The Impact of Weight-bearing Exercise, Non-Weight-bearing Exercise, and Cardiovascular Stress on Biochemical Markers of Cartilage Turnover in Patients With Mild to Moderate Knee Osteoarthritis: A Sequential, Cross-Over, Clinical Study.

OBJECTIVE: To investigate how running, cycling, and sedentary cardiovascular stress impact biomarkers of cartilage turnover acutely in subjects with knee osteoarthritis (OA). DESIGN: This was a sequential, cross-over, clinical study. Forty subjects with primary knee OA underwent moderate-to-high-intensity cycling, running, and adrenaline infusion on separate days. Blood was sampled before, during, and at 6-time points after intervention. On a control day, similar samples were taken. Biomarkers of type II collagen degradation (C2M, T2CM, Coll2-1, Coll2-1NO2), formation (PRO-C2), and aggrecan degradation (ARGS) were measured. RESULTS: Mean age was 60.4 years, 40% were male, 45% had cumulated Kellgren-Lawrence (KL)-grade (Right + Left knee) of 2 to 3 and 55% had 4 to 6. Analyzing overall changes, area under the curve was significantly lower compared with resting values for ARGS and C2M after cycling and for ARGS after running. Considering individual time points, peak changes in biomarker levels showed reduction in C2M shortly following cycling (T20min = -12.3%, 95% confidence interval [CI]: -19.3% to -5.2%). PRO-C2 increased during cycling (T10min = 14.0%, 95% CI = 4.1% to 23.8%) and running (T20min = 16.5%, 95% CI = 4.3% to 28.6%). T2CM decreased after cycling (T50min = -19.9%, 95% CI = -29.2% to -10.6%), running (T50min = -22.8%, 95% CI = -32.1% to -13.5%), and infusion of adrenaline (peak, T50min = -9.8%, 95% CI = -20.0% to 0.4%). A latent increase was seen in Coll2-1 240 minutes after running (T260min = 21.7%, 95% CI = -1.6% to 45.1%). CONCLUSION: Exercise had an impact on cartilage markers, but it did not suggest any detrimental effect on cartilage. Changes following adrenaline infusion suggest a sympathomimetic influence on the serological composition of biomarkers.

The efficacy and safety of a fixed-dose combination of apocynin and paeonol, APPA, in symptomatic knee OA: A double-blind, randomized, placebo-controlled, clinical trial.

OBJECTIVE: Apocynin (AP) and paeonol (PA) are low molecular weight phenolic compounds with a broad array of anti-inflammatory and immunoregulatory effects. This study assessed of a fixed-dose combination of APPA in people with symptomatic knee osteoarthritis (OA). METHODS: A multi-center, randomized, placebo-controlled, double-blind phase 2a trial enrolled participants with radiographic knee OA (Kellgren-Lawrence, KL, grades 2-3) and pain ≥40/100 on WOMAC pain subscale, and evaluated the efficacy and safety of oral APPA over a 28-day period. APPA 800 mg or matching placebo was administered twice daily in a 1:1 ratio. Post-hoc analyses explored the response to APPA in sub-groups with more severe pain and structural severity. RESULTS: The two groups were comparable at baseline; 152 subjects were enrolled and 148 completed the trial. There was no statistically significant difference between groups with respect to the primary outcome, WOMAC pain (mean difference between groups was -0.89, 95% CI: -5.62, 3.84, p = 0.71), nor WOMAC function or WOMAC total. However, predefined subgroup analyses of subjects with symptoms compatible with neuroplastic/neuropathic pain features showed a statistically significant effect of APPA compared to placebo. Adverse events (mainly gastrointestinal) were mild to moderate. CONCLUSION: Treatment with APPA 800 mg twice daily for 28 days in subjects with symptomatic knee OA was not associated with significant symptom improvement compared to placebo. The treatment was well-tolerated and safe. While the study was not powered for such analysis, pre-planned subgroup analyses showed a significant effect of APPA in subjects with neuroplastic pain/severe OA, indicating that further research in the effects of APPA in appropriate patients is warranted.

Exploring High-Purity Multiparton Scattering at Hadron Colliders.

Multiparton interactions are a fascinating phenomenon that occur in almost every high-energy hadron-hadron collision yet are remarkably difficult to study quantitatively. In this Letter, we present a strategy to optimally disentangle multiparton interactions from the primary scattering in a collision. That strategy enables probes of multiparton interactions that are significantly beyond the state of the art, including their characteristic momentum scale, the interconnection between primary and secondary scatters, and the pattern of three and potentially even more simultaneous hard scatterings. This opens a path to powerful new constraints on multiparton interactions for LHC phenomenology and to the investigation of their rich field-theoretical structure.

Associations between single-question Visual Analogue Scale pain score and weight-bearing and non-weight-bearing domains of Western Ontario and McMaster Universities Arthritis Index pain: data from 2 phase 3 clinical trials.

Introduction: Visual Analogue Scale (VAS) and the pain subscale of the Western Ontario and McMaster Universities Arthritis Index (WOMAC) are commonly used measuring tools of osteoarthritis (OA) pain. Objectives: The objective of this cross-sectional study was to explore the associations between single-question VAS pain and the weight-bearing and non-weight-bearing domains of WOMAC pain. Methods: Data from 2093 patients with OA participating in 2 phase 3 clinical trials were included for post hoc analyses. Univariate Pearson correlations and comparison of r values were made using z statistics obtained using the Fisher r to z test for all items of the VAS pain scale, the WOMAC pain subscale, the weight-bearing and non-weight-bearing constructs of WOMAC pain subscale, and by subgroups of WOMAC pain quintiles and Kellgren-Lawrence grades. Results: The correlations between VAS pain and WOMAC pain were significant (r = 0.67, P < 0.001) with a slope of 0.57 (95% confidence interval [CI]: 0.54-0.61). A similar correlation was found for weight-bearing pain (r = 0.68, P < 0.001, slope: 0.62 (95% CI: 0.59-0.65) but significantly lower for non-weight-bearing pain (r = 0.55, P < 0.001, slope: 0.49 (95% CI: 0.46-0.52). The degree of disagreement between the 2 instruments seemed to be lesser in the extreme ends of the scales, and the observed association between Kellgren-Lawrence grade and disagreement between VAS and WOMAC was driven by non-weight-bearing pain. Conclusion: In conclusion, VAS pain and WOMAC pain subscale correlation was found to be moderate and the VAS pain scale correlated more accurately with the WOMAC pain weight-bearing questions. This constitutes novel insight into patient with OA pain reporting.

A biomarker perspective on the acute effect of exercise with and without impact on joint tissue turnover: an exploratory randomized cross-over study.

PURPOSE: To investigate acute changes in biochemical markers of bone and cartilage turnover in response to moderate intensity exercise with and without joint impact in healthy human subjects. METHODS: A randomized, cross-over, exploratory, clinical study was conducted. Twenty healthy subjects with no history of joint trauma completed 30 min interventions of standardized moderate intensity cycling and running as well as a resting intervention 1 week apart. Blood samples were taken immediately before, four times after exercise and again the next day. Urine was sampled, before, after and the next day. On the day of rest, samples were taken at timepoints similar to the days of exercise. Markers of type I (CTX-I), II (C2M, CTX-II) and VI (C6M) collagen degradation, cartilage oligomeric matrix protein (COMP) and procollagen C-2 (PRO-C2) was measured. TRIAL REGISTRATION NUMBER: NCT04542655, 02 September 2020, retrospectively registered. RESULTS: CTX-I was different from cycling (4.2%, 95%CI: 0.4-8.0%, p = 0.03) and resting (6.8%, 95%CI: 2.9-10.7%, p = 0.001) after running and the mean change in COMP was different from cycling (10.3%, 95%CI: 1.1-19.5%, p = 0.03), but not from resting (8.6%, 95%CI: - 0.7-17.8%, p = 0.07) after running. Overall, changes in other biomarkers were not different between interventions. CONCLUSION: In this exploratory study, running, but not cycling, at a moderate intensity and duration induced acute changes in biomarkers of bone and cartilage extra-cellular matrix turnover.

Genomic prediction of yield and root development in wheat under changing water availability.

BACKGROUND: Deeper roots help plants take up available resources in deep soil ensuring better growth and higher yields under conditions of drought. A large-scale semi-field root phenotyping facility was developed to allow a water availability gradient and detect potential interaction of genotype by water availability gradient. Genotyped winter wheat lines were grown as rows in four beds of this facility, where indirect genetic effects from neighbors could be important to trait variation. The objective was to explore the possibility of genomic prediction for grain-related traits and deep root traits collected via images taken in a minirhizotron tube under each row of winter wheat measured. RESULTS: The analysis comprised four grain-related traits: grain yield, thousand-kernel weight, protein concentration, and total nitrogen content measured on each half row that were harvested separately. Two root traits, total root length between 1.2 and 2 m depth and root length in four intervals on each tube were also analyzed. Two sets of models with or without the effects of neighbors from both sides of each row were applied. No interaction between genotypes and changing water availability were detected for any trait. Estimated genomic heritabilities ranged from 0.263 to 0.680 for grain-related traits and from 0.030 to 0.055 for root traits. The coefficients of genetic variation were similar for grain-related and root traits. The prediction accuracy of breeding values ranged from 0.440 to 0.598 for grain-related traits and from 0.264 to 0.334 for root traits. Including neighbor effects in the model generally increased the estimated genomic heritabilities and accuracy of predicted breeding values for grain yield and nitrogen content. CONCLUSIONS: Similar relative amounts of additive genetic variance were found for both yield traits and root traits but no interaction between genotypes and water availability were detected. It is possible to obtain accurate genomic prediction of breeding values for grain-related traits and reasonably accurate predicted breeding values for deep root traits using records from the semi-field facility. Including neighbor effects increased the estimated additive genetic variance of grain-related traits and accuracy of predicting breeding values. High prediction accuracy can be obtained although heritability is low.

Author Correction: Genomic prediction and GWAS of yield, quality and disease-related traits in spring barley and winter wheat.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genomic prediction and GWAS of yield, quality and disease-related traits in spring barley and winter wheat.

Genome-wide association study (GWAS) and genomic prediction (GP) are extensively employed to accelerate genetic gain and identify QTL in plant breeding. In this study, 1,317 spring barley and 1,325 winter wheat breeding lines from a commercial breeding program were genotyped with the Illumina 9 K barley or 15 K wheat SNP-chip, and phenotyped in multiple years and locations. For GWAS, in spring barley, a QTL on chr. 4H associated with powdery mildew and ramularia resistance were found. There were several SNPs on chr. 4H showing genome-wide significance with yield traits. In winter wheat, GWAS identified two SNPs on chr. 6A, and one SNP on chr. 1B, significantly associated with quality trait moisture, as well as one SNP located on chr. 5B associated with starch content in the seeds. The significant SNPs identified by multiple trait GWAS were generally the same as those found in single trait GWAS. GWAS including genotype-location information in the model identified significant SNPs in each tested location, which were not found previously when including all locations in the GWAS. For GP, in spring barley, GP using the Bayesian Power Lasso model had higher accuracy than ridge regression BLUP in powdery mildew and yield traits, whereas the prediction accuracies were similar using Bayesian Power Lasso model and rrBLUP for yield traits in winter wheat.

Evaluation of serum ARGS neoepitope as an osteoarthritis biomarker using a standardized model for exercise-induced cartilage extra cellular matrix turnover.

Objective: To propose a standardized model for exercise-induced cartilage turnover and investigate residual levels and dynamics of biomarker serum ARGS (sARGS) in primary osteoarthritis (OA) patients and a supportive group of young healthy subjects. Method: The trial is a randomized, cross-over, exploratory study with interventions of exercise and inactivity. 20 subjects with knee OA, as well as 20 young healthy subjects (mean age 25.7 years (range; 19-30), 50% male), underwent cycling, running and resting interventions on separate days one week apart. Blood samples were taken at baseline, immediately, 1, 2, 3 and 24 h after activity start. sARGS was measured by sandwich ELISA. Results: Intraclass correlation between visits were 0.97 and 0.77 for the OA and healthy group, respectively. An acute drop in sARGS in response to high-intensity exercise was observed in both groups. Minute acute sARGS increase was observed in OA subjects in response to moderate intensity running and cycling, which normalized within 24 h. In healthy subjects an acute drop in sARGS was seen immediately after running, but not cycling, and no other changes were observed. A negative correlation between baseline Kellgren-Lawrence (KL) grade and baseline sARGS (r = -0.69, p = 0.002) in OA was found. A negative correlation between age and sARGS was found in healthy subjects (r = -0.67, p = <0.002). Conclusion: sARGS sensitivity to physical activity is considered low and sARGS is a reproducible and stable marker. Minute acute increases in sARGS were observed in the hours following moderate intensity exercise.

Genomic Prediction and Genome-Wide Association Studies of Flour Yield and Alveograph Quality Traits Using Advanced Winter Wheat Breeding Material.

Use of genetic markers and genomic prediction might improve genetic gain for quality traits in wheat breeding programs. Here, flour yield and Alveograph quality traits were inspected in 635 F6 winter wheat breeding lines from two breeding cycles. Genome-wide association studies revealed single nucleotide polymorphisms (SNPs) on chromosome 5D significantly associated with flour yield, Alveograph P (dough tenacity), and Alveograph W (dough strength). Additionally, SNPs on chromosome 1D were associated with Alveograph P and W, SNPs on chromosome 1B were associated with Alveograph P, and SNPs on chromosome 4A were associated with Alveograph L (dough extensibility). Predictive abilities based on genomic best linear unbiased prediction (GBLUP) models ranged from 0.50 for flour yield to 0.79 for Alveograph W based on a leave-one-out cross-validation strategy. Predictive abilities were negatively affected by smaller training set sizes, lower genetic relationship between lines in training and validation sets, and by genotype-environment (G×E) interactions. Bayesian Power Lasso models and genomic feature models resulted in similar or slightly improved predictions compared to GBLUP models. SNPs with the largest effects can be used for screening large numbers of lines in early generations in breeding programs to select lines that potentially have good quality traits. In later generations, genomic predictions might be used for a more accurate selection of high quality wheat lines.

Genome-Wide Association Studies and Comparison of Models and Cross-Validation Strategies for Genomic Prediction of Quality Traits in Advanced Winter Wheat Breeding Lines.

The aim of the this study was to identify SNP markers associated with five important wheat quality traits (grain protein content, Zeleny sedimentation, test weight, thousand-kernel weight, and falling number), and to investigate the predictive abilities of GBLUP and Bayesian Power Lasso models for genomic prediction of these traits. In total, 635 winter wheat lines from two breeding cycles in the Danish plant breeding company Nordic Seed A/S were phenotyped for the quality traits and genotyped for 10,802 SNPs. GWAS were performed using single marker regression and Bayesian Power Lasso models. SNPs with large effects on Zeleny sedimentation were found on chromosome 1B, 1D, and 5D. However, GWAS failed to identify single SNPs with significant effects on the other traits, indicating that these traits were controlled by many QTL with small effects. The predictive abilities of the models for genomic prediction were studied using different cross-validation strategies. Leave-One-Out cross-validations resulted in correlations between observed phenotypes corrected for fixed effects and genomic estimated breeding values of 0.50 for grain protein content, 0.66 for thousand-kernel weight, 0.70 for falling number, 0.71 for test weight, and 0.79 for Zeleny sedimentation. Alternative cross-validations showed that the genetic relationship between lines in training and validation sets had a bigger impact on predictive abilities than the number of lines included in the training set. Using Bayesian Power Lasso instead of GBLUP models, gave similar or slightly higher predictive abilities. Genomic prediction based on all SNPs was more effective than prediction based on few associated SNPs.

Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines.

Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phenotyping all the material produced but only a subset of it named training population (TP). However, genotyping of all the accessions under analysis is needed and, therefore, optimizing TP dimension and genotyping strategy is pivotal to implement GP in commercial breeding schemes. Here, we explored the optimum TP size and we integrated pedigree records and genome wide association studies (GWAS) results to optimize the genotyping strategy. A total of 988 advanced wheat breeding lines were genotyped with the Illumina 15K SNPs wheat chip and phenotyped across several years and locations for yield, lodging, and starch content. Cross-validation using the largest possible TP size and all the SNPs available after editing (~11k), yielded predictive abilities (rGP) ranging between 0.5-0.6. In order to explore the Training population size, rGP were computed using progressively smaller TP. These exercises showed that TP of around 700 lines were enough to yield the highest observed rGP. Moreover, rGP were calculated by randomly reducing the SNPs number. This showed that around 1K markers were enough to reach the highest observed rGP. GWAS was used to identify markers associated with the traits analyzed. A GWAS-based selection of SNPs resulted in increased rGP when compared with random selection and few hundreds SNPs were sufficient to obtain the highest observed rGP. For each of these scenarios, advantages of adding the pedigree information were shown. Our results indicate that moderate TP sizes were enough to yield high rGP and that pedigree information and GWAS results can be used to greatly optimize the genotyping strategy.

A randomized, double-blind, multicenter, placebo-controlled study to evaluate the efficacy and safety of oral salmon calcitonin in the treatment of osteoporosis in postmenopausal women taking calcium and vitamin D.

This randomized, double-blind, placebo-controlled phase III study was conducted to assess the efficacy and safety of oral calcitonin (SMC021) for the treatment of postmenopausal osteoporosis. A total of 4665 postmenopausal women with osteoporosis were randomized 1:1 to receive calcium and vitamin D plus either SMC021 tablets (0.8mg/d) or placebo for 36months. The primary endpoint was the proportion of patients with a new vertebral fracture. The two groups were well balanced at baseline with regards to demographic and clinical data. No effect of SMC021 on preventing new vertebral fractures was observed, nor was any effect seen on new hip or non-vertebral fractures. Women receiving SMC021 had a mean 1.02% (±0.12%) increase in lumbar spine bone mineral density (BMD) compared with a mean 0.18% (±0.12%) increase in the placebo group by the end of the study (p<0.0001). Similarly, small increases in BMD were observed at the femoral neck and hip in both groups. Levels of the biomarkers of bone turnover, urinary CTX-I and CTX-II, were 15% lower in the SMC021 group than in the placebo arm at 12 and 24months, but not at 36months. No change in quality of life between groups, assessed by the Qualeffo-14 questionnaire, was observed in either group between baseline and month 36. Pharmacokinetics analysis confirmed exposure to SMC021, but the drug levels were markedly lower than expected. Approximately 92% of subjects in each treatment group experienced an adverse event (AE), the majority of which were mild or moderate in intensity. AEs associated with SMC021 were primarily of gastrointestinal origin and included nausea, vomiting and abdominal pain, as well as hot flushes which were the reason for the slightly higher drop-out rate in the active treatment arm compared to placebo. The number of severe AEs was low in both groups. Thirty-five deaths were reported but none were considered treatment-related. Due to the lack of efficacy in preventing fractures, the development of the orally formulated calcitonin was terminated despite the promising results in earlier studies.

Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice.

Vernalization, a period of low temperature to induce transition from vegetative to reproductive state, is an important environmental stimulus for many cool season grasses. A key gene in the vernalization pathway in grasses is the VRN1 gene. The objective of this study was to identify causative polymorphism(s) at the VRN1 locus in perennial ryegrass (Lolium perenne) for variation in vernalization requirement. Two allelic Bacterial Artificial Chromosome clones of the VRN1 locus from the two genotypes Veyo and Falster with contrasting vernalization requirements were identified, sequenced, and characterized. Analysis of the allelic sequences identified an 8.6-kb deletion in the first intron of the VRN1 gene in the Veyo genotype which has low vernalization requirement. This deletion was in a divergent recurrent selection experiment confirmed to be associated with genotypes with low vernalization requirement. The region surrounding the VRN1 locus in perennial ryegrass showed microcolinearity to the corresponding region on chromosome 3 in Oryza sativa with conserved gene order and orientation, while the micro-colinearity to the corresponding region in Triticum monococcum was less conserved. Our study indicates that the first intron of the VRN1 gene, and in particular the identified 8.6 kb region, is an important regulatory region for vernalization response in perennial ryegrass.

Vernalization response of Phleum pratense and its relationships to stem lignification and floral transition.

BACKGROUND: Timothy is a long-day grass species well adapted for cultivation in northern latitudes. It produces elongating tillers not only in spring growth but also later in summer. As the quantity and quality of harvested biomass is dictated by canopy architecture and the proportion of stem-forming flowering tillers, the regulation of flowering is of great interest in forage grass production. METHODS: Canopy architecture, stem morphology and freezing tolerance of vernalized timothy were investigated in greenhouse and field experiments. The molecular control of development was examined by analysing the relationship between apex development and expression of timothy homologues of the floral inducer VRN1 and repressor VRN2. KEY RESULTS: True stem formation and lignification of the sclerenchyma ring occur in both vernalized and regrowing stems irrespective of the developmental stage of the apex. The stems had, however, divergent morphology. Vernalization enhanced flowering, and the expression of the VRN1 homologue was elevated when the apex had passed into the reproductive stage. High VRN1 homologue expression was not associated with reduction in freezing tolerance and the expression coincided with increased levels of the floral repressor VRN2 homologue. Field experiments supported the observed linkage between the upregulation of the VRN1 homologue and the transition to the reproductive stage in vernalized tillers. The upregulation of putative VRN1 or VRN2 genes was restricted to vernalized tillers in the spring yield and, thus, not detected in non-vernalized tillers of the second yield; so-called regrowth. CONCLUSIONS: The formation of a lignified sclerenchyma ring that efficiently reduces the digestibility of the stem was not related to apex development but rather to a requirement for mechanical support. The observed good freezing tolerance of reproductive timothy tillers could be one important adaptation mechanism ensuring high yields in northern conditions. Both VRN1 and VRN2 homologues required a vernalization signal for expression so the development of yield-forming tillers in regrowth was regulated independently of the studied genes.

Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.).

BACKGROUND: OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover. RESULTS: Variation in genomic sequences coding for COMT, CCoAOMT1, and CCoAOMT2 was analyzed in relation to stover cell wall digestibility for a panel of 40 European forage maize inbred lines, and re-analyzed for a panel of 34 lines from a published French study. Different methodologies for association analysis were performed and compared. Across association methodologies, a total number of 25, 12, 1, 6 COMT polymorphic sites were significantly associated with DNDF, OMD, NDF, and WSC, respectively. Association analysis for CCoAOMT1 and CCoAOMT2 identified substantially fewer polymorphic sites (3 and 2, respectively) associated with the investigated traits. Our re-analysis on the 34 lines from a published French dataset identified 14 polymorphic sites significantly associated with cell wall digestibility, two of them were consistent with our study. Promising polymorphisms putatively causally associated with variability of cell wall digestibility were inferred from the total number of significantly associated SNPs/Indels. CONCLUSIONS: Several polymorphic sites for three O-methyltransferase loci were associated with stover cell wall digestibility. All three tested genes seem to be involved in controlling DNDF, in particular COMT. Thus, considerable variation among Bm3 wildtype alleles can be exploited for improving cell-wall digestibility. Target sites for functional markers were identified enabling development of efficient marker-based selection strategies.

High levels of linkage disequilibrium and associations with forage quality at a phenylalanine ammonia-lyase locus in European maize (Zea mays L.) inbreds.

Forage quality of maize is influenced by both the content and structure of lignin in the cell wall. Phenylalanine Ammonia-Lyase (PAL) catalyzes the first step in lignin biosynthesis in plants; the deamination of L-phenylalanine to cinnamic acid. Successive enzymatic steps lead to the formation of three monolignols, constituting the complex structure of lignin. We have cloned and sequenced a PAL genomic sequence from 32 maize inbred lines currently employed in forage maize breeding programs in Europe. Low nucleotide diversity and excessive linkage disequilibrium (LD) was identified at this PAL locus, possibly reflecting selective constrains resulting from PAL being the first enzyme in the monolignol, and other, pathways. While the association analysis was affected by extended LD and population structure, several individual polymorphisms were associated with neutral detergent fiber (not considering population structure) and a single polymorphism was associated with in vitro digestibility of organic matter (considering population structure).

Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.).

The timing of transition from vegetative growth to flowering is important in nature as well as in agriculture. One of several pathways influencing this transition in plants is the gibberellin (GA) pathway. In maize (Zea mays L.), the Dwarf8 (D8) gene has been identified as an orthologue of the gibberellic acid-insensitive (GAI) gene, a negative regulator of GA response in Arabidopsis. Nine intragenic polymorphisms in D8 have been linked with variation in flowering time of maize. We tested the general applicability of these polymorphisms as functional markers in an independent set of inbred lines. Single nucleotide primer extension (SNuPe) and gel-based indel markers were developed, and a set of 71 elite European inbred lines were phenotyped for flowering time and plant height across four environments. To control for population structure, we genotyped the plant material with 55 simple sequence repeat markers evenly distributed across the genome. When population structure was ignored, six of the nine D8 polymorphisms were significantly associated with flowering time and none with plant height. However, when population structure was taken into consideration, an association with flowering time was only detected in a single environment, whereas an association across environments was identified between a 2-bp indel in the promoter region and plant height. As the number of lines with different haplotypes within subpopulations was a limiting factor in the analysis, D8 alleles would need to be compared in isogenic backgrounds for a reliable estimation of allelic effects.

Functional markers in plants.

Different approaches (including association studies) have recently been adopted for the functional characterization of allelic variation in plants and to identify sequence motifs affecting phenotypic variation. We propose the term 'functional markers' for DNA markers derived from such functionally characterized sequence motifs. Functional markers are superior to random DNA markers such as RFLPs, SSRs and AFLPs owing to complete linkage with trait locus alleles. We outline the definition, development, application and prospects of functional markers.