Genetic regions determine tolerance to nitrogen deficiency in European elite bread wheats grown under contrasting nitrogen stress scenarios.

KEY MESSAGE: Clustering 24 environments in four contrasting nitrogen stress scenarios enabled the detection of genetic regions determining tolerance to nitrogen deficiency in European elite bread wheats. Increasing the nitrogen use efficiency of wheat varieties is an important goal for breeding. However, most genetic studies of wheat grown at different nitrogen levels in the field report significant interactions with the genotype. The chromosomal regions possibly involved in these interactions are largely unknown. The objective of this study was to quantify the response of elite bread wheat cultivars to different nitrogen field stress scenarios and identify genomic regions involved in this response. For this purpose, 212 elite bread wheat varieties were grown in a multi-environment trial at different nitrogen levels. Genomic regions associated with grain yield, protein concentration and grain protein deviation responses to nitrogen deficiency were identified. Environments were clustered according to adjusted means for grain yield, yield components and grain protein concentration. Four nitrogen availability scenarios were identified: optimal condition, moderate early deficiency, severe late deficiency, and severe continuous deficiency. A large range of tolerance to nitrogen deficiency was observed among varieties, which were ranked differently in different nitrogen deficiency scenarios. The well-known negative correlation between grain yield and grain protein concentration also existed between their respective tolerance indices. Interestingly, the tolerance indices for grain yield and grain protein deviation were either null or weakly positive meaning that breeding for the two traits should be less difficult than expected. Twenty-two QTL regions were identified for the tolerance indices. By selecting associated markers, these regions may be selected separately or combined to improve the tolerance to N deficiency within a breeding programme.

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.

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection.

There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker-trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.

Identification of QTLs affecting post-anthesis heat stress responses in European bread wheat.

KEY MESSAGE: The response of a large panel of European elite wheat varieties to post-anthesis heat stress is influenced by 17 QTL linked to grain weight or the stay-green phenotype. Heat stress is a critical abiotic stress for winter bread wheat (Triticum aestivum L.) especially at the flowering and grain filling stages, limiting its growth and productivity in Europe and elsewhere. The breeding of new high-yield and stress-tolerant wheat varieties requires improved understanding of the physiological and genetic bases of heat tolerance. To identify genomic areas associated with plant and grain characteristics under heat stress, a panel of elite European wheat varieties (N = 199) was evaluated under controlled conditions in 2016 and 2017. A split-plot design was used to test the effects of high temperature for ten days after flowering. Flowering time, leaf chlorophyll content, the number of productive spikes, grain number, grain weight and grain size were measured, and the senescence process was modeled. Using genotyping data from a 280 K SNP chip, a genome-wide association study was carried out to test the main effect of each SNP and the effect of SNP × treatment interaction. Genotype × treatment interactions were mainly observed for grain traits measured on the main shoots and tillers. We identified 10 QTLs associated with the main effect of at least one trait and seven QTLs associated with the response to post-anthesis heat stress. Of these, two main QTLs associated with the heat tolerance of thousand-kernel weight were identified on chromosomes 4B and 6B. These QTLs will be useful for breeders to improve grain yield in environments where terminal heat stress is likely to occur.

Using environmental clustering to identify specific drought tolerance QTLs in bread wheat (T. aestivum L.).

KEY MESSAGE: Environmental clustering helps to identify QTLs associated with grain yield in different water stress scenarios. These QTLs could be useful for breeders to improve grain yields and increase genetic resilience in marginal environments. Drought is one of the main abiotic stresses limiting winter bread wheat growth and productivity around the world. The acquisition of new high-yielding and stress-tolerant varieties is therefore necessary and requires improved understanding of the physiological and genetic bases of drought resistance. A panel of 210 elite European varieties was evaluated in 35 field trials. Grain yield and its components were scored in each trial. A crop model was then run with detailed climatic data and soil water status to assess the dynamics of water stress in each environment. Varieties were registered from 1992 to 2011, allowing us to test timewise genetic progress. Finally, a genome-wide association study (GWAS) was carried out using genotyping data from a 280 K SNP chip. The crop model simulation allowed us to group the environments into four water stress scenarios: an optimal condition with no water stress, a post-anthesis water stress, a moderate-anthesis water stress and a high pre-anthesis water stress. Compared to the optimal water condition, grain yield losses in the stressed conditions were 3.3%, 12.4% and 31.2%, respectively. This environmental clustering improved understanding of the effect of drought on grain yields and explained 20% of the G × E interaction. The greatest genetic progress was obtained in the optimal condition, mostly represented in France. The GWAS identified several QTLs, some of which were specific of the different water stress patterns. Our results make breeding for improved drought resistance to specific environmental scenarios easier and will facilitate genetic progress in future environments, i.e., water stress environments.

A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.).

KEY MESSAGE: This study identified 333 genomic regions associated to 28 traits related to nitrogen use efficiency in European winter wheat using genome-wide association in a 214-varieties panel experimented in eight environments. Improving nitrogen use efficiency is a key factor to sustainably ensure global production increase. However, while high-throughput screening methods remain at a developmental stage, genetic progress may be mainly driven by marker-assisted selection. The objective of this study was to identify chromosomal regions associated with nitrogen use efficiency-related traits in bread wheat (Triticum aestivum L.) using a genome-wide association approach. Two hundred and fourteen European elite varieties were characterised for 28 traits related to nitrogen use efficiency in eight environments in which two different nitrogen fertilisation levels were tested. The genome-wide association study was carried out using 23,603 SNP with a mixed model for taking into account parentage relationships among varieties. We identified 1,010 significantly associated SNP which defined 333 chromosomal regions associated with at least one trait and found colocalisations for 39 % of these chromosomal regions. A method based on linkage disequilibrium to define the associated region was suggested and discussed with reference to false positive rate. Through a network approach, colocalisations were analysed and highlighted the impact of genomic regions controlling nitrogen status at flowering, precocity, and nitrogen utilisation on global agronomic performance. We were able to explain 40 ± 10 % of the total genetic variation. Numerous colocalisations with previously published genomic regions were observed with such candidate genes as Ppd-D1, Rht-D1, NADH-Gogat, and GSe. We highlighted selection pressure on yield and nitrogen utilisation discussing allele frequencies in associated regions.

A multi-environmental study of recent breeding progress on nitrogen use efficiency in wheat (Triticum aestivum L.).

KEY MESSAGE: By comparing 195 varieties in eight trials, this study assesses nitrogen use efficiency improvement in high and low nitrogen conditions in European winter wheat over the last 25 years. In a context where European agriculture practices have to deal with environmental concerns and nitrogen (N) fertiliser cost, nitrogen use efficiency (NUE) has to be improved. This study assessed genetic progress in winter wheat (Triticum aestivum L.) NUE. Two hundred and twenty-five European elite varieties were tested in four environments under two levels of N. Global genetic progress was assessed on additive genetic values and on genotype × N interaction, covering 25 years of European breeding. To avoid sampling bias, quality, precocity and plant height were added as covariates in the analyses when needed. Genotype × environment interactions were highly significant for all the traits studied to such an extent that no additive genetic effect was detected on N uptake. Genotype × N interactions were significant for yield, grain protein content (GPC), N concentration in straw, N utilisation, and NUE. Grain yield improvement (+0.45 % year(-1)) was independent of the N treatment. GPC was stable, thus grain nitrogen yield was improved (+0.39 % year(-1)). Genetic progress on N harvest index (+0.12 % year(-1)) and on N concentration in straw (-0.52 % year(-1)) possibly revealed improvement in N remobilisation. There has been an improvement of NUE additive genetic value (+0.33 % year(-1)) linked to better N utilisation (+0.20 % year(-1)). Improved yield stability was detected as a significant improvement of NUE in low compared to high N conditions. The application of these results to breeding programs is discussed.

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

Dominant-negative activity of a Brca1 truncation mutant: effects on proliferation, tumorigenicity in vivo, and chemosensitivity in a mouse ovarian cancer cell line.

In order to generate an in vitro mouse model for the study of human ovarian cancers, we compared the effects of a truncated Brca1 mutant expression on cellular phenotype with those of a full-length sense and antisense Brca1 expression in the ID-8 mouse epithelial ovarian cancer cell line. The examined cellular processes include proliferation, tumorigenicity in syngeneic mice in vivo and sensitivity/resistance to several cytotoxic drugs. We found that the expression of a spontaneous truncated Brca1 mutant in ID-8 cells which contain two endogenous wild-type Brca1 alleles led to a dominant-negative effect of Brca1, demonstrated by an increase in tumorigenicity in vivo and in chemosensitivity. Expression of a truncated Brca1 mutant in a mouse epithelial ovarian cancer cell line could thus provide a powerful in vitro model for the study of human BRCA1-related ovarian tumorigenesis.