Catherine Giauffret

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds ( Zea mays L.)

Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix–best linear unbiased predictions model (RA–BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request.

The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L

An understanding of the genetic determinism of frost tolerance is a prerequisite for the development of frost tolerant cultivars for cold northern areas. In legumes, it is not known to which extent vernalization requirement or photoperiod responsiveness are necessary for the development of frost tolerance. In pea (Pisum sativum L.) however, the flowering locus Hr is suspected to influence winter frost tolerance by delaying floral initiation until after the main winter freezing periods have passed. The objective of this study was to dissect the genetic determinism of frost tolerance in pea by QTL analysis and to assess the genetic linkage between winter frost tolerance and the Hr locus. A population of 164 recombinant inbred lines (RILs), derived from the cross Champagne x Terese was evaluated both in the greenhouse and in field conditions to characterize the photoperiod response from which the allele at the Hr locus was inferred. In addition, the population was also assessed for winter frost tolerance in 11 field conditions. Six QTL were detected, among which three were consistent among the different experimental conditions, confirming an oligogenic determinism of frost tolerance in pea. The Hr locus was found to be the peak marker for the highest explanatory QTL of this study. This result supports the hypothesis of the prominent part played by the photoperiod responsiveness in the determinism of frost tolerance for this species. The consistency of three QTL makes these positions interesting targets for marker-assisted selection.

Fine Mapping and Haplotype Structure Analysis of a Major Flowering Time Quantitative Trait Locus on Maize Chromosome 10

Flowering time is a major adaptive trait in plants and an important selection criterion for crop species. In maize, however, little is known about its molecular basis. In this study, we report the fine mapping and characterization of a major quantitative trait locus located on maize chromosome 10, which regulates flowering time through photoperiod sensitivity. This study was performed in near-isogenic material derived from a cross between the day-neutral European flint inbred line FV286 and the tropical short-day inbred line FV331. Recombinant individuals were identified among a large segregating population and their progenies were scored for flowering time. Combined genotypic characterization led to delimit the QTL to an interval of 170 kb and highlighted an unbalanced recombination pattern. Two bacterial artificial chromosomes (BACs) covering the region were analyzed to identify putative candidate genes, and synteny with rice, sorghum, and brachypodium was investigated. A gene encoding a CCT domain protein homologous to the rice Ghd7 heading date regulator was identified, but its causative role was not demonstrated and deserves further analyses. Finally, an association study showed a strong level of linkage disequilibrium over the region and highlighted haplotypes that could provide useful information for the exploitation of genetic resources and marker-assisted selection in maize.

Relative contributions of light interception and radiation use efficiency to the reduction of maize productivity under cold temperatures

Maize (Zea mays L.) is a chill-susceptible crop cultivated in northern latitude environments. The detrimental effects of cold on growth and photosynthetic activity have long been established. However, a general overview of how important these processes are with respect to the reduction of productivity reported in the field is still lacking. In this study, a model-assisted approach was used to dissect variations in productivity under suboptimal temperatures and quantify the relative contributions of light interception (PARc) and radiation use efficiency (RUE) from emergence to flowering. A combination of architectural and light transfer models was used to calculate light interception in three field experiments with two cold-tolerant lines and at two sowing dates. Model assessment confirmed that the approach was suitable to infer light interception. Biomass production was strongly affected by early sowings. RUE was identified as the main cause of biomass reduction during cold events. Furthermore, PARc explained most of the variability observed at flowering, its relative contributions being more or less important according to the climate experienced. Cold temperatures resulted in lower PARc, mainly because final leaf length and width were significantly reduced for all leaves emerging after the first cold occurrence. These results confirm that virtual plants can be useful as fine phenotyping tools. A scheme of action of cold on leaf expansion, light interception and radiation use efficiency is discussed with a view towards helping breeders define relevant selection criteria.

Fortune telling: metabolic markers of plant performance

Background In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC–MS, LC–MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory evaluation and crop yield have been obtained.Aim of review(i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding.Key messageUsing examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance.

Association mapping for cold tolerance in two large maize inbred panels.

BackgroundBreeding for cold tolerance in maize promises to allow increasing growth area and production in temperate zones. The objective of this research was to conduct genome-wide association analyses (GWAS) in temperate maize inbred lines and to find strategies for pyramiding genes for cold tolerance. Two panels of 306 dent and 292 European flint maize inbred lines were evaluated per se and in testcrosses under cold and control conditions in a growth chamber. We recorded indirect measures for cold tolerance as the traits number of days from sowing to emergence, relative leaf chlorophyll content or quantum efficiency of photosystem II. Association mapping for identifying genes associated to cold tolerance in both panels was based on genotyping with 49,585 genome-wide single nucleotide polymorphism (SNP) markers.ResultsWe found 275 significant associations, most of them in the inbreds evaluated per se, in the flint panel, and under control conditions. A few candidate genes coincided between the current research and previous reports. A total of 47 flint inbreds harbored the favorable alleles for six significant quantitative trait loci (QTL) detected for inbreds per se evaluated under cold conditions, four of them had also the favorable alleles for the main QTL detected from the testcrosses. Only four dent inbreds (EZ47, F924, NK807 and PHJ40) harbored the favorable alleles for three main QTL detected from the evaluation of the dent inbreds per se under cold conditions. There were more QTL in the flint panel and most of the QTL were associated with days to emergence and ΦPSII.ConclusionsThese results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection.

The thermoluminescence 'afterglow' band as a sensitive indicator of abiotic stresses in plants

Single turn-over xenon flashes induce a thermoluminescence (TL) B-band centred near 35 °C. The far-red illumination of leaves at non-freezing temperatures induces a band peaking at around 45 °C (afterglow or AG-band), together with a downshifted B-band peaking between 15 °C and 28 °C. In control, unfrozen wheat plants, the Tmax of the B-band induced after 30 s far-red light at 0 °C was approx. 15-18 °C. In maize plants grown under the same conditions, this far-red-induced downshift was not so strong, since the B-band peaked at 28 - 30 °C. Both a decline in the AG-band and a reversal of the downshift of the B-band were observed after short-term freezing in several plant species. There was usually a sudden drop in the AG-band below a critical freezing temperature. However, while in wheat plants a weak TL emission could be seen between 40-50 °C in frozen samples, in cold-sensitive maize plants this was completely suppressed and only the B-band could be detected. In cold-hardened wheat plants the temperature at which the AG-band was suppressed was lower than in non-hardened plants. Drought and short-term heat stress also affect the AG-band. As the AG-band was found to be more sensitive to several types of stresses than the B-band, it can be used as a sensitive stress indicator. However, the behaviour of the AG-band depends on several factors (for example the age of the leaf, etc.), which must be controlled if different species or varieties are to be compared

A size‐mediated effect can compensate for transient chilling stress affecting maize (Zea mays) leaf extension

*In this study, we examined the impact of transient chilling in maize (Zea mays). We investigated the respective roles of the direct effects of stressing temperatures and indirect whorl size-mediated effects on the growth of leaves chilled at various stages of development. *Cell production, individual leaf extension and final leaf size of plants grown in a glasshouse under three temperature regimes (a control and two short chilling transfers) were studied using two genotypes contrasting in terms of their architecture. *The kinetics of all the leaves emerging after the stress were affected, but not all final leaf lengths were affected. No size-mediated propagation of an initial growth reduction was observed, but a size-mediated effect was associated with a longer duration of leaf elongation which compensated for reduced leaf elongation rates when leaves were stressed during their early growth. Both cell division and cell expansion contributed to explaining cold-induced responses at the leaf level. *These results demonstrate that leaf elongation kinetics and final leaf length are under the control of processes at the n - 1 (cell proliferation and expansion) and n + 1 (whorl size signal) scales. Both levels may respond to chilling stress with different time lags, making it possible to buffer short-term responses.

The use of MapPop1.0 for choosing a QTL mapping sample from an advanced backcross population

QTL detection is a good way to assess the genetic basis of quantitative traits such as the plant response to its environment, but requires large mapping populations. Experimental constraints, however, may require a restriction of the population size, risking a decrease in the quality level of QTL mapping. The purpose of this paper was to test if an advanced backcross population sample chosen by MapPop 1.0 could limit the effect of size restriction and improve the QTL detection when compared to random samples. We used the genotypic and phenotypic data obtained for 280 genotypes, considered as the reference population. The “MapPop sample” of 100 genotypes was first compared to the reference population, and genetic maps, genotypic and phenotypic data and QTL results were analysed. Despite the increase in donor allele frequency in the MapPop sample, this did not lead to an increase of the genetic map length or a biased phenotypic distribution. Three QTL among the 10 QTL found in the reference population were also detected in the MapPop sample. Next, the MapPop sample results were compared to those from 500 random samples of the same size. The main conclusion was that the MapPop software avoided the selection of biased samples and the detection of false QTL and appears particularly interesting to select a sample from an unbalanced population.

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding

IntroductionIn Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context.ObjectivesUsing an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass.MethodsThirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping.ResultsNMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance.ConclusionAfter validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.