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To clean or not to clean phenotypic datasets for outlier plants in genetic analyses?
No full textBased on case studies, we discuss the extent to which genome-wide association studies (GWAS) are affected by outlier plants, i.e. those deviating from the expected distribution on a multi-criteria basis. Using a raw dataset consisting of daily measurements of leaf area, biomass, and plant height for thousands of plants, we tested three different cleaning methods for their effects on genetic analyses. No-cleaning resulted in the highest number of dubious quantitative trait loci, especially at loci with highly unbalanced allelic frequencies. A trade-off was identified between the risk of false-positives (with no-cleaning and/or a low threshold for minor allele frequency) and the risk of missing interesting rare alleles. Cleaning can lower the risk of the latter by making it possible to choose a higher threshold in GWAS
Unraveling the effects of the gut microbiota composition and function on horse endurance physiology
No full textGradual responses of grapevine yield components and carbon status to nitrogen supply
No full textAim: Nitrogen is a major element conditioning grapevine growth, yield and aromatic profiles of berries and wines. Different tools can be used in order to detect differences in N status of the plant, including direct measurements of soil, plant nitrogen status (eg. petiole; must), or indirect observations of plant nutritional status such as leaf transmittance or reflectance (eg. SPAD; NDVI). However, the relationships between these indicators of nitrogen status and the overall plant functioning over vintages remain poorly known. The present study aimed at quantifying key vegetative and reproductive responses to plant nitrogen status over two successive seasons under different nitrogen supply levels.
Methods and results: Potted plants of Sauvignon Blanc grafted onto SO4 were grown outdoors in 2017 and 2018 with no water limitation. Four mineral nitrogen fertilization levels (equivalent to 0 kg of N ha-1 or 0U, 20U, 40U, 80U) and one organic nitrogen fertilization level (40U) were imposed in 2017. These treatments were doubled in 2018 to increase the degree of nitrogen supply and consequently, the range of observed effects on plant growth and yield. Plant nitrogen status (SPAD) was monitored weekly during both growing cycles. Yield components were determined over the two seasons. Lastly, plant carbon status was addressed through dynamic measurement of plant development and photosynthesis, and destructive measurement of dry matter accumulation and carbon storage in annual and perennial organs at flowering, veraison and harvest.
The SPAD values progressively decreased under lower N supply (0N) during the first year (from 31 to 16) and they were more than halved between the maximum and the minimum N treatments straight after budburst in year two (40 for 160N and 19 for 0N). Then, the differences in SPAD values among treatments were maintained up to harvest (2018). The gradient of N status resulted in a gradient of berry numbers per inflorescence (from 180 to 34 berries/inflorescence for 80N and 0N, respectively in 2018) and of individual berry dry matter at harvest (from 0.13 to 0.41 g for 160N and 0N, respectively in 2018). Quantitative relationships between N status and the relative reductions (% of reduction per %SPAD decrease) in terms of C gain (leaf area, photosynthesis), C growth (shoot, berry, trunk and root dry matter) and C storage (trunk and root) were fitted at flowering, veraison and harvest. The reduction in C gain under lower N supply was mainly related to the decrease in total leaf area before flowering (-1.64%). Although the photosynthesis rate tended to decrease under N deficiency over the season, it only poorly contributed to the reduction in C gain. The whole plant C growth was inhibited when N status decreased (-1.13% at harvest), due to the inhibition of shoot dry matter before veraison (-1.81%) and to a lower extent, to the lower dry matter in berries (-0.80%), trunks (-0.42%) and roots (-0.84%) at harvest. Part of the reduction in root dry matter was related to the lower starch reserves (-0.31%) at harvest. Interestingly, starch reserves tended to be higher under organic N supply than mineral N supply.
Conclusion: The present results provided a general framework of carbon gain and use over time (within and between seasons) as impacted by N supply levels and form. Such a framework will be useful when building a model of the pluri-annual dynamics of carbon balance related to yield elaboration in grapevines
The microvine, a model to study the effect of temperature on grapevine latent bud development and fruitfulness
No full textAim: The success of inflorescence primordia initiation and differentiation within latent buds (i.e. bud fruitfulness) is a critical issue for grapevine yield sustainability under climate change. The aim of the present study was to track the timing and rate of inflorescence development in latent buds along the cane and to quantify their responses to elevated day/night (D/N) temperatures.
Methods and Results: The experiments were conducted under controlled conditions, using the microvine model, which is suitable for establishment in small areas. Two imagery methods for analyzing bud anatomy were assessed: light microscopy and x-ray microtomography. Light microscopy was laborious, but it was the most accurate method for investigating organogenesis in the primordial shoot of the latent bud. In plants grown in a greenhouse (D/N, 25°C/15°C), the number of phytomer primordia in latent buds increased linearly from the apical to the basal buds on the cane. A maximum of six phytomers and two inflorescence primordia were observed beneath the 20th bud position that is, slightly fewer than usually reported with macrovines. The first and second inflorescences started to differentiate at the 14th and 18th bud position, respectively. Temperature increases in the growth chamber (D/N, 20–30°C/15–25°C) only slightly changed the final number of preformed phytomers and the probability of inflorescence primordia differentiation per bud. However, elevated temperature sharply accelerated and thereby shortened development of the latent bud primordial shoot, resulting in differentiation of the first inflorescence primordia straight from the fifth bud position. Based on the spatiotemporal conversion of bud position into thermal time, the first inflorescence started to differentiate 332 growing degree days (°Cd) (or 41 days) after bud emergence at D/N 20°C/15°C, and only 98°Cd (or 5 days) after bud emergence at D/N 35°C/25°C. Finally, the number of preformed phytomers was shown to correlate with primary bud length and cane diameter, independent of temperature. These easily measured variables may be used as indicators of bud developmental stage and potential bud fruitfulness in further studies using the microvine.
Conclusions: The microvine appears to be suitable for parameterizing a developmental model of grapevine latent buds under controlled environmental conditions and when evaluating the response to elevated D/N temperatures.
Significance and impact of the study: The precise description of the timing and rate of differentiation of phytomers and inflorescences opens new perspectives for understanding the molecular processes underlying the response of bud fruitfulness to environmental constraints
Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies
No full textBackground: Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays).
Results: The effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution).
Conclusions : Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions
Environmentally mediated reproductive success predicts breeding dispersal decisions in an early successional amphibian
No full textDispersal is a central mechanism in ecology and evolution. Dispersal evolution is driven by a trade-off between costs and benefits, which is influenced by interindividual variability and local environmental conditions (context-dependent dispersal). Many studies have investigated how dispersal decisions may be influenced by environmental factors, including density, predation and interspecific competition. Yet few have attempted to examine how habitat disturbance may affect the dispersal process in spatially structured populations. In early successional species, one might expect individuals to adjust their dispersal decisions based on two main factors that potentially have an influence on reproductive success: patch size and the level of patch disturbance. In this study, we examined how these two factors affect breeding success and dispersal decisions in an early successional amphibian, the yellow-bellied toad, Bombina variegata. To this end, we used capture-recapture data collected on a spatially structured population occupying 28 breeding patches. We took advantage of recent developments in multievent capture-recapture models to detect signs of context-dependent dispersal. The results revealed that the probability of successful reproduction and the number of newly metamorphosed individuals increased with both the size and the proportion of disturbance of a patch. In addition, our results showed that the factors affecting breeding success also influenced breeding dispersal probability. Large patch size negatively influenced emigration probability; in contrast, it positively influenced immigration probability. Equally, higher disturbance had a strong negative influence on emigration probability and slightly positively affected immigration probability. These findings strongly suggest that individuals make context-dependent dispersal decisions, adjusted to maximize future fitness prospects in a patch, allowing them to better cope with rapid changes in environmental conditions resulting from the ecological succession process. This opens new areas of potential research into the role of dispersal in organism specialization along an ecological succession gradient
Excessive assimilation of ammonium by plastidic glutamine synthetase is a major cause of ammonium toxicity in Arabidopsis thaliana
No full textPlants use nitrate and ammonium in the soil as their main nitrogen sources. Recently, ammonium has attracted attention due to evidence suggesting that, in C3 species, an elevated CO2 environment inhibits nitrate assimilation. However, high concentrations of ammonium as the sole nitrogen source for plants causes impaired growth, i.e. ammonium toxicity. Although ammonium toxicity has been studied for a long time, the primary cause remains to be elucidated. Here, we show that ammonium assimilation in plastids rather than ammonium accumulation is a primary cause for toxicity. Our genetic screen of ammonium-tolerant Arabidopsis lines with enhanced shoot growth identified plastidic GLUTAMINE SYNTHETASE 2 (GLN2) as the causal gene. Our reciprocal grafting of wild-type and GLN2 or GLN1;2-deficient lines suggested that shoot GLN2 activity results
34 in ammonium toxicity, whilst root GLN1;2 activity prevents it. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress responsive genes. Application of an alkaline ammonia solution to the toxic ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress in the shoot. This fundamental insight provides a framework for enhanced understanding of ammonium toxicity in plants
Biomarkers and algorithms for diagnosis of ovarian cancer: CA125, HE4, RMI and ROMA, a review.
No full textOvarian cancer is the 5th leading cause of death for women with cancer worldwide. In more than 70% of cases, it is only diagnosed at an advanced stage. Our study aims to give an update on the biological markers for diagnosing ovarian cancer, specifically HE4, CA 125, RMI and ROMA algorithms.Serum CA125 assay has low sensitivity in the early stages and can be increased in certain conditions such as menstruation or endometriosis. The level of HE4 is overexpressed in ovarian tumors. Its specificity is 94% and its level is not affected by endometriosis cysts. The combined measures of CA125 and HE4 have proved to be highly efficient with an area under the curve (AUC) of up to 0.96. Furthermore, this combined measure of CA125 can correct the variations in HE4 which are due to smoking or contraception combining estrogen plus progestin. While the specificity of RMI sometimes reaches 92%, the rather low AUC of 0.86 does not make it the best diagnostic tool. The specificity of ROMA is lower than HE4 (84% compared to 94%).To date, the most efficient biological diagnostic tool to diagnose ovarian cancer is the combination of CA125 and HE4
Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude
No full textIn plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Variation of these traits with elevation defines a syndrome of adaptation to altitude with plants that flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains with increasing elevation. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding