - nbs-lrr proteins - phytophthora-infestans - disease-resistance - r-gene - nucleotide-binding - field-resistance - lycopersicon-esculentum - nicotiana-benthamiana
Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of potato. Resistance (R) genes from the wild species Solanum demissum have been used by breeders to generate late-blight-resistant cultivars but resistance was soon overcome by the pathogen. A more recent screening of a large number of wild species has led to the identification of novel sources of resistance, many of which are currently being characterized further. Here, we report on the cloning of dominant Rpi genes from S. venturii. Rpi-vnt1.1 and Rpi-vnt1.3 were mapped to chromosome 9 using nucleotide binding site (NBS) profiling. Subsequently, a Tm-22-based allele mining strategy was used to clone both genes. Rpi-vnt1.1 and Rpi-vnt1.3 belong to the coiled-coil NBS leucine-rich repeat (LRR) class of plant R genes and encode predicted peptides of 891 and 905 amino acids (aa), respectively, which share 75% amino acid identity with the Tomato mosaic virus resistance protein Tm-22 from tomato. Compared with Rpi-vnt1.1, Rpi-vnt1.3 harbors a 14-aa insertion in the N-terminal region of the protein and two different amino acids in the LRR domain. Despite these differences, Rpi-vnt1.1 and Rpi-vnt1.3 genes have the same resistance spectrum
Breeding Value Estimation for Fat Percentage Using Dense Markers on Bos taurus Autosome 14
Roos, S. de; Schrooten, C. ; Mullaart, E. ; Calus, M.P.L. ; Veerkamp, R.F. - \ 2007
Journal of Dairy Science 90 (2007)10. - ISSN 0022-0302 - p. 4821 - 4829.
quantitative trait locus - milk-production - linkage disequilibrium - bovine chromosome-14 - dgat1 - cattle - prediction - haplotypes - mutation - genetics
Prediction of breeding values using whole-genome dense marker maps for genomic selection has become feasible with the advances in DNA chip technology and the discovery of thousands of single nucleotide polymorphisms in genome-sequencing projects. The objective of this study was to compare the accuracy of predicted breeding values from genomic selection (GS), selection without genetic marker information (BLUP), and gene-assisted selection (GEN) on real dairy cattle data for 1 chromosome. Estimated breeding values of 1,300 bulls for fat percentage, based on daughter performance records, were obtained from the national genetic evaluation and used as phenotypic data. All bulls were genotyped for 32 genetic markers on chromosome 14, of which 1 marker was the causative mutation in a gene with a large effect on fat percentage. In GS, the data were analyzed with a multiple quantitative trait loci (QTL) model with haplotype effects for each marker bracket and a polygenic effect. Identical-by-descent probabilities based on linkage and linkage disequilibrium information were used to model the covariances between haplotypes. A Bayesian method using Gibbs sampling was used to predict the presence of a putative QTL and the effects of the haplotypes in each marker bracket. In BLUP, the haplotype effects were removed from the model, whereas in GEN, the haplotype effects were replaced by the effect of the genotype at the known causative mutation. The breeding values from the national genetic evaluation were treated as true breeding values because of their high accuracy and were used to compute the accuracy of prediction for GS, BLUP, and GEN. The allele substitution effect for the causative mutation, obtained from GEN, was 0.35% fat. The accuracy of the predicted breeding values for GS (0.75) was as high as for GEN (0.75) and higher than for BLUP (0.51). When some markers close to the QTL were omitted from the model, the accuracy of prediction was only slightly lower, around 0.72. The removal of all markers within 8 cM from the QTL reduced the accuracy to 0.64, which was still much higher than BLUP. It is concluded that, when applied to 1 chromosome and if genetic markers close to the QTL are available, the presented model for GS is as accurate as GEN.
The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea
Finkers, H.J. ; Heusden, A.W. van; Meijer-Dekens, R.G. ; Kan, J.A.L. van; Maris, P.C. ; Lindhout, P. - \ 2007
Theoretical and Applied Genetics 114 (2007)6. - ISSN 0040-5752 - p. 1071 - 1080.
quantitative trait locus - lycopersicon-hirsutum la407 - recombinant inbred lines - cultivated tomato - advanced backcross - genomic library - genes - fruit - esculentum - pennellii
Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus has been identified in accessions of wild relatives of tomato such as Solanum habrochaites LYC4. In a previous F-2 mapping study, three QTLs conferring resistance to B. cinerea (Rbcq1, Rbcq2 and Rbcq4a) were identified. As it was probable that this study had not identified all QTLs involved in resistance we developed an introgression line (IL) population (n = 30), each containing a S. habrochaites introgression in the S. lycopersicum cv. Moneymaker genetic background. On average each IL contained 5.2% of the S. habrochaites genome and together the lines provide an estimated coverage of 95%. The level of susceptibility to B. cinerea for each of the ILs was assessed in a greenhouse trial and compared to the susceptible parent S. lycopersicum cv. Moneymaker. The effect of the three previously identified loci could be confirmed and seven additional loci were detected. Some ILs contains multiple QTLs and the increased resistance to B. cinerea in these ILs is in line with a completely additive model. We conclude that this set of QTLs offers good perspectives for breeding of B. cinerea resistant cultivars and that screening an IL population is more sensitive for detection of QTLs conferring resistance to B. cinerea than the analysis in an F-2 population.