Flowering time control in European winter wheat

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Genotyping by sequencing; a strategy for identification and mapping of induced mutation in newly developed wheat mutant lines

Exposing genetic material with physical mutagens can create novel genetic resources capable of combating different stresses. High throughput GBS-DArTseq™ assay was deployed to estimate genetic diversity of 33 newly developed stable wheat mutants as compared to the wild type. The identified 1,57,608 PAVs markers were randomly distributed across wheat chromosomes and sub-genomes with the highest number detected on Chr-7D (2877) and Chr-7B (2711). The B sub-genome contained the most PAVs followed by D and A-sub genome. Among mutant lines, Pb-M-2061 and Pb-M-59 had the highest PAV count, while Pb-M-605 and Pb-M-196 had the lowest. A total of 7,910 PAVs were consistently present over all replicates, with 3,252 specifically present in mutants and absent in wild type. The maximum PAVs (1480) were found in Pb-M-1027 and Pb-M-1323 (656). Functional characterization revealed that out of 3,252, 1,238 were found in wheat transcriptome database that contained 152 characterized and 1,196 uncharacterized genes. COGs and GO-terms analysis linked many PAVs with pathways involving signaling, metabolism and defense. Maximum number of gene-containing PAVs were identified in Pb-M-1027, Pb-M-2302 and Pb-M-1323 which were involved in tolerance to diseases and abiotic stresses, improved photosynthetic efficiency, larger grain size, increased grain yield and harvest index pathways. This study provides valuable insights into the genetic diversity and potential agronomic benefits of PAVs in wheat mutant lines. These findings can help molecular geneticist and breeders for exploiting the induced genetic diversity for unravelling the genetic circuits as well as exploiting in wheat breeding for developing resilient cultivars.

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

KEY MESSAGE

PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.

Natural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat

Heat stress threatens global wheat (Triticum aestivum) production, causing dramatic yield losses worldwide. Identifying heat tolerance genes and comprehending molecular mechanisms are essential. Here, we identify a heat tolerance gene, TaSG-D1E286K, in Indian dwarf wheat (Triticum sphaerococcum), which encodes an STKc_GSK3 kinase. TaSG-D1E286K improves heat tolerance compared to TaSG-D1 by enhancing phosphorylation and stability of downstream target TaPIF4 under heat stress condition. Additionally, we reveal evolutionary footprints of TaPIF4 during wheat selective breeding in China, that is, InDels predominantly occur in the TaPIF4 promoter of Chinese modern wheat cultivars and result in decreased expression level of TaPIF4 in response to heat stress. These sequence variations with negative effect on heat tolerance are mainly introduced from European germplasm. Our study provides insight into heat stress response mechanisms and proposes a potential strategy to improve wheat heat tolerance in future.

Field response and molecular screening of European wheat germplasm against powdery mildew at the Himalayan region of Pakistan

Wheat powdery mildew possesses a significant threat to wheat crops not only on a global scale but also in the northern region of Pakistan. Recognizing the need for effective measures, the exploration and utilization of exotic germplasm take on critical importance. To address this, a series of trials were made to investigate the response of 30 European (EU) lines, in addition to the local checks (Siran, Atta-Habib (AH) and Ghanimat-e-IBGE) against wheat powdery mildew at the Himalayan region of Pakistan. The study involved field testing from 2018 to 2022 across multiple locations, resulting in 38 different environments (location × year). In addition to field evaluations, molecular genotyping was also performed. The disease was absent on the tested lines during 2018, 2019, and 2020 whereas it ranged from 0 to 100% at Chitral location during 2021, where 100% was observed only for one EU wheat line "Matrix." The disease prevailed only at Gilgit location (0-60% for EU wheat line "F236") and at Nagar location (0-10% for EU wheat lines Substance and Nelson) during the disease season of 2022. Most of the EU wheat lines showed very low ACI values, due to an overall low disease pressure. Matrix showed the maximum ACI (1.54) followed by Ritter (1.25) and Bli_autrichion (0.87), whereas the minimum (0.1) was for Substance, JB_Asano, and KWS_Loft followed by Canon (0.19), all exhibiting partial resistance. The molecular marker-based screening revealed that Pm38 was the most prevalent and detected in 100% of wheat lines followed by Pm39 (60%) and Pm8 (30%). Six wheat lines (20%) possessed all three Pm genes (Pm8, Pm38, and Pm39) concurrently. The variability observed in this study can be utilized in future breeding efforts aimed at developing resistant wheat varieties.

Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize

KEY MESSAGE

Multi-trial genome wide association study of plasticity indices allow to detect QTLs specifically involved in the genotype x water availability interaction. Concerns regarding high maize yield losses due to increasing occurrences of drought events are growing, and breeders are still looking for molecular markers for drought tolerance. However, the genetic determinism of traits in response to drought is highly complex and identification of causal regions is a tremendous task. Here, we exploit the phenotypic data obtained from four trials carried out on a phenotyping platform, where a diversity panel of 254 maize hybrids was grown under well-watered and water deficit conditions, to investigate the genetic bases of the drought response in maize. To dissociate drought effect from other environmental factors, we performed multi-trial genome-wide association study on well-watered and water deficit phenotypic means, and on phenotypic plasticity indices computed from measurements made for six ecophysiological traits. We identify 102 QTLs and 40 plasticity QTLs. Most of them were new compared to those obtained from a previous study on the same dataset. Our results show that plasticity QTLs cover genetic regions not identified by QTLs. Furthermore, for all ecophysiological traits, except one, plasticity QTLs are specifically involved in the genotype by water availability interaction, for which they explain between 60 and 100% of the variance. Altogether, QTLs and plasticity QTLs captured more than 75% of the genotype by water availability interaction variance, and allowed to find new genetic regions. Overall, our results demonstrate the importance of considering phenotypic plasticity to decipher the genetic architecture of trait response to stress.

Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley

The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.

GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat

In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01357-5.

Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations

Plant breeders have indirectly selected for variation at circadian-associated loci in many of the world's major crops, when breeding to increase yield and improve crop performance. Using an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, we investigated how variation in circadian clock-associated genes contributes to the regulation of heading date in UK and European winter wheat (Triticum aestivum) varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidates for the Earliness per se (Eps) D1 and B1 loci under field conditions. We then confirmed a single-nucleotide polymorphism within the coding region of TaELF3-B1 as a candidate polymorphism underlying the Eps-B1 locus. We found that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1 is, instead, an allele that lies within an introgression region containing an inversion relative to the Chinese Spring D genome. Using Triticum turgidum cv. Kronos carrying loss-of-function alleles of TtELF3, we showed that ELF3 regulates heading, with loss of a single ELF3 homoeologue sufficient to alter heading date. These studies demonstrated that ELF3 forms part of the circadian oscillator; however, the loss of all homoeologues was required to affect circadian rhythms. Similarly, loss of functional LUX ARRHYTHMO (LUX) in T. aestivum, an orthologue of a protein partner of Arabidopsis (Arabidopsis thaliana) ELF3, severely disrupted circadian rhythms. ELF3 and LUX transcripts are not co-expressed at dusk, suggesting that the structure of the wheat circadian oscillator might differ from that of Arabidopsis. Our demonstration that alterations to ELF3 homoeologues can affect heading date separately from effects on the circadian oscillator suggests a role for ELF3 in cereal photoperiodic responses that could be selected for without pleiotropic deleterious alterations to circadian rhythms.

Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

The dynamics of plant development not only has an impact on ecological adaptation but also contributes to the realization of genetically determined yield potentials in various environments. Dissecting the genetic determinants of plant development becomes urgent due to the global climate change, which can seriously affect and even disrupt the locally adapted developmental patterns. In order to determine the role plant developmental loci played in local adaptation and yield formation, a panel of 188 winter and facultative wheat cultivars from diverse geographic locations were characterized with the 15K Illumina Single Nucleotide Polymorphism (SNP) chip and functional markers of several plant developmental genes and included into a multiseason field experiment. Genome-wide association analyses were conducted on five consecutive developmental phases spanning from the first node appearance to full heading together with various grain yield-related parameters. The panel was balanced for the PPD-D1 photoperiod response gene, which facilitated the analyses in the two subsets of photoperiod-insensitive and -sensitive genotypes in addition to the complete panel. PPD-D1 was the single highest source, explaining 12.1%-19.0% of the phenotypic variation in the successive developmental phases. In addition, 21 minor developmental loci were identified, each one explaining only small portions of the variance, but, together, their effects amounted to 16.6%-50.6% of phenotypic variance. Eight loci (2A_27, 2A_727, 4A_570, 5B_315, 5B_520, 6A_26, 7A_1-(VRN-A3), and 7B_732) were independent of PPD-D1. Seven loci were only detectable in the PPD-D1-insensitive genetic background (1A_539, 1B_487, 2D_649, 4A_9, 5A_584-(VRN-A1), 5B_571-(VRN-B1), and 7B_3-(VRN-B3)), and six loci were only detectable in the sensitive background, specifically 2A_740, 2D_25, 3A_579, 3B_414, 7A_218, 7A_689, and 7B_538. The combination of PPD-D1 insensitivity and sensitivity with the extremities of early or late alleles in the corresponding minor developmental loci resulted in significantly altered and distinct plant developmental patterns with detectable outcomes on some yield-related traits. This study examines the possible significance of the above results in ecological adaptation.

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

Choosing the right tool: Leveraging of plant genetic resources in wheat (Triticum aestivum L.) benefits from selection of a suitable genomic prediction model

Genomic prediction of genebank accessions benefits from the consideration of additive-by-additive epistasis and subpopulation-specific marker effects. Wheat (Triticum aestivum L.) and other species of the Triticum genus are well represented in genebank collections worldwide. The substantial genetic diversity harbored by more than 850,000 accessions can be explored for their potential use in modern plant breeding. Characterization of these large number of accessions is constrained by the required resources, and this fact limits their use so far. This limitation might be overcome by engaging genomic prediction. The present study compared ten different genomic prediction approaches to the prediction of four traits, namely flowering time, plant height, thousand grain weight, and yellow rust resistance, in a diverse set of 7745 accession samples from Germany's Federal ex situ genebank at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben. Approaches were evaluated based on prediction ability and robustness to the confounding influence of strong population structure. The authors propose the wide application of extended genomic best linear unbiased prediction due to the observed benefit of incorporating additive-by-additive epistasis. General and subpopulation-specific additive ridge regression best linear unbiased prediction, which accounts for subpopulation-specific marker-effects, was shown to be a good option if contrasting clusters are encountered in the analyzed collection. The presented findings reaffirm that the trait's genetic architecture as well as the composition and relatedness of the training set and test set are major driving factors for the accuracy of genomic prediction.

Plant clock modifications for adapting flowering time to local environments

During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.

Identification of QTLs for wheat heading time across multiple-environments

KEY MESSAGE

The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays it. A genome-wide scan of marker-trait associations with heading date detected two QTL: an adapted allele at locus TaHd102 on chromosome 5A that has a consistent effect on HD in German cultivars in multiple environments and a non-adapted allele at locus TaHd044 on chromosome 3A that accelerates flowering by 5.6 days. TaHd102 and TaHd044 explain 13.8% and 33% of the genetic variance, respectively. The interplay of the climatic variables led to the detection of environment specific association responding to temperature in lower latitudes and photoperiod in higher ones. Another locus TaHd098 on chromosome 5A showed epistatic interactions with 15 known regulators of flowering time when non-adapted cultivars from outside Germany were included in the analysis.

Do lower nitrogen fertilization levels require breeding of different types of cultivars in triticale?

The comparably low genotype-by-nitrogen level interaction suggests that selection in early generations can be done under high-input conditions followed by selection under different nitrogen levels to identify genotypes ideally suited for the target environment. Breeding high-yielding, nitrogen-efficient crops is of utmost importance to achieve greater agricultural sustainability. The aim of this study was to evaluate nitrogen use efficiency (NUE) of triticale, investigate long-term genetic trends and the genetic architecture, and develop strategies for NUE improvement by breeding. For this, we evaluated 450 different triticale genotypes under four nitrogen fertilization levels in multi-environment field trials for grain yield, protein content, starch content and derived indices. Analysis of temporal trends revealed that modern cultivars are better in exploiting the available nitrogen. Genome-wide association mapping revealed a complex genetic architecture with many small-effect QTL and a high level of pleiotropy for NUE-related traits, in line with phenotypic correlations. Furthermore, the effect of some QTL was dependent on the nitrogen fertilization level. High correlations of each trait between N levels and the rather low genotype-by-N-level interaction variance showed that generally the same genotypes perform well over different N levels. Nevertheless, the best performing genotype was always a different one. Thus, selection in early generations can be done under high nitrogen fertilizer conditions as these provide a stronger differentiation, but the final selection in later generations should be conducted with a nitrogen fertilization as in the target environment.

GWAS for main effects and epistatic interactions for grain morphology traits in wheat

In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length-width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017-2018, 2018-2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01164-w.

Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies

Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

Using a gene-based phenology model to identify optimal flowering periods of spring wheat in irrigated mega-environments

To maximize the grain yield of spring wheat, flowering needs to coincide with the optimal flowering period (OFP) by minimizing frost and heat stress on reproductive development. This global study conducted a comprehensive modelling analysis of genotype, environment, and management to identify the OFPs for sites in irrigated mega-environments of spring wheat where the crop matures during a period of increasing temperatures. We used a gene-based phenology model to conduct long-term simulation analysis with parameterized genotypes to identify OFPs and optimal sowing dates for sites in irrigated mega-environments, considering the impacts of frost and heat stress on yield. The validation results showed that the gene-based model accurately predicted wheat heading dates across global wheat environments. The long-term simulations indicated that frost and heat stress significantly advanced or delayed OFPs and shrank the durations of OFPs in irrigated mega-environments when compared with OFPs where the model excluded frost and heat stress impacts. The simulation results (incorporating frost and heat penalties on yield) also showed that earlier flowering generally resulted in higher yields, and early sowing dates and/or early flowering genotypes were suggested to achieve early flowering. These results provided an interpretation of the regulation of wheat flowering to the OFP by the selection of sowing date and cultivar to achieve higher yields in irrigated mega-environments.

Effect of Flowering Time-Related Genes on Biomass, Harvest Index, and Grain Yield in CIMMYT Elite Spring Bread Wheat

Simple Summary

Allelic variants of vernalization (Vrn), photoperiod (Ppd), and earliness per se (Eps) genes in two panels of elite spring wheat were used to estimate their effects on the phenological stages, biomass (BM), harvest index (HI), and grain yield (YLD). Major spring alleles of Vrn-1 had the largest effect on shortening the time to anthesis, while the Ppd-insensitive allele Ppd-D1a had the most significant positive effect on YLD. Furthermore, alleles at recently identified loci TaTOE-B1 and TaFT3-B1 promoted between 3.8% and 7.6% higher YLD and 4.2% and 10.2% higher HI in the two panels. Further, when the possible effects of the TaTOE-B1 and TaFT3-B1 alleles on the sink and source traits were explored, the favorable allele at TaTOE-B1 showed positive effects on several sink traits related mainly to the grain number. Favorable alleles at TaFT3-B1 followed a different pattern, with positive effects on the traits related to grain weight. The results of this study expanded the wheat breeders’ toolbox in the quest to breed better-adapted and higher-yielding wheat cultivars.

Abstract

Grain yield (YLD) is a function of the total biomass (BM) and of partitioning the biomass by grains, i.e., the harvest index (HI). The most critical developmental stage for their determination is the flowering time, which mainly depends on the vernalization requirement (Vrn) and photoperiod sensitivity genes (Ppd) loci. Allelic variants at the Vrn, Ppd, and earliness per se (Eps) genes of elite spring wheat genotypes included in High Biomass Association Panel (HiBAP) I and II were used to estimate their effects on the phenological stages BM, HI, and YLD. Each panel was grown for two consecutive years in Northwest Mexico. Spring alleles at Vrn-1 had the largest effect on shortening the time to anthesis, and the Ppd-insensitive allele Ppd-D1a had the most significant positive effect on YLD in both panels. In addition, alleles at TaTOE-B1 and TaFT3-B1 promoted between 3.8% and 7.6% higher YLD and 4.2% and 10.2% higher HI in HiBAP I and II, respectively. When the possible effects of the TaTOE-B1 and TaFT3-B1 alleles on the sink and source traits were explored, the favorable allele at TaTOE-B1 showed positive effects on several sink traits mainly related to grain number. The favorable alleles at TaFT3-B1 followed a different pattern, with positive effects on the traits related to grain weight. The results of this study expanded the wheat breeders’ toolbox in the quest to breed better-adapted and higher-yielding wheat cultivars.

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries' breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms 'response-to-auxin' and 'response-to-wounding.' Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat

A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01240-1.

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.

Genetic dissection of days to flowering via genome-wide association studies in Turkish common bean germplasm

Common bean is a nutrient-dense legume crop serving as a source of food for millions of people. Characterization of unexplored common bean germplasm to unlock the phenotypic and genetic variations is still needed to explore the breeding potential of this crop. The current study aimed to dissect the genetic basis having association for days to flowering (DF). A total of 188 common bean accessions collected from 19 provinces of Turkey were used as plant material under five environments and two locations. Analysis of variance (ANOVA) revealed that genotypes and genotype by environment interaction have significant effects on DF. A total of 10 most stable accessions were evaluated from stability analysis. Overall maximum (75) and minimum (54) DF were observed for Hakkari-51 and Mus-46 accessions, respectively. The implemented constellation plot divided studied germplasm according to their DF and growth habit. A total of 7900 DArTseq markers were used for association analysis. Mixed linear model using the Q + K Model resulted a total of 18 DArTseq markers from five environments. DArT-8668385 marker identified in Bolu during 2016 was also associated with DF in Sivas during 2017. Combined data of five years resulted a total of four markers (DArT-22346534, DArT-3369768, DArT-3374613, and DArT-3370801) having significant association ( p  <  0.01 ) for DF. DArT-22346534 present on Pv 08 accounted a maximum of 9.89% variation to the studied trait. A total of four putative candidate genes were predicted from sequences reflecting homology to identified four DArTseq markers. We envisage that exploitation of identified DArTseq markers will hopefully beneficial for the development of new common bean varieties having better adaptation ability to changing climatic conditions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01029-8.

Comparative Performance of High-Yielding European Wheat Cultivars Under Contrasting Mediterranean Conditions

Understanding the interaction between genotype performance and the target environment is the key to improving genetic gain, particularly in the context of climate change. Wheat production is seriously compromised in agricultural regions affected by water and heat stress, such as the Mediterranean basin. Moreover, wheat production may be also limited by the nitrogen availability in the soil. We have sought to dissect the agronomic and physiological traits related to the performance of 12 high-yield European bread wheat varieties under Mediterranean rainfed conditions and different levels of N fertilization during two contrasting crop seasons. Grain yield was more than two times higher in the first season than the second season and was associated with much greater rainfall and lower temperatures. However, the nitrogen effect was rather minor. Genotypic effects existed for the two seasons. While several of the varieties from central/northern Europe yielded more than those from southern Europe during the optimal season, the opposite trend occurred in the dry season. The varieties from central/northern Europe were associated with delayed phenology and a longer crop cycle, while the varieties from southern Europe were characterized by a shorter crop cycle but comparatively higher duration of the reproductive period, associated with an earlier beginning of stem elongation and a greater number of ears per area. However, some of the cultivars from northern Europe maintained a relatively high yield capacity in both seasons. Thus, KWS Siskin from the UK exhibited intermediate phenology, resulting in a relatively long reproductive period, together with a high green area throughout the crop cycle.

Deoxynivalenol Occurrence in Triticale Crops in Romania during the 2012-2014 Period with Extreme Weather Events

This article aims to evaluate deoxynivalenol occurrence in triticale crops in Romania in years with extreme weather events (2012: Siberian anticyclone with cold waves and heavy snowfall; 2013 and 2014: “Vb” cyclones with heavy precipitation and floods in spring). The deoxynivalenol level in triticale samples (N = 236) was quantified by ELISA. In Romania, the extreme weather events favoured deoxynivalenol occurrence in triticale in Transylvania and the Southern Hilly Area (44–47° N, 22–25° E) with a humid/balanced-humid temperate continental climate, luvisols and high/very high risk of floods. Maximum deoxynivalenol contamination was lower in the other regions, although heavy precipitation in May–July 2014 was higher, with chernozems having higher aridity. Multivariate analysis of the factors influencing deoxynivalenol occurrence in triticale showed at least a significant correlation for all components of variation source (agricultural year, agricultural region, average of deoxynivalenol, average air temperature, cumulative precipitation, soil moisture reserve, aridity indices) (p-value < 0.05). The spatial and geographic distribution of deoxynivalenol in cereals in the countries affected by the 2012–2014 extreme weather events revealed a higher contamination in Central Europe compared to southeastern and eastern Europe. Deoxynivalenol occurrence in cereals was favoured by local and regional agroclimatic factors and was amplified by extreme weather events.

A multiple species, continent-wide, million-phenotype agronomic plant dataset

A critical shortage of ‘big’ agronomic data is placing an unnecessary constraint on the conduct of public agronomic research, imparting barriers to model development and testing. Here, we address this problem by providing a large non-relational database of agronomic trials, linked to intensive management and observational data, run under a unified experimental framework. The National Variety Trials (NVTs) represent a decade-long experimental trial network, conducted across thousands of Australian field sites using highly standardised randomised controlled designs. The NVTs contain over a million machine-measured phenotypic observations, aggregated from density-controlled populations containing hundreds of millions of plants and thousands of released plant varieties. These data are linked to hundreds of thousands of metadata observations including standardised soil tests, fertiliser and pesticide input data, crop rotation data, prior farm management practices, and in-field sensors. Finally, these data are linked to a suite of ground and remote sensing observations, arranged into interpolated daily- and ten-day aggregated time series, to capture the substantial diversity in vegetation and environmental patterns across the continent-spanning NVT network.

Measurement(s)	grain yield trait • protein content • days to flowering trait • Glucosinolate • plant structure development stage
Technology Type(s)	specimen harvest quantity • Mass Spectrometry • agronomic process
Sample Characteristic - Organism	Pisum sativum • Secale cereale x Triticum aestivum • Triticum aestivum • Brassica napus • Avena sativa • Lens culinaris • Cicer arietinum • Lupinus angustifolius • Vicia faba
Sample Characteristic - Environment	cultivated environment
Sample Characteristic - Location	Australia

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13709956

Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background

Earliness per se (Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature and therefore determining the likely Eps × temperature interaction is needed for each newly identified Eps gene. We studied two NILs differing in the newly identified Eps-7D (carrying insensitive Ppd-D1 in the background) under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 and 24 h). Eps-7D affected time to anthesis as expected and the Eps-7D-late allele extended both the period before and after terminal spikelet. The interaction effect of Eps-7D × temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with the late or early allele was affected by the growing temperature (i.e., difference was least at 18 °C and largest at 9 °C), and the differences caused due to temperature sensitivity were influenced by photoperiod. The rate of leaf initiation was faster in NIL with Eps-7D-early than with the late allele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs. Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.

Phenology and Floret Development as Affected by the Interaction between Eps-7D and Ppd-D1

Earliness per se (Eps) genes may play a critical role in further improving wheat adaptation and fine-tuning wheat development to cope with climate change. There are only few studies on the detailed effect of Eps on wheat development and fewer on the interaction of Eps with the environment and other genes determining time to anthesis. Furthermore, it seems relevant to study every newly discovered Eps gene and its probable interactions as the mechanisms and detailed effects of each Eps may be quite different. In the present study, we evaluated NILs differing in the recently identified Eps-7D as well as in Ppd-D1 at three temperature regimes (9, 15 and 18 °C) under short day. The effect of Eps-7D on time to anthesis as well as on its component phases varied both qualitatively and quantitatively depending on the allelic status of Ppd-D1 and temperature, being larger in a photoperiod-sensitive background. A more noticeable effect of Eps-7D (when combined with Ppd-D1b) was realised during the late reproductive phase. Consequently, the final leaf number was not clearly altered by Eps-7D, while floret development of the labile florets (florets 2 and 3 in this case, depending on the particular spikelet) was favoured by the action of the Eps-7D-late allele, increasing the likelihood of particular florets to become fertile, and consequently, improving spike fertility when combined with Ppd-D1b.

Root characteristics of spring wheat under drip irrigation and their relationship with aboveground biomass and yield

The objectives of this two-year field experiment were (1) to study the effect of irrigation frequency and irrigation amount on the root characteristics of drip-irrigated spring wheat (Triticum aestivum L.) and (2) to determine the relationship between these root characteristics and aboveground biomass and yield. A split-plot design was used with two wheat cultivars (Xinchun 6 and Xinchun 22). The irrigation treatments consisted of three irrigation intervals (D_1, 13 d; D₂, 10 d; and D₃, 7 d) and three water amounts (W1, 3750 m³/ha; W2, 6000 m³/ha; and W3, 8250 m³/ha). The results showed that root length density (RLD) and root weight density (RWD) were greater at 0–20 cm than at 20–40 cm at flowering. The RLD was greater in D1 and D2 than in D3 in the shallow soil layer and did not differ among the treatments with different irrigation frequencies in deep soil. The RLD at the 0–20 cm depth of W3 was 17.9% greater than that of W2 and 53.8% greater than that of W1, and the RLD trend was opposite at the 20–40 cm depth. The root–shoot ratio was significantly higher in D2 than in the other treatment, whereas the RLD, RWD, leaf Pn and LAI were significantly greater in D3. Leaf Pn and LAI both increased as the irrigation amount increased. Regression analysis showed a natural logarithmic relationship between RWD and aboveground biomass (R² > 0.60, P < 0.05) and binomial relationships of the RWD at 0–20 cm depth (R² = 0.43, P < 0.05) and the RLD at 20–40 cm depth (R² = 0.34, P < 0.05) with grain yield. We found that with the optimum irrigation amount (W2), increasing drip irrigation frequency can increase wheat root length and root weight and aboveground biomass accumulation, thereby improving yield and water use efficiency.

Characterizing Winter Wheat Germplasm for Fusarium Head Blight Resistance Under Accelerated Growth Conditions

Fusarium head blight (FHB) is one of the economically important diseases of wheat as it causes severe yield loss and reduces grain quality. In winter wheat, due to its vernalization requirement, it takes an exceptionally long time for plants to reach the heading stage, thereby prolonging the time it takes for characterizing germplasm for FHB resistance. Therefore, in this work, we developed a protocol to evaluate winter wheat germplasm for FHB resistance under accelerated growth conditions. The protocol reduces the time required for plants to begin heading while avoiding any visible symptoms of stress on plants. The protocol was tested on 432 genotypes obtained from a breeding program and a genebank. The mean area under disease progress curve for FHB was 225.13 in the breeding set and 195.53 in the genebank set, indicating that the germplasm from the genebank set had higher resistance to FHB. In total, 10 quantitative trait loci (QTL) for FHB severity were identified by association mapping. Of these, nine QTL were identified in the combined set comprising both genebank and breeding sets, while two QTL each were identified in the breeding set and genebank set, respectively, when analyzed separately. Some QTLs overlapped between the three datasets. The results reveal that the protocol for FHB evaluation integrating accelerated growth conditions is an efficient approach for FHB resistance breeding in winter wheat and can be even applied to spring wheat after minor modifications.

Genetic Architecture of Cereal Leaf Beetle Resistance in Wheat

Wheat production can be severely damaged by endemic and invasive insect pests. Here, we investigated resistance to cereal leaf beetle in a panel of 876 winter wheat cultivars, and dissected the genetic architecture underlying this insect resistance by association mapping. We observed an effect of heading date on cereal leaf beetle infestation, with earlier heading cultivars being more heavily infested. Flag leaf glaucousness was also found to be correlated with resistance. In line with the strong effect of heading time, we identified Ppd-D1 as a major quantitative trait locus (QTL), explaining 35% of the genotypic variance of cereal leaf beetle resistance. The other identified putative QTL explained much less of the genotypic variance, suggesting a genetic architecture with many small-effect QTL, which was corroborated by a genomic prediction approach. Collectively, our results add to our understanding of the genetic control underlying insect resistances in small-grain cereals.

Identification of the vernalization gene VRN-B1 responsible for heading date variation by QTL mapping using a RIL population in wheat

BACKGROUND

Heading time is one of the most important agronomic traits in wheat, as it largely affects both adaptation to different agro-ecological conditions and yield potential. Identification of genes underlying the regulation of wheat heading and the development of diagnostic markers could facilitate our understanding of genetic control of this process.

RESULTS

In this study, we developed 400 recombinant inbred lines (RILs) by crossing a γ-ray-induced early heading mutant (eh1) with the late heading cultivar, Lunxuan987. Bulked Segregant Analysis (BSA) of both RNA and DNA pools consisting of various RILs detected a quantitative trait loci (QTL) for heading date located on chromosomes 5B, and further genetic linkage analysis limited the QTL to a 3.31 cM region. We then identified a large deletion in the first intron of the vernalization gene VRN-B1 in eh1, and showed it was associated with the heading phenotype in the RIL population. However, it is not the mutation loci that resulted in early heading phonotype in the mutant compared to that of wildtype. RNA-seq analysis suggested that Vrn-B3 and several newly discovered genes, including beta-amylase 1 (BMY1) and anther-specific protein (RTS), were highly expressed in both the mutant and early heading pool with the dominant Vrn-B1 genotype compared to that of Lunxuan987 and late heading pool. Enrichment analysis of differentially expressed genes (DEGs) identified several key pathways previously reported to be associated with flowering, including fatty acid elongation, starch and sucrose metabolism, and flavonoid biosynthesis.

CONCLUSION

The development of new markers for Vrn-B1 in this study supplies an alternative solution for marker-assisted breeding to optimize heading time in wheat and the DEGs analysis provides basic information for VRN-B1 regulation study.

Identification of Quantitative Trait Loci Relating to Flowering Time, Flag Leaf and Awn Characteristics in a Novel Triticum dicoccum Mapping Population

Tetraploid landraces of wheat harbour genetic diversity that could be introgressed into modern bread wheat with the aid of marker-assisted selection to address the genetic diversity bottleneck in the breeding genepool. A novel bi-parental Triticum turgidum ssp. dicoccum Schrank mapping population was created from a cross between two landrace accessions differing for multiple physiological traits. The population was phenotyped for traits hypothesised to be proxies for characteristics associated with improved photosynthesis or drought tolerance, including flowering time, awn length, flag leaf length and width, and stomatal and trichome density. The mapping individuals and parents were genotyped with the 35K Wheat Breeders’ single nucleotide polymorphism (SNP) array. A genetic linkage map was constructed from 104 F4 individuals, consisting of 2066 SNPs with a total length of 3295 cM and an average spacing of 1.6 cM. Using the population, 10 quantitative trait loci (QTLs) for five traits were identified in two years of trials. Three consistent QTLs were identified over both trials for awn length, flowering time and flag leaf width, on chromosomes 4A, 7B and 5B, respectively. The awn length and flowering time QTLs correspond with the major loci Hd and Vrn-B3, respectively. The identified marker-trait associations could be developed for marker-assisted selection, to aid the introgression of diversity from a tetraploid source into modern wheat for potential physiological trait improvement.

Large genetic yield potential and genetic yield gap estimated for wheat in Europe

Improving yield potential and closing the yield gap are important to achieve global food security. Europe is the largest wheat producer, delivering about 35% of wheat globally, but European wheat's yield potential from genetic improvements is as yet unknown. We estimated wheat 'genetic yield potential', i.e. the yield of optimal or ideal genotypes in a target environment, across major wheat growing regions in Europe by designing in silico ideotypes. These ideotypes were optimised for current climatic conditions and based on optimal physiology, constrained by available genetic variation in target traits. A 'genetic yield gap' in a location was estimated as the difference between the yield potential of the optimal ideotype compared with a current, well-adapted cultivar. A large mean genetic yield potential (11-13 t ha-1) and genetic yield gap (3.5-5.2 t ha-1) were estimated under rainfed conditions in Europe. In other words, despite intensive wheat breeding efforts, current local cultivars were found to be far from their optimum, meaning that a large genetic yield gap still exists in European wheat. Heat and drought tolerance around flowering, optimal canopy structure and phenology, improved root water uptake and reduced leaf senescence under drought were identified as key traits for improvement. Closing this unexploited genetic yield gap in Europe through crop improvements and genetic adaptations could contribute towards global food security.

Genome-wide association and epistatic interactions of flowering time in soybean cultivar

Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.

Characterization of the Genetic Architecture for Fusarium Head Blight Resistance in Durum Wheat: The Complex Association of Resistance, Flowering Time, and Height Genes

Durum wheat is an economically important crop for Canadian farmers. Fusarium head blight (FHB) is one of the most destructive diseases that threatens durum production in Canada. FHB reduces yield and end-use quality and most commonly contaminates the grain with the fungal mycotoxin deoxynivalenol, also known as DON. Serious outbreaks of FHB can occur in durum wheat in Canada, and combining genetic resistance with fungicide application is a cost effective approach to control this disease. However, there is limited variation for genetic resistance to FHB in elite Canadian durum cultivars. To explore and identify useful genetic FHB resistance variation for the improvement of Canadian durum wheat, we assembled an association mapping (AM) panel of diverse durum germplasms and performed genome wide association analysis (GWAS). Thirty-one quantitative trait loci (QTL) across all 14 chromosomes were significantly associated with FHB resistance. On 3BS, a stable QTL with a larger effect for resistance was located close to the centromere of 3BS. Three haplotypes of Fhb1 QTL were identified, with an emmer wheat haplotype contributing to disease susceptibility. The large number of QTL identified here can provide a rich resource to improve FHB resistance in commercially grown durum wheat. Among the 31 QTL most were associated with plant height and/or flower time. QTL 1A.1, 1A.2, 3B.2, 5A.1, 6A.1, 7A.3 were associated with FHB resistance and not associated or only weakly associated with flowering time nor plant height. These QTL have features that would make them good targets for FHB resistance breeding.

Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat

In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.

Agronomic and Physiological Traits, and Associated Quantitative Trait Loci (QTL) Affecting Yield Response in Wheat (Triticum aestivum L.): A Review

Enhanced grain yield has been achieved in bread wheat (Triticum aestivum L.) through development and cultivation of superior genotypes incorporating yield-related agronomic and physiological traits derived from genetically diverse and complementary genetic pool. Despite significant breeding progress, yield levels in wheat have remained relatively low and stagnant under marginal growing environments. There is a need for genetic improvement of wheat using yield-promoting morpho-physiological attributes and desired genotypes under the target production environments to meet the demand for food and feed. This review presents breeding progress in wheat for yield gains using agronomic and physiological traits. Further, the paper discusses globally available wheat genetic resources to identify and select promising genotypes possessing useful agronomic and physiological traits to enhance water, nutrient-, and radiation-use efficiency to improve grain yield potential and tolerance to abiotic stresses (i.e. elevated CO2, high temperature, and drought stresses). Finally, the paper highlights quantitative trait loci (QTL) linked to agronomic and physiological traits to aid breeding of high-performing wheat genotypes.

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

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.

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat

Background

Heading time is an important adaptive trait in durum wheat. In hexaploid wheat, Photoperiod-1 (Ppd) loci are essential regulators of heading time, with Ppd-B1 conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome Ppd-D1 locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat.

Results

In this study, we employed a panel of 328 diverse European durum genotypes that were evaluated for heading time at five environments. Genome-wide association mapping identified six putative QTL, with a major QTL on chromosome 2B explaining 26.2% of the genotypic variance. This QTL was shown to correspond to copy number variation at Ppd-B1, for which two copy number variants appear to be present. The higher copy number confers earlier heading and was more frequent in the heat and drought prone countries of lower latitude. In addition, two other QTL, corresponding to Vrn-B3 (TaFT) and Ppd-A1, were found to explain 9.5 and 5.3% of the genotypic variance, respectively.

Conclusions

Our results revealed the yet unknown role of copy number variation of Ppd-B1 as the major source underlying the variation in heading time in European durum wheat. The observed geographic patterns underline the adaptive value of this polymorphism and suggest that it is already used in durum breeding to tailor cultivars to specific target environments. In a broader context our findings provide further support for a more widespread role of copy number variation in mediating abiotic and biotic stress tolerance in plants.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0768-2) contains supplementary material, which is available to authorized users.

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. The aims of this study were thus to compare the merit of marker-assisted selection using the major frost tolerance QTL Fr-A2 with genomic prediction for winter hardiness and frost tolerance, and to assess the potential of combining both measures with a genomic selection index using a high density marker map or a reduced set of pre-selected markers. Cross-validation within two training populations phenotyped for frost tolerance and winter hardiness underpinned the importance of Fr-A2 for frost tolerance especially when upweighting its effect in genomic prediction models, while a combined genomic selection index increased the prediction accuracy for an independent validation population in comparison to training with winter hardiness data alone. The prediction accuracy could moreover be maintained with pre-selected marker sets, which is highly relevant when employing cost reducing fingerprinting techniques such as targeted genotyping-by-sequencing. Genomic selection showed thus large potential to improve or maintain the performance of winter wheat for these difficult, costly, and laborious to phenotype traits.

The Photoperiod-Insensitive Allele Ppd-D1a Promotes Earlier Flowering in Rht12 Dwarf Plants of Bread Wheat

The gibberellin-responsive dwarfing gene Rht12 can significantly reduce plant height without changing seedling vigor and substantially increase ear fertility in bread wheat (Triticum aestivum. L). However, Rht12 delays heading date and anthesis date, hindering the use of Rht12 in wheat improvement. To promote early flowering of the Rht12 dwarf plants, the photoperiod-insensitive allele Ppd-D1a was introduced through a cross between Jinmai47 (Ppd-D1a) and Karcagi (Rht12). The results showed that Ppd-D1a can rescue the delaying effect of Rht12 on flowering time and promote earlier flowering by 9.0 days (163.2°Cd) in the Rht12 dwarf plants by shortening the late reproduction phase. Plant height was reduced by Rht12 (43.2%) and Ppd-D1a (10.9%), achieving dwarf plants with higher lodging resistance. Ear fertility, like the grain number per spike, was significantly increased by Rht12 (21.3%), while it was reduced by Ppd-D1a (6.5%). However, thousand kernel weight was significantly reduced by Rht12 (12.9%) but significantly increased by Ppd-D1a (16.9%). Finally, plant yield was increased by 16.4 and 8.2%, and harvest index was increased by 24.9 and 15.4% in the Rht12 dwarf lines and tall lines with Ppd-D1a, respectively. Clearly, there was an additive interaction between Rht12 and Ppd-D1 and the introduction of Ppd-D1a advanced the flowering time and improved the yield traits of Rht12 dwarf plants, suggesting that the combination of Rht12 and Ppd-D1a would be conducive to the successful use of Rht12 in wheat breeding programs.

Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components

Phenotypic and genetic analysis of six spike and kernel characteristics in wheat revealed geographic patterns as well as long-term trends arising from breeding progress, particularly in regard to spikelet fertility, i.e. the number of kernels per spikelet, a grain yield component that appears to underlie the increase in the number of kernels per spike. Wheat is a staple crop of global relevance that faces continuous demands for improved grain yield. In this study, we evaluated a panel of 407 winter wheat cultivars for six characteristics of spike and kernel development. All traits showed a large genotypic variation and had high heritabilities. We observed geographic patterns for some traits in addition to long-term trends showing a continuous increase in the number of kernels per spike. This breeding progress is likely due to the increase in spikelet fertility, i.e. the number of kernels per spikelet. While the number of kernels per spike and spikelet fertility were significantly positively correlated, both traits showed a significant negative correlation with thousand-kernel weight. Genome-wide association mapping identified only small- and moderate-effect QTL and an effect of the phenology loci Rht-D1 and Ppd-D1 on some of the traits. The allele frequencies of some QTL matched the observed geographic patterns. The quantitative inheritance of all traits with contributions of additional small-effect QTL was substantiated by genomic prediction. Taken together, our results suggest that some of the examined traits were already the basis of grain yield progress in wheat in the past decades. A more targeted exploitation of the available variation, potentially coupled with genomic approaches, may assist wheat breeding in continuing to increase yield levels globally.

Allelic variation of vernalization and photoperiod response genes in a diverse set of North American high latitude winter wheat genotypes

The major physiological determinants of wheat (Triticum aestivum L.) phenology in a given area are a response to vernalization temperature and day length, which are at least in part, regulated by the allelic variation at the vernalization (VRN) and photoperiod (PPD) loci, respectively. Characterization of the existing genetic variation for plant phenology in winter wheat can assist breeding programs improve adaptation to local environments and to optimize wheat phenology for the changing climate. The objectives of this research were to characterize the allelic variation at the major VRN and PPD loci in a diverse panel of high latitude winter wheat genotypes (n = 203) and to associate the allelic variation with phenologic, agronomic and adaptation traits. The panel was genotyped using allele-specific markers at vernalization (VRN-A1, VRN-B1, VRN-D1 and VRN-B3) and photoperiod (PPD-A1, PPD-B1, and PPD-D1) loci and phenotyped for agronomically-important traits. Though photoperiod sensitivity was more prevalent, most of the variation in the phenology of the winter wheat panel was explained by allelic variation at PPD-D1, PPD-A1, and the interaction between these loci. While a typical high latitude winter wheat genotype is one that carries winter alleles at all major VRN loci and photoperiod sensitive alleles at the major PPD loci, in lower latitudes where winters are milder, the presence of one or two photoperiod insensitive alleles seems to contribute to higher yield and wider adaptation.

Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.

A population of wheat multiple synthetic derivatives: an effective platform to explore, harness and utilize genetic diversity of Aegilops tauschii for wheat improvement

The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding. Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding.

Genetic dissection of pre-anthesis sub-phase durations during the reproductive spike development of wheat

Flowering time is an important factor affecting grain yield in wheat. In this study, we divided reproductive spike development into eight sub-phases. These sub-phases have the potential to be delicately manipulated to increase grain yield. We measured 36 traits with regard to sub-phase durations, determined three grain yield-related traits in eight field environments and mapped 15 696 single nucleotide polymorphism (SNP, based on 90k Infinium chip and 35k Affymetrix chip) markers in 210 wheat genotypes. Phenotypic and genetic associations between grain yield traits and sub-phase durations showed significant consistency (Mantel test; r = 0.5377, P < 0.001). The shared quantitative trait loci (QTLs) revealed by the genome-wide association study suggested a close association between grain yield and sub-phase duration, which may be attributed to effects on spikelet initiation/spikelet number (double ridge to terminal spikelet stage, DR-TS) and assimilate accumulation (green anther to anthesis stage, GA-AN). Moreover, we observed that the photoperiod-sensitivity allele at the Ppd-D1 locus on chromosome 2D markedly extended all sub-phase durations, which may contribute to its positive effects on grain yield traits. The dwarfing allele at the Rht-D1 (chromosome 4D) locus altered the sub-phase duration and displayed positive effects on grain yield traits. Data for 30 selected genotypes (from among the original 210 genotypes) in the field displayed a close association with that from the greenhouse. Most importantly, this study demonstrated specific connections to grain yield in narrower time windows (i.e. the eight sub-phases), rather than the entire stem elongation phase as a whole.