Quantitative Trait Locus Association Research Articles

An integrated network of microRNA and gene expression in ovarian cancer.

BackgroundOvarian cancer is a deadly female reproductive cancer. Understanding the biological mechanisms underlying ovarian cancer could help lead to quicker and more accurate diagnosis and more effective treatments. Both changes in microRNA(miRNA) expression and miRNA/mRNA dysregulation have been associated with ovarian cancer. With the availability of whole-genome miRNA and mRNA sequencing we now have new potentials to study these associations. In this study, we performed a comprehensive analysis of miRNA and mRNA expression in ovarian cancer using an integrative network approach combined with association analysis.ResultsWe developed an integrative approach to construct a network that illustrates the complex interplay among miRNA and gene expression from a systems perspective. Our method is composed of expanding networks from eQTL associations, building network associations in eQTL analysis, and then combine the networks into an integrated network. This integrated network takes account of miRNA expression quantitative trait loci (eQTL) associations, miRNAs and their targets, protein-protein interactions, co-expressions among miRNAs and genes respectively. Applied to the ovarian cancer data set from The Cancer Genome Atlas (TCGA), we created an integrated network with 167 nodes containing 108 miRNA-target interactions and 145 from protein-protein interactions, starting from 44 initial eQTLs. This integrated network encompassed 26 genes and 14 miRNAs associated with cancer. In particular, 11 genes and 12 miRNAs in the integrated network are associated with ovarian cancer.ConclusionWe demonstrated an integrated network approach that integrates multiple data sources at a systems level. We applied this approach to the TCGA ovarian cancer dataset, and constructed a network that provided a more inclusive view of miRNA and gene expression in ovarian cancer. This network included four separate types of interactions among miRNAs and genes. Simply analyzing each interaction component in isolation, such as the eQTL associations, the miRNA-target interactions or the protein-protein interactions, would create a much more limited network than the integrated one.

Stories and Challenges of Genome Wide Association Studies in Livestock - A Review.

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

Breeding of a target genotype variety based on identified chalkiness marker-QTL associations in rice (Oryza sativa L.).

The aim of this study was to breed a target genotype variety based on the identified chalkiness marker-QTL (quantitative trait locus) associations in rice. First, a permanent mapping population of rice that consisted of 525 recombinant inbred lines (RILs), which were derived from Zhenshan 97/Minghui 63, was used to identify QTLs with additive effects for rice quantitative traits and percentage of grain chalkiness (PGC). Subsequently, based on the identified QTLs in rice, the molecular marker 68923-PGC was selected to screen the low chalkiness rice line. Then, using the integration of molecular marker breeding and traditional breeding, we analyzed the genotype and phenotype of inbred lines from 525 RILs; we identified one rice variety with particularly high yields, good taste, and broad adaptability. The new variety was temporarily named RIL10, which was a high quality, high yield, and broadly adaptable variety, and it is predominantly a feature that has contributed to its geographical adaptability, which would be planted from 35°E to 18°E in Chinain China, where 2/3 of rice production occurs. RIL10 was a marker-assisted selection breeding achievement for producing a high quality, high yield, and broadly adaptable rice variety.

Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population.

BackgroundA previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. Since that time, the genomic resources available for such analyses have improved substantially. An updated NAM genetic linkage map has a nearly six-fold greater marker density than the previous map and the combined SNPs and read-depth variants (RDVs) from maize HapMaps 1 and 2 provided 28.5 M genomic variants for association analysis, 17 fold more than HapMap 1. In addition, phenotypic values of the NAM RILs were re-estimated to account for environment-specific flowering time covariates and a small proportion of lines were dropped due to genotypic data quality problems. Comparisons of original and updated QTL and GWAS results confound the effects of linkage map density, GWAS marker density, population sample size, and phenotype estimates. Therefore, we evaluated the effects of changing each of these parameters individually and in combination to determine their relative impact on marker-trait associations in original and updated analyses.ResultsOf the four parameters varied, map density caused the largest changes in QTL and GWAS results. The updated QTL model had better cross-validation prediction accuracy than the previous model. Whereas joint linkage QTL positions were relatively stable to input changes, the residual values derived from those QTL models (used as inputs to GWAS) were more sensitive, resulting in substantial differences between GWAS results. The updated NAM GWAS identified several candidate genes consistent with previous QTL fine-mapping results.ConclusionsThe highly polygenic nature of resistance to SLB complicates the identification of causal genes. Joint linkage QTL are relatively stable to perturbations of data inputs, but their resolution is generally on the order of tens or more Mbp. GWAS associations have higher resolution, but lower power due to stringent thresholds designed to minimize false positive associations, resulting in variability of detection across studies. The updated higher density linkage map improves QTL estimation and, along with a much denser SNP HapMap, greatly increases the likelihood of detecting SNPs in linkage with causal variants. We recommend use of the updated genetic resources and results but emphasize the limited repeatability of small-effect associations.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1068) contains supplementary material, which is available to authorized users.

Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans.

Fever predicts clinical outcomes in sepsis, trauma and during cardiovascular stress, yet the genetic determinants are poorly understood. We used an integrative genomics approach to identify novel genomic determinants of the febrile response to experimental endotoxemia. We highlight multiple integrated lines of evidence establishing the clinical relevance of this novel fever locus. Through genome-wide association study (GWAS) of evoked endotoxemia (lipopolysaccharide (LPS) 1 ng/kg IV) in healthy subjects of European ancestry we discovered a locus on chr7p11.2 significantly associated with the peak febrile response to LPS (top single nucleotide polymorphism (SNP) rs7805622, P = 2.4 × 10(-12)), as well as with temperature fluctuation over time. We replicated this association in a smaller independent LPS study (rs7805622, P = 0.03). In clinical translation, this locus was also associated with temperature and mortality in critically ill patients with trauma or severe sepsis. The top GWAS SNPs are not located within protein-coding genes, but have significant cis-expression quantitative trait loci (eQTL) associations with expression of a cluster of genes ∼400 kb upstream, several of which (SUMF2, CCT6A, GBAS) are regulated by LPS in vivo in blood cells. LPS- and cold-treatment of adipose stromal cells in vitro suggest genotype-specific modulation of eQTL candidate genes (PSPH). Several eQTL genes were up-regulated in brown and white adipose following cold exposure in mice, highlighting a potential role in thermogenesis. Thus, through genomic interrogation of experimental endotoxemia, we identified and replicated a novel fever locus on chr7p11.2 that modulates clinical responses in trauma and sepsis, and highlight integrated in vivo and in vitro evidence for possible novel cis candidate genes conserved across human and mouse.

Miscanthus: a case study for the utilization of natural genetic variation

Cultivars ofMiscanthusused as bioenergy crops or tested in trials are largely clonally propagated, wild sourced genotypes or clonally propagated F1 hybrids. One of the most productive taxa is the sterile triploidM.× giganteus. Little domestication or breeding has been undertaken and there is huge potential to utilize the extensive genetic resources of the genus for crop improvement. The challenge is to generate new highly adapted genotypes suitable for a range of environments. Production on marginal land, not used for food crops, is particularly desirable, but presents many barriers to crop breeders, as these are largely unproductive and/or stressful environments. This article outlines progress made in characterizing natural genetic variation inMiscanthusincluding next-generation single-nucleotide polymorphism genotyping, quantitative trait locus analysis and association mapping. It also explains how this knowledge is being used to develop novel genotypes suited for growth in a broad range of agricultural and marginal lands by defining breeding pools, generating novel crosses, manipulating polyploidy and applying genomic selection approaches.

Quantitative trait loci and genetic association analysis reveals insights into complex pearl quality traits in donor silver-lipped pearl oysters

Abstract Pearl oysters are commercially farmed for their gemstone quality pearls worldwide and are an important animal model for understanding bivalve biology. However, despite their economic and scientific significance, limited quantitative genetic studies have been undertaken to identify genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). Over the last decade, pearling industries worldwide have shown strong interest in genetic stock improvement aiming to increase the production of high quality ‘South Sea’ pearls. However, before genetic breeding programmes can be initiated, the genetic architecture of such traits needs to be elucidated. This study investigates the genetic architecture of complex pearl quality traits (pearl size, weight, surface complexion and colour) and presents the first putative quantitative trait loci (QTL) and genetic associations to these commercially important pearl quality traits. To identify QTL and genetic associations to pearl quality traits, a total of 2114 pearl grading records were recorded over 342 pearl oysters. Utilising these phenotypic records, this study provides strong evidence that pearl quality traits have a low to moderate additive genetic component ( h 2 from 0.14 to 0.34) and supports previous quantitative genetic studies that these traits are polygenic in nature. A total of nine putative QTL and 25 marker associations for pearl colour, one QTL for pearl surface complexion and three genetic associations to pearl size and weight were identified using 11 half-sib families. The majority of QTL and genetic associations were detected for pearl colour whereby the most prominent QTL were located within a 2 cM interval on LG10. QTL in this region were mapped for four out of five sub-categories of pearl colour and explained from 32% to 46.1% of the phenotypic variation observed in pearl colour. Segregation in multiple families provides further support that genes localised to this region have significant effects on pearl colour. The segregation of these preliminary QTL and detection of genetic associations provide insights into the genetic architecture of pearl quality traits and will direct further research into the establishment of genetic breeding programmes for pearl quality within the Pinctada maxima pearling industry.

Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow.

Our current understanding of speciation is often based on considering a relatively small number of genes, sometimes in isolation of one another. Here, we describe a possible emergent genome process involving the aggregate effect of many genes contributing to the evolution of reproductive isolation across the speciation continuum. When a threshold number of divergently selected mutations of modest to low fitness effects accumulate between populations diverging with gene flow, nonlinear transitions can occur in which levels of adaptive differentiation, linkage disequilibrium, and reproductive isolation dramatically increase. In effect, the genomes of the populations start to "congeal" into distinct entities representing different species. At this stage, reproductive isolation changes from being a characteristic of specific, divergently selected genes to a property of the genome. We examine conditions conducive to such genome-wide congealing (GWC), describe how to empirically test for GWC, and highlight a putative empirical example involving Rhagoletis fruit flies. We conclude with cautious optimism that the models and concepts discussed here, once extended to large numbers of neutral markers, may provide a framework for integrating information from genome scans, selection experiments, quantitative trait loci mapping, association studies, and natural history to develop a deeper understanding of the genomics of speciation.

Is the Alcohol Deprivation Effect Genetically Mediated? Studies with HXB/BXH Recombinant Inbred Rat Strains

Two features of alcohol addiction that have been widely studied in animal models are relapse drinking following periods of alcohol abstinence and the escalation of alcohol consumption after chronic continuous or intermittent alcohol exposure. The genetic contribution to these phenotypes has not been systematically investigated. HXB/BXH recombinant inbred (RI) rat strains were given access to alcohol sequentially as follows: alcohol (10%) as the only fluid for 1 week; alcohol (10%) and water in a 2-bottle choice paradigm for 7 weeks ("pre-alcohol deprivation effect [ADE] alcohol consumption"); 2 weeks of access to water only (alcohol deprivation); and 2 weeks of reaccess to 10% alcohol and water ("post-ADE alcohol consumption"). The periods of deprivation and reaccess to alcohol were repeated 3 times. The ADE was defined as the amount of alcohol consumed in the first 24 hours after deprivation minus the average daily amount of alcohol consumed in the week prior to deprivation. Heritability of the phenotypes was determined by analysis of variance, and quantitative trait loci (QTLs) were identified. All strains showed increased alcohol consumption, compared to the predeprivation period, in the first 24 hours after each deprivation (ADE). Broad-sense heritability of the ADEs was low (ADE1, 9.1%; ADE2, 26.2%; ADE3, 16.3%). Alcohol consumption levels were relatively stable over weeks 2 to 7. Post-ADE alcohol consumption levels consistently increased in some strains and were decreased or unchanged in others. Heritability of pre- and post-ADE alcohol consumption was high and increased over time (week 2, 38.5%; week 7, 51.1%; week 11, 56.8%; week 15, 63.3%). QTLs for pre- and post-ADE alcohol consumption were similar, but the strength of the QTL association with the phenotype decreased over time. In the HXB/BXH RI rat strains, genotypic variance does not account for a large proportion of phenotypic variance in the ADE phenotype (low heritability), suggesting a role of environmental factors. In contrast, a large proportion of the variance across the RI strains in pre- and post-ADE alcohol consumption is due to genetically determined variance (high heritability).

English

Protein and fat percent as content of milk are high-priority criteria for financial aims and selection of programs in dairy cattle. In order to incorporate information on marker- quantitative trait locus (QTL) associations, QTL detection and parameter estimation should also be performed. Microsatellite markers are most valuable markers in association studies between different loci with the production traits. With the aim of analysis markers previously identified by other researchers in QTLs of milk fat and protein percent traits in Iranian Holstein dairy cattle sample population, we use ten microsatellite markers on chromosomes 1, 6, 7 and 20. All microsatellite markers were genotype in 156 dairy cattle which have at least one year data of milk fat and protein record using 6 to 8% polyacrylamide gel electrophoreses determined with silver nitrate staining. We find 7, 5 and 8 out of 10 markers showing significant effect on milk fat percent in 1 to 120, 120 to 240 and 240 to 360 milking days, respectively. Our results show 6, 8 and 9 out of 10 markers have significant effect on protein percent in 1 to 120, 120 to 240 and 240 to 360 milking days respectively.   Key words: Fat percent, Iranian Holstein cattle, microsatellites, milking days, protein percent, quantitative trait locus (QTL).

Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.

Modifying plant cell walls for bioenergy production.

Abstract Predictions about future supply of crude oil, increase in greenhouse gases and burgeoning human population have recently necessitated a search for sustainable and environmentally responsible sources of alternative energy. Bioconversion of organic biomass, largely derived from plant residues, to biofuels has been viewed as one of the most attractive avenues of research. More than half of the plant biomass produced on earth consists of cell walls that are enriched in carbohydrate polymers such as cellulose and hemicellulose. Breakdown of these carbohydrate polymers by pre-treatments and cellulolytic enzymes to monomer sugars (saccharification) which is followed by fermentation of sugars to bioethanol is one of the favoured ways of producing biofuels. Presence of phenolic compounds in form of lignin hinders access of cell wall degrading enzymes to carbohydrates, and genetic engineering of genes and metabolic pathways involved in cell wall formation could dramatically alter the outcome for biofuel production. In recent years, several reports have described such approaches that improve saccharification efficiency and this review discusses some of those advances. Another approach is to use quantitative trait locus (QTL) mapping and/or association mapping to identify genes/molecular markers that are associated with cell wall polymer synthesis. These candidate genes can be used for marker-assisted breeding and/or could be manipulated using transgenic approaches. A combination of these techniques is likely to provide novel tools in producing feedstocks for efficient use of selected plant biomass in biofuel production.

High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method—2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.

Human CLOCK gene-associated attention deficit hyperactivity disorder-related features in healthy adults: quantitative association study using Wender Utah Rating Scale

Circadian rhythm disturbance is highly prevalent in attention deficit hyperactivity disorder (ADHD). Recently, the association between the CLOCK gene and ADHD has been demonstrated in clinical samples, and the CLOCK gene's role was thought to be mediated by rhythm dysregulation. Meanwhile, ADHD has been suggested as the extreme end of a continuously distributed trait that can be found in the general population. Therefore, we examined two possibilities: (1) an ADHD-related continuous trait may be associated with the CLOCK gene, and (2) this association may be mediated by the degree of individuals' evening preference. To explore these possibilities, we performed a quantitative trait locus association study with a sample of 1,289 healthy adults. The Wender Utah Rating Scale (WURS) and the Composite Scale of Morningness (CSM) were utilized to measure the quantitative traits. Quantitative association analysis was performed using PLINK software. We found that rs1801260 (=T3111C) was associated with WURS scores in both allele-wise (p = 0.018) and haplotype-wise analyses (range of p values: 0.0155-0.0171) in male participants only. After controlling for the CSM total score as a covariate, the strength of the association did not change at all, suggesting that the association was not mediated by evening preference. Despite the very weak association signal, our results provide evidence that the CLOCK gene's association with ADHD in clinical samples may be generalizable to traits measured in the normal population. However, as our results failed to show a mediating role of evening preference, ongoing efforts are needed to identify the mechanisms by which the CLOCK gene determines ADHD-related traits.

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

BackgroundThe olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey.Methodology/Principal FindingsNext-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers.Conclusions/SignificanceThis study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype.

Haplotype, molecular marker and phenotype effects associated with mineral nutrient and grain size traits of TaGS1a in wheat

Glutamine synthetase (GS) is a key enzyme in the formation of the amino acid glutamine during N assimilation. The characterization of GS genes and the development of functional markers are important for marker-assisted selection (MAS) in wheat breeding programs. In the present study, the full-length genomic DNA (gDNA) sequence of TaGS1a was obtained from 60 wheat varieties. TaGS1a comprises 3415bp and has eleven exons and ten introns. Nine single nucleotide polymorphisms (SNPs) and two insertions and deletions of DNA segments (InDels) were detected in introns, resulting two haplotypes: Hap 1 and Hap 2. A cleaved amplified polymorphic sequence (CAPS) marker was developed to distinguish the two haplotypes. The TaGS1a-CAPS marker was located on chromosome 6D using Chinese Spring nullisomic–tetrasomic lines, and mapped at 2.5 cM from the SSR marker barc1121b in a RIL population. The completely corresponding results between quantitative trait locus (QTL) analysis and association analysis suggested that the TaGS1a gene had functions for grain size traits, including thousand grain weight (TGW), grain width (GW), grain height (GH), GL/GW ratio (GLW), factor form density (FFD), grain area (GA) and grain volume (GV) during maturity stage, and for the ratio of root/shoot for dry weight and nitrogen, phosphorus, potassium contents (RSDW, RSNC, RSPC and RSKC) during seedling stage.

Marker-assisted versus phenotypic selection for iron-deficiency chlorosis in soybean

Iron-deficiency chlorosis (IDC) is an important agronomic trait when soybean (Glycine max (L.) Merr.) is planted on calcareous soil. Breeders need confirmation that marker-QTL (quantitative trait loci) associations developed using association mapping, will be effective in a different set of genotypes than the ones used to identify those markers. Marker-QTL associations that had previously been identified in separate mapping experiments were evaluated. Marker-assisted selection (MAS) was compared to phenotypic selection (PS) to evaluate the association mapping approach to identifying markers. The PS or MAS criteria were used to select the 20 most IDC-tolerant and IDC-susceptible lines, based on three 2009 selection sites. Three sites in 2010 were used as validation to compare the effectiveness of the different selection criteria. A random sample (RS) was generated as a control. When validation was conducted averaged across three 2010 sites, PS was the best method to select for IDC with a mean of 1.78, compared to MAS with a mean of 2.05. Since PS was so effective the process of genotyping, which is required for MAS, was unnecessary. The additive effects of QTL that had been estimated from the original mapping experiments were biased upward when compared to QTL effects estimated from the 2009 data. Also, many markers in the target population of experimental lines did not have a gene frequency of 0.5, which greatly reduced the effectiveness of MAS.

Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping

Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length.

Dissection of complex traits in forest trees — opportunities for marker-assisted selection

Due to their long reproductive cycles and the time to expression of mature traits, marker-assisted selection is particularly attractive for tree breeding. In this review, we discuss different approaches used for developing markers and propose a method for application of markers in low linkage disequilibrium (LD) populations. Identification of useful markers for application in tree breeding is mainly based on two approaches, quantitative trait locus (QTL) mapping and association genetic studies. While several studies have identified significant markers, effect of the individual markers is low making it difficult to utilize them in breeding programs. Recently, genomic selection (GS) was proposed for overcoming some of these difficulties. In GS, high density markers are used for predicting phenotypes from genotypes. Currently small effective populations with high LD are being tested for GS in tree breeding. For wider application, GS needs to be applied in low LD populations which are found in many tree breeding programs. Here we propose an approach in which the significant markers from association studies may be used for developing prediction models in low LD populations using the same methods as in GS. Preliminary analyses indicate that a modest numbers of markers may be sufficient for developing prediction models in low LD populations. GS based on large numbers of random markers or small numbers of associated markers is poised to make marker-assisted selection a reality in forest tree breeding.

The peach (Prunus persica L. Batsch) genome harbours 10 KNOX genes, which are differentially expressed in stem development, and the class 1 KNOPE1 regulates elongation and lignification during primary growth

The KNOTTED-like (KNOX) genes encode homeodomain transcription factors and regulate several processes of plant organ development. The peach (Prunus persica L. Batsch) genome was found to contain 10 KNOX members (KNOPE genes); six of them were experimentally located on the Prunus reference map and the class 1 KNOPE1 was found to link to a quantitative trait locus (QTL) for the internode length in the peach×Ferganensis population. All the KNOPE genes were differentially transcribed in the internodes of growing shoots; the KNOPE1 mRNA abundance decreased progressively from primary (elongation) to secondary growth (radial expansion). During primary growth, the KNOPE1 mRNA was localized in the cortex and in the procambium/metaphloem zones, whereas it was undetected in incipient phloem and xylem fibres. KNOPE1 overexpression in the Arabidopsis bp4 loss-of-function background (35S:KNOPE1/bp genotype) restored the rachis length, suggesting, together with the QTL association, a role for KNOPE1 in peach shoot elongation. Several lignin biosynthesis genes were up-regulated in the bp4 internodes but repressed in the 35S:KNOPE1/bp lines similarly to the wild type. Moreover, the lignin deposition pattern of the 35S:KNOPE1/bp and the wild-type internodes were the same. The KNOPE1 protein was found to recognize in vitro one of the typical KNOX DNA-binding sites that recurred in peach and Arabidopsis lignin genes. KNOPE1 expression was inversely correlated with that of lignin genes and lignin deposition along the peach shoot stems and was down-regulated in lignifying vascular tissues. These data strongly support that KNOPE1 prevents cell lignification by repressing lignin genes during peach stem primary growth.