Diversity matters in wheat mixtures: A genomic survey of the impact of genetic diversity on the performance of 12 way durum wheat mixtures grown in two contrasted and controlled environments.

In ecology, an increase in genetic diversity within a community in natural ecosystems increases its productivity, while in evolutionary biology, kinship selection predicts that relatedness on social traits improves fitness. Varietal mixtures, where different genotypes are grown together, show contrasting results, especially for grain yield where both positive and negative effects of mixtures have been reported. To understand the effect of diversity on field performance, we grew 96 independent mixtures each composed with 12 durum wheat (Triticum turgidum ssp. durum Thell.) inbred lines, under two contrasting environmental conditions for water availability. Using dense genotyping, we imputed allelic frequencies and a genetic diversity index on more than 96000 loci for each mixture. We then analyzed the effect of genetic diversity on agronomic performance using a genome-wide approach. We explored the stress gradient hypothesis, which proposes that the greater the unfavourable conditions, the more beneficial the effect of diversity on mixture performance. We found that diversity on average had a negative effect on yield and its components while it was beneficial on grain weight. There was little support for the stress gradient theory. We discuss how to use genomic data to improve the assembly of varietal mixtures.

Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits.

Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios.

Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection.

Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.

Wheat individual grain-size variance originates from crop development and from specific genetic determinism.

Wheat grain yield is usually decomposed in the yield components: number of spikes / m2, number of grains / spike, number of grains / m2 and thousand kernel weight (TKW). These are correlated one with another due to yield component compensation. Under optimal conditions, the number of grains per m2 has been identified as the main determinant of yield. However, with increasing occurrences of post-flowering abiotic stress associated with climate change, TKW may become severely limiting and hence a target for breeding. TKW is usually studied at the plot scale as it represents the average mass of a grain. However, this view disregards the large intra-genotypic variance of individual grain mass and its effect on TKW. The aim of this study is to investigate the determinism of the variance of individual grain size. We measured yield components and individual grain size variances of two large genetic wheat panels grown in two environments. We also carried out a genome-wide association study using a dense SNPs array. We show that the variance of individual grain size partly originates from the pre-flowering components of grain yield; in particular it is driven by canopy structure via its negative correlation with the number of spikes per m2. But the variance of final grain size also has a specific genetic basis. The genome-wide analysis revealed the existence of QTL with strong effects on the variance of individual grain size, independently from the other yield components. Finally, our results reveal some interesting drivers for manipulating individual grain size variance either through canopy structure or through specific chromosomal regions.

Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.).

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat.

VERNALIZATION1 controls developmental responses of winter wheat under high ambient temperatures.

Low temperatures are required to regulate the transition from vegetative to reproductive growth via a pathway called vernalization. In wheat, vernalization predominantly involves the cold upregulation of the floral activator VERNALIZATION1 (VRN1). Here, we have used an extreme vernalization response, identified through studying ambient temperature responses, to reveal the complexity of temperature inputs into VRN-A1, with allelic inter-copy variation at a gene expansion of VRN-A1 modulating these effects. We find that the repressors of the reproductive transition, VERNALIZATION2 (VRN2) and ODDSOC2, are re-activated when plants experience high temperatures during and after vernalization. In addition, this re-activation is regulated by photoperiod for VRN2 but was independent of photoperiod for ODDSOC2 We also find this warm temperature interruption affects flowering time and floret number and is stage specific. This research highlights the important balance between floral activators and repressors in coordinating the response of a plant to temperature, and that the absence of warmth is essential for the completion of vernalization. This knowledge can be used to develop agricultural germplasm with more predictable vernalization responses that will be more resilient to variable growth temperatures.

Different grain-filling rates explain grain-weight differences along the wheat ear.

Thousand grain weight is one of the components determining wheat grain yield. It represents the average value of individual grain weights which depends on position within the ear and on positon within the spikelet. Our objective was to quantify the influences of individual floret anthesis date, of carpel weight at anthesis and of rate and duration of grain filling, on variation in individual final grain weight. Two bread wheat cultivars were grown in a greenhouse and their ears were sampled from anthesis through to harvest. Each ear was divided into three parts-basal, central and apical-where the two proximal grains were dissected from each of two spikelets. We analysed (i) the flowering time shift within the ear and within the spikelet; and (ii) the growth kinetics during grain filling in relation to position along the ear. For both cultivars, florets located in the central part of the ear were the first to reach anthesis followed by those in the apical part and then the basal part. Within a spikelet, the floret located nearest the rachis flowered first followed by the more distal ones. We found no significant systematic effect of flowering time-shift on final grain weight. Nevertheless, grains in the central part were heavier than the basal ones (9.75% smaller) and than the apical ones (18.25% smaller). These differences were explained mainly by differences in mean grain filling rates. Analysis of growth kinetics enabled an improved explanation of the variability of individual grain weight along the ear.

Effects of ambient temperature in association with photoperiod on phenology and on the expressions of major plant developmental genes in wheat (Triticum aestivum L.).

In addition to its role in vernalization, temperature is an important environmental stimulus in determining plant growth and development. We used factorial combinations of two photoperiods (16H, 12H) and three temperature levels (11, 18 and 25 °C) to study the temperature responses of 19 wheat cultivars with established genetic relationships. Temperature produced more significant effects on plant development than photoperiod, with strong genotypic components. Wheat genotypes with PPD-D1 photoperiod sensitive allele were sensitive to temperature; their development was delayed by higher temperature, which intensified under non-inductive conditions. The effect of temperature on plant development was not proportional; it influenced the stem elongation to the largest extent, and warmer temperature lengthened the lag phase between the detection of first node and the beginning of intensive stem elongation. The gene expression patterns of VRN1, VRN2 and PPD1 were also significantly modified by temperature, while VRN3 was more chronologically regulated. The associations between VRN1 and VRN3 gene expression with early apex development were significant in all treatments but were only significant for later plant developmental phases under optimal conditions (16H and 18 °C). Under 16H, the magnitude of the transient peak expression of VRN2 observed at 18 and 25 °C associated with the later developmental phases.

Bread Wheat (Triticum aestivum L.) Grain Protein Concentration Is Related to Early Post-Flowering Nitrate Uptake under Putative Control of Plant Satiety Level.

The strong negative correlation between grain protein concentration (GPC) and grain yield (GY) in bread wheat complicates the simultaneous improvement of these traits. However, earlier studies have concluded that the deviation from this relationship (grain protein deviation or GPD) has strong genetic basis. Genotypes with positive GPD have an increased ability to uptake nitrogen (N) during the post-flowering period independently of the amount of N taken up before flowering, suggesting that genetic variability for N satiety could enable the breakage of the negative relationship. This study is based on two genotypes markedly contrasted for GPD grown under semi-hydroponic conditions differentiated for nitrate availability both before and after flowering. This allows exploration of the genetic determinants of post-flowering N uptake (PANU) by combining whole plant sampling and targeted gene expression approaches. The results highlights the correlation (r² = 0.81) with GPC of PANU occurring early during grain development (flowering-flowering + 250 degree-days) independently of GY. Early PANU was in turn correlated (r² = 0.80) to the stem-biomass increment after flowering through its effect on N sink activity. Differences in early PANU between genotypes, despite comparable N statuses at flowering, suggest that genetic differences in N satiety could be involved in the establishment of the GPC. Through its strong negative correlation with genes implied in N assimilation, root nitrate concentration appears to be a good marker for evaluating instantaneous plant N demand, and may provide valuable information on the genotypic N satiety level. This trait may help breeders to identify genotypes having high GPC independently of their GY.

Post-flowering nitrate uptake in wheat is controlled by N status at flowering, with a putative major role of root nitrate transporter NRT2.1.

In bread wheat (Triticum aestivum L.), the simultaneous improvement of both yield and grain protein is difficult because of the strong negative relationship between these two traits. However, some genotypes deviate positively from this relationship and this has been linked to their ability to take up nitrogen (N) during the post-flowering period, regardless of their N status at flowering. The physiological and genetic determinants of post-flowering N uptake relating to N satiety are poorly understood. This study uses semi-hydroponic culture of cv. Récital under controlled conditions to explore these controls. The first objective was to record the effects of contrasting N status at flowering on post-flowering nitrate (NO3⁻) uptake under non-limiting NO3⁻ conditions, while following the expression of key genes involved in NO3⁻ uptake and assimilation. We found that post-flowering NO3⁻ uptake was strongly influenced by plant N status at flowering during the first 300-400 degree-days after flowering, overlapping with a probable regulation of nitrate uptake exerted by N demand for growth. The uptake of NO3⁻ correlated well with the expression of the gene TaNRT2.1, coding for a root NO3⁻ transporter, which seems to play a major role in post-flowering NO3⁻ uptake. These results provide a useful knowledge base for future investigation of genetic variability in post-flowering N uptake and may lead to concomitant gains in both grain yield and grain protein in wheat.

Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model.

Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.

Acclimation of leaf nitrogen to vertical light gradient at anthesis in wheat is a whole-plant process that scales with the size of the canopy.

Vertical leaf nitrogen (N) gradient within a canopy is classically considered as a key adaptation to the local light environment that would tend to maximize canopy photosynthesis. We studied the vertical leaf N gradient with respect to the light gradient for wheat (Triticum aestivum) canopies with the aims of quantifying its modulation by crop N status and genetic variability and analyzing its ecophysiological determinants. The vertical distribution of leaf N and light was analyzed at anthesis for 16 cultivars grown in the field in two consecutive seasons under two levels of N. The N extinction coefficient with respect to light (b) varied with N supply and cultivar. Interestingly, a scaling relationship was observed between b and the size of the canopy for all the cultivars in the different environmental conditions. The scaling coefficient of the b-green area index relationship differed among cultivars, suggesting that cultivars could be more or less adapted to low-productivity environments. We conclude that the acclimation of the leaf N gradient to the light gradient is a whole-plant process that depends on canopy size. This study demonstrates that modeling leaf N distribution and canopy expansion based on the assumption that leaf N distribution parallels that of the light is inappropriate. We provide a robust relationship accounting for vertical leaf N gradient with respect to vertical light gradient as a function of canopy size.

The quantitative response of wheat vernalization to environmental variables indicates that vernalization is not a response to cold temperature.

The initiation of flowering is a crucial trait that allows temperate plants to flower in the favourable conditions of spring. The timing of flowering initiation is governed by two main mechanisms: vernalization that defines a plant's requirement for a prolonged exposure to cold temperatures; and photoperiod sensitivity defining the need for long days to initiate floral transition. Genetic variability in both vernalization and photoperiod sensitivity largely explains the adaptability of cultivated crop plants such as bread wheat (Triticum aestivum L.) to a wide range of climatic conditions. The major genes controlling wheat vernalization (VRN1, VRN2, and VRN3) and photoperiod sensitivity (PPD1) have been identified, and knowledge of their interactions at the molecular level is growing. However, the quantitative effects of temperature and photoperiod on these genes remain poorly understood. Here it is shown that the distinction between the temperature effects on organ appearance rate and on vernalization sensu stricto is crucial for understanding the quantitative effects of the environmental signal on wheat flowering. By submitting near isogenic lines of wheat differing in their allelic composition at the VRN1 locus to various temperature and photoperiod treatments, it is shown that, at the whole-plant level, the vernalization process has a positive response to temperature with complex interactions with photoperiod. In addition, the phenotypic variation associated with the presence of different spring homoeoalleles of VRN1 is not induced by a residual vernalization requirement. The results demonstrate that a precise definition of vernalization is necessary to understand and model temperature and photoperiod effects on wheat flowering. It is suggested that this definition should be used as the basis for gene expression studies and assessment of functioning of the wheat flowering gene network, including an explicit account of the quantitative effect of environmental variables.

Anthesis date mainly explained correlations between post-anthesis leaf senescence, grain yield, and grain protein concentration in a winter wheat population segregating for flowering time QTLs.

The genetic variability of the duration of leaf senescence during grain filling has been shown to affect both carbon and nitrogen acquisition. In particular, maintaining green leaves during grain filling possibly leads to increased grain yield, but its associated effect on grain protein concentration has not been studied. The aim of this study was to dissect the genetic factors contributing to correlations observed at the phenotypic level between leaf senescence during grain filling, grain protein concentration, and grain yield in winter wheat. With this aim in view, an analysis of quantitative trait locus (QTL) co-locations for these traits was carried out on a doubled haploid mapping population grown in a large multienvironment trial network. Pleiotropic QTLs affecting leaf senescence and grain yield and/or grain protein concentration were identified on chromosomes 2D, 2A, and 7D. These were associated with QTLs for anthesis date, showing that the phenotypic correlations with leaf senescence were mainly explained by flowering time in this wheat population. Study of the allelic effects of these pleiotropic QTLs showed that delaying leaf senescence was associated with increased grain yield or grain protein concentration depending on the environments considered. It is proposed that this differential effect of delaying leaf senescence on grain yield and grain protein concentration might be related to the nitrogen availability during the post-anthesis period. It is concluded that the benefit of using leaf senescence as a selection criterion to improve grain protein concentration in wheat cultivars may be limited and would largely depend on the targeted environments, particularly on their nitrogen availability during the post-anthesis period.

Deviation from the grain protein concentration-grain yield negative relationship is highly correlated to post-anthesis N uptake in winter wheat.

In plants, carbon and nitrogen (N) economies are intimately linked at the physiological and biochemical level. The strong genetic negative correlation between grain yield and grain protein concentration observed in various cereals is an illustration of this inter-relationship. Studies have shown that deviation from this negative relationship (grain protein deviation or GPD) has a genetic basis, but its physiological basis is still poorly understood. This study analysed data on 27 genotypes grown in multienvironment field trials, representing a wide range of agricultural practices and climatic conditions. The objective was to identify physiological processes related to the genetic variability in GPD. Under most environments, GPD was significantly related to post-anthesis N uptake independently of anthesis date and total N at anthesis. The underlying physiological trait might be related to genotypic differences in either access to soil N, regulation of N uptake by plant N status, or ability to maintain root activity during the grain-filling period. GPD is an interesting potential target in breeding as it appears to be relatively robust across different environments and would be valuable in increasing total N uptake by maturity.