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.

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

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.

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.

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

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.)

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.

Complexes between nuclear factor-κB p65 and signal transducer and activator of transcription 3 are key actors in inducing activation-induced cytidine deaminase expression and immunoglobulin A production in CD40L plus interleukin-10-treated human blood B cells

The signal transducer and activator of transcription 3 (STAT3) transcription factor pathway plays an important role in many biological phenomena. STAT3 transcription is triggered by cytokine-associated signals. Here, we use isolated human B cells to analyse the role of STAT3 in interleukin (IL)-10 induced terminal B cell differentiation and in immunoglobulin (Ig)A production as a characteristic readout of IL-10 signalling. We identified optimal conditions for inducing in-vitro IgA production by purified blood naive B cells using IL-10 and soluble CD40L. We show that soluble CD40L consistently induces the phosphorylation of nuclear factor (NF)-κB p65 but not of STAT3, while IL-10 induces the phosphorylation of STAT3 but not of NF-κB p65. Interestingly, while soluble CD40L and IL-10 were synergistic in driving the terminal maturation of B cells into IgA-producing plasma cells, they did not co-operate earlier in the pathway with regard to the transcription factors NF-κB p65 or STAT3. Blocking either NF-κB p65 or STAT3 profoundly altered the production of IgA and mRNA for activation-induced cytidine deaminase (AID), an enzyme strictly necessary for Ig heavy chain recombination. Finally, the STAT3 pathway was directly activated by IL-10, while IL-6, the main cytokine otherwise known for activating the STAT3 pathway, did not appear to be involved in IL-10-induced-STAT3 activation. Our results suggest that STAT3 and NF-κB pathways co-operate in IgA production, with soluble CD40L rapidly activating the NF-κB pathway, probably rendering STAT3 probably more reactive to IL-10 signalling. This novel role for STAT3 in B cell development reveals a potential therapeutic or vaccine target for eliciting IgA humoral responses at mucosal interfaces.

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.

Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays

hBRCA1 is involved in 20-45% of inherited breast cancer cases and is implicated in many mechanisms involved in response to DNA damage. To date, BRCA1 orthologs have been characterized in vertebrate genomes only. We have identified the ortholog of BRCA1 in Arabidopsis thaliana. AtBRCA1 is a 5.5 kb part of the locus At4g21070. The corresponding mRNA of 3.5 kb is composed of 14 exons and encodes a 941 amino acid protein (104 kDa). AtBRCA1, which has one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain, shows a high similarity to hBRCA1 in these motifs and has the same characteristic molecular organization. We have also identified a putative ortholog in rice (OsBRCA1). With 941 and 968 amino acids, respectively, AtBRCA1 and OsBRCA1 are the shortest members of the BRCA1 family, and may represent a plant specificity. AtBRCA1 is expressed ubiquitously in plant tissues, at levels depending on organ type, with highest levels in flower buds and exponentially growing cell cultures. Increase of mRNA levels in all plant tissues 1 h after irradiation with the highest induction level of approximately 150 times for a 100 Gy dose is consistent with a putative role of AtBRCA1 in DNA repair and in cell-cycle control.

Inhibition of BRCA1 leads to increased chemoresistance to microtubule-interfering agents, an effect that involves the JNK pathway

We have developed ribozymes (Rz) that inhibit BRCA1 expression in order to study the role of this gene in chemosensitivity. Two Rz, targeting positions 358 or 5282 of the BRCA1 mRNA, were cloned into the retroviral vector LXSN and lipofected into the breast cancer cell-line HBL100. We obtained 79-99% inhibition of BRCA1 expression, as determined by real-time quantitative PCR and by Western blotting. Decreased expression of BRCA1 led to sensitivity to the DNA damaging agents cisplatin and etoposide, resistance to the microtubule-interfering agents (MIA) taxol and vincristine. The molecular mechanism of resistance to MIA was investigated further by determining the status of the JNK pathway. We found that JNK1 expression was elevated, while JNK2 expression was decreased in Rz-expressing clones compared to controls. We have quantified the mRNA levels of BRCA1, JNK1, 2, MEK-4, -7 and c-jun after treatment with MIA. Vincristine treatment of control cells resulted in transcriptional repression of BRCA1, while the JNK1, 2, MEK-4, -7 and c-jun genes were induced. In Rz-treated cells, only JNK1 and MEK-4 were expressed and none was induced after MIA treatment. We then studied the phosphorylation of c-jun, a downstream effector of the JNK pathway. We observed a strong increase in phosphorylated c-jun after MIA treatment of the control cells but not in BRCA1-Rz treated cells, suggesting inhibition of the JNK pathway. These results show that the BRCA1-JNK pathway is involved in the cytotoxic response to MIA treatment, and inhibition of BRCA1 leads to transcriptional modifications of the JNK pathway.

Molecular pathways involved in response to ionizing radiation of ID-8 mouse ovarian cancer cells expressing exogenous full-length Brca1 or truncated Brca1 mutant

BRCA1 germline mutations have been linked to the development of hereditary breast and ovarian cancers. Recent studies suggest that BRCA1 may function in the regulation of basic cellular processes, including gene transcription, and sensing and/or repair of DNA damage. To further delineate the BRCA1 upstream and downstream steps involved in its role in the cellular response to ionizing radiation, we compared the effects of expression of an exogenous full-length Brca1 with those of a truncated Brca1 mutant in the ID-8 mouse ovarian cancer cell line after irradiation. We found that expression of both full-length and truncated Brca1 increased resistance to ionizing radiation. Expression of truncated, but not full-length, Brca1 then allowed us to identify new potential downstream targets of mutated BRCA1 like MAPK/ERK pathway members and also key genes involved in mutated BRCA1 signaling pathway response to ionizing radiation such as p53 and p21WAF1/CIP1. We therefore established an in vitro mouse model for studying the molecular effects of human BRCA1 germline mutations.

Real-time PCR quantification of full-length and exon 11 spliced BRCA1 transcripts in human breast cancer cell lines

Germline alterations of the BRCA1 tumor suppressor gene have been implicated at least in half of familial breast cancers. Nevertheless, in sporadic breast cancer no mutation of this gene has been characterized to date. In sporadic breast tumors, other BRCA1 gene loss of function mechanisms, such as down-regulation of gene expression, have been suggested. In an effort to better understand the relationship between BRCA1 expression and malignant transformation, we have adapted the new real-time quantitative PCR method based on a 5' nuclease assay and the use of doubly labeled fluorescent TaqMan probes to quantify BRCA1 mRNA. We have compared expression of BRCA1 mRNA with or without exon 11 in the normal breast epithelial cell line MCF10a and in three cancer cell lines (MCF-7, MDA-MB231 and HBL100) by comparing two methods of quantification: the comparative C(T) and the standard curve. We found that the full length BRCA1 mRNA, which encodes the functional nuclear protein, was down-regulated in tumor cells when compared with MCF10a cells.