Delimitation of the Earliness per se D1 (Eps-D1) flowering gene to a subtelomeric chromosomal deletion in bread wheat (Triticum aestivum)

Identification of Quantitative Trait Loci Associated with Plant Adaptation Traits Using Nested Association Mapping Population

This study evaluated 290 recombinant inbred lines (RILs) of the nested association mapping (NAM) population from the UK. The population derived from 24 families, where a common parent was "Paragon," one of the UK's spring wheat cultivar standards. All genotypes were tested in two regions of Kazakhstan at the Kazakh Research Institute of Agriculture and Plant Industry (KRIAPI, Almaty region, Southeast Kazakhstan, 2019-2022 years) and Alexandr Barayev Scientific-Production Center for Grain Farming (SPCGF, Shortandy, Akmola region, Northern Kazakhstan, 2019-2022 years). The studied traits consisted of plant adaptation-related traits, including heading date (HD, days), seed maturation date (SMD, days), plant height (PH, cm), and peduncle length (PL, cm). In addition, the yield per m2 was analyzed in both regions. Based on a field evaluation of the population in northern and southeastern Kazakhstan and using 10,448 polymorphic SNP (single-nucleotide polymorphism) markers, the genome-wide association study (GWAS) allowed for detecting 74 QTLs in four studied agronomic traits (HD, SMD, PH, and PL). The literature survey suggested that 16 of the 74 QTLs identified in our study had also been detected in previous QTL mapping studies and GWASs for all studied traits. The results will be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.

A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat

Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.

Revisiting the role and mechanism of ELF3 in circadian clock modulation

The gene encoding EARLY FLOWERING3 (ELF3) is necessary for photoperiodic flowering and the normal regulation of circadian rhythms. It provides important information at the cellular level to uncover the biological mechanisms that improve plant growth and development. ELF3 interactions with transcription factors such as BROTHER OF LUX ARRHYTHMO (BOA), LIGHT-REGULATED WD1 (LWD1), PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), PHYTOCHROME-INTERACTING FACTOR 7 (PIF7), and LUX ARRHYTHMO (LUX) suggest a role in evening complex (EC) independent pathways, demanding further investigation to elucidate the EC-dependent versus EC-independent mechanisms. The ELF3 regulation of flowering time about photoperiod and temperature variations can also optimize crop cultivation across diverse latitudes. In this review paper, we summarize how ELF3's role in the circadian clock and light-responsive flowering control in crops offers substantial potential for scientific advancement and practical applications in biotechnology and agriculture. Despite its essential role in crop adaptation, very little is known in many important crops. Consequently, comprehensive and targeted research is essential for extrapolating ELF3-related insights from Arabidopsis to other crops, utilizing both computational and experimental methodologies. This research should prioritize investigations into ELF3's protein-protein interactions, post-translational modifications, and genomic targets to elucidate its contribution to accurate circadian clock regulation.

Identification of the causal mutation in early heading mutant of bread wheat (Triticum aestivum L.) using MutMap approach

In bread wheat (Triticum aestivum L.), fine-tuning the heading time is essential to maximize grain yield. Photoperiod-1 (Ppd-1) and VERNALIZATION 1 (Vrn-1) are major genes affecting photoperiod sensitivity and vernalization requirements, respectively. These genes have predominantly governed heading timing. However, Ppd-1 and Vrn-1 significantly impact heading dates, necessitating another gene that can slightly modify heading dates for fine-tuning. In this study, we developed an early heading mutant from the ethyl methanesulfonate-mutagenized population of the Japanese winter wheat cultivar "Kitahonami." MutMap analysis identified a nonsense mutation in the clock component gene Wheat PHYTOCLOCK 1/LUX ARRHYTHMO (WPCL-D1) as the probable SNP responsible for the early heading mutant on chromosome 3D. Segregation analysis using F2 and F3 populations confirmed that plants carrying the wpcl-D1 allele headed significantly earlier than those with the functional WPCL-D1. The early heading mutant exhibited increased expression levels of Ppd-1 and circadian clock genes, such as WPCL1 and LATE ELONGATED HYPOCOTYL (LHY). Notably, the transcript accumulation levels of Ppd-A1 and Ppd-D1 were influenced by the copy number of the functional WPCL1 gene. These results suggest that a loss-of-function mutation in WPCL-D1 is the causal mutation for the early heading phenotype. Adjusting the functional copy number of WPCL1 will be beneficial in fine-tuning of heading dates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01478-5.

Molecular Markers Help with Breeding for Agronomic Traits of Spring Wheat in Kazakhstan and Siberia

The Kazakhstan-Siberia Network for Spring Wheat Improvement (KASIB) was established in 2000, forming a collaboration between breeding and research programs through biannual yield trials. A core set of 142 genotypes from 15 breeding programs was selected, genotyped for 81 DNA functional markers and phenotyped for 10 agronomic traits at three sites in Kazakhstan (Karabalyk, Shortandy and Shagalaly) and one site in Russia (Omsk) in 2020-2022. The study aim was to identify markers demonstrating significant effects on agronomic traits. The average grain yield of individual trials varied from 118 to 569 g/m2. Grain yield was positively associated with the number of days to heading, plant height, number of grains per spike and 1000-kernel weight. Eight DNA markers demonstrated significant effects. The spring-type allele of the Vrn-A1 gene accelerated heading by two days (5.6%) and was present in 80% of the germplasm. The winter allele of the Vrn-A1 gene significantly increased grain yield by 2.7%. The late allele of the earliness marker per se, TaMOT1-D1, delayed development by 1.9% and increased yield by 4.5%. Translocation of 1B.1R was present in 21.8% of the material, which resulted in a 6.2% yield advantage compared to 1B.1B germplasm and a reduction in stem rust severity from 27.6 to 6.6%. The favorable allele of TaGS-D1 increased both kernel weight and yield by 2-3%. Four markers identified in ICARDA germplasm, ISBW2-GY (Kukri_c3243_1065, 3B), ISBW3-BM (TA004946-0577, 1B), ISBW10-SM2 (BS00076246_51, 5A), ISBW11-GY (wsnp_Ex_c12812_20324622, 4A), showed an improved yield in this study of 3-4%. The study recommends simultaneous validation and use of selected markers in KASIB's network.

Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time

KEY MESSAGE

We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.

PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon

Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.

Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus

Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.

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.

A 'wiring diagram' for sink strength traits impacting wheat yield potential

Identifying traits for improving sink strength is a bottleneck to increasing wheat yield. The interacting processes determining sink strength and yield potential are reviewed and visualized in a set of 'wiring diagrams', covering critical phases of development (and summarizing known underlying genetics). Using this framework, we reviewed and assembled the main traits determining sink strength and identified research gaps and potential hypotheses to be tested for achieving gains in sink strength. In pre-anthesis, grain number could be increased through: (i) enhanced spike growth associated with optimized floret development and/or a reduction in specific stem-internode lengths and (ii) improved fruiting efficiency through an accelerated rate of floret development, improved partitioning between spikes, or optimized spike cytokinin levels. In post-anthesis, grain, sink strength could be augmented through manipulation of grain size potential via ovary size and/or endosperm cell division and expansion. Prospects for improving spike vascular architecture to support all rapidly growing florets, enabling the improved flow of assimilate, are also discussed. Finally, we considered the prospects for enhancing grain weight realization in relation to genetic variation in stay-green traits as well as stem carbohydrate remobilization. The wiring diagrams provide a potential workspace for breeders and crop scientists to achieve yield gains in wheat and other field crops.

A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800

The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars.

Allelic Variations in Phenology Genes of Eastern U.S. Soft Winter and Korean Winter Wheat and Their Associations with Heading Date

Wheat heading time is genetically controlled by phenology genes including vernalization (Vrn), photoperiod (Ppd) and earliness per se (Eps) genes. Characterization of the existing genetic variation in the phenology genes of wheat would provide breeding programs with valuable genetic resources necessary for the development of wheat varieties well-adapted to the local environment and early-maturing traits suitable for double-cropping system. One hundred forty-nine eastern U.S. soft winter (ESW) and 32 Korean winter (KW) wheat genotypes were characterized using molecular markers for Vrn, Ppd, Eps and reduced-height (Rht) genes, and phenotyped for heading date (HD) in the eastern U.S. region. The Ppd-D1 and Rht-D1 genes exhibited the highest genetic diversity in ESW and KW wheat, respectively. The genetic variations for HD of ESW wheat were largely contributed by Ppd-B1, Ppd-D1 and Vrn-D3 genes. The Rht-D1 gene largely contributed to the genetic variation for HD of KW wheat. KW wheat headed on average 14 days earlier than ESW wheat in each crop year, largely due to the presence of the one-copy vrn-A1 allele in the former. The development of early-maturing ESW wheat varieties could be achieved by selecting for the one-copy vrn-A1 and vrn-D3a alleles in combination with Ppd-B1a and Ppd-D1a photoperiod insensitive alleles.

Advancing understanding of oat phenology for crop adaptation

Oat (Avena sativa) is an annual cereal grown for forage, fodder and grain. Seasonal flowering behaviour, or phenology, is a key contributor to the success of oat as a crop. As a species, oat is a vernalization-responsive long-day plant that flowers after winter as days lengthen in spring. Variation in both vernalization and daylength requirements broadens adaptation of oat and has been used to breed modern cultivars with seasonal flowering behaviours suited to different regions, sowing dates and farming practices. This review examines the importance of variation in oat phenology for crop adaptation. Strategies to advance understanding of the genetic basis of oat phenology are then outlined. These include the potential to transfer knowledge from related temperate cereals, particularly wheat (Triticum aestivum) and barley (Hordeum vulgare), to provide insights into the potential molecular basis of variation in oat phenology. Approaches that use emerging genomic resources to directly investigate the molecular basis of oat phenology are also described, including application of high-resolution genome-wide diversity surveys to map genes linked to variation in flowering behaviour. The need to resolve the contribution of individual phenology genes to crop performance by developing oat genetic resources, such as near-isogenic lines, is emphasised. Finally, ways that deeper knowledge of oat phenology can be applied to breed improved varieties and to inform on-farm decision-making are outlined.

Circadian regulation of the transcriptome in a complex polyploid crop

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

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.

Multi-donor × elite-based populations reveal QTL for low-lodging wheat

Low-lodging high-yielding wheat germplasm and SNP-tagged novel alleles for lodging were identified in a process that involved selecting donors through functional phenotyping for underlying traits with a designed phenotypic screen, and a crossing strategy involving multiple-donor × elite populations. Lodging is a barrier to achieving high yield in wheat. As part of a study investigating the potential to breed low-lodging high-yielding wheat, populations were developed crossing four low-lodging high-yielding donors selected based on lodging related traits, with three cultivars. Lodging was evaluated in single rows in an early generation and subsequently in plots in 2 years with contrasting lodging environment. A large number of lines lodged less than their recurrent parents, and some were also higher yielding. Heritability for lodging was high, but the genetic correlation between contrasting environments was intermediate-low. Lodging genotypic rankings in single rows did not correlate well with plots. Populations from the highest lodging background were genotyped (90 K iSelect BeadChip array). Fourteen markers on nine chromosomes were associated with lodging, differing under high- versus low-lodging conditions. Of the fourteen markers, ten were found to co-locate with previously identified QTL for lodging-related traits or at homoeologous locations for previously identified lodging-related QTL, while the remaining four markers (in chromosomes 2D, 4D, 7B and 7D) appear to map to novel QTL for lodging. Lines with more favourable markers lodged less, suggesting value in these markers as a selection tool. This study demonstrates that the combination of donor functional phenotyping, screen design and crossing strategy can help identify novel alleles in germplasm without requiring extensive bi-parental populations.

Functional characterization of genes with daily expression patterns in common wheat

Our findings suggest most wheat biological processes are under the control of the daily expressed genes. Plant circadian rhythms represent daily changes in the activity of various processes, which are based on changes in the levels of gene expression and protein synthesis. In wheat, some key components of plant circadian clock have been identified, but there is little data on the daily expression and interactions of these genes. To study the common wheat daily transcriptome, RNA sequencing was performed. Using these data, genes expressed in daily pattern and the metabolic pathways controlled by them were identified: responses to stimuli and nutrients, transport, photoperiodism, photomorphogenesis, synthesis and degradation of different metabolites, and regulation of the processes of RNA synthesis. It was shown that a significant part of the transcriptome can vary greatly daily. Five expression patterns were identified. They were characterized by peaks at different time points and described the genes underlying these patterns. The analysis of the enrichment of gene ontology terms with various patterns allowed us to describe the main metabolic pathways in each group. Wheat homologs of the genes related to circadian clock in Arabidopsis were identified. Most of them were represented by three homoeologous genes expressed uniformly. Comparison of their expression patterns demonstrated a shift in the expression peaks for some core and accessory genes; the majority of wheat circadian genes were expressed in accordance with Arabidopsis homologs. This may indicate a similar functional role of these genes in wheat.

The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome

The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.

Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat

Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.

Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10⁻¹⁴) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.

Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations

In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.

Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study

Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.

Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

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.

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.

Resolving a QTL complex for height, heading, and grain yield on chromosome 3A in bread wheat

Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that 'late' alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation.

Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat

Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.

Temperature response of wheat affects final height and the timing of stem elongation under field conditions

In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.

Temperature response of wheat affects final height and the timing of stem elongation under field conditions

In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.

Phenology and related traits for wheat adaptation

Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.

Earliness per se×temperature interaction: consequences on leaf, spikelet, and floret development in wheat

Wheat adaptation can be fine-tuned by earliness per se (Eps) genes. Although the effects of Eps genes are often assumed to act independently of the environment, previous studies have shown that they exhibit temperature sensitivity. The number of leaves and phyllochron are considered determinants of flowering time and the numerical components of yield include spikelets per spike and fertile floret number within spikelets. We studied the dynamics of leaf, spikelet, and floret development in near isogenic lines with either late or early alleles of Eps-D1 under seven temperature regimes. Leaf appearance dynamics were modulated by temperature, and Eps alleles had a greater effect on the period from flag leaf to heading than phyllochron. In addition, the effects of the Eps alleles on spikelets per spike were minor, and more related to spikelet plastochron than the duration of the early reproductive phase. However, fertile floret number was affected by the interaction between Eps alleles and temperature. So, at 9 °C, Eps-early alleles had more fertile florets than Eps-late alleles, at intermediate temperatures there was no significant difference, and at 18 °C (the highest temperature) the effect was reversed, with lines carrying the late allele producing more fertile florets. These effects were mediated through changes in floret survival; there were no clear effects on the maximum number of floret primordia.

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r ² = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (F _st ) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.

Haplotype block analysis of an Argentinean hexaploid wheat collection and GWAS for yield components and adaptation

BACKGROUND

Increasing wheat (Triticum aestivum L.) production is required to feed a growing human population. In order to accomplish this task a deeper understanding of the genetic structure of cultivated wheats and the detection of genomic regions significantly associated with the regulation of important agronomic traits are necessary steps. To better understand the genetic basis and relationships of adaptation and yield related traits, we used a collection of 102 Argentinean hexaploid wheat cultivars genotyped with the 35k SNPs array, grown from two to six years in three different locations. Based on SNPs data and gene-related molecular markers, we performed a haplotype block characterization of the germplasm and a genome-wide association study (GWAS).

RESULTS

The genetic structure of the collection revealed four subpopulations, reflecting the origin of the germplasm used by the main breeding programs in Argentina. The haplotype block characterization showed 1268 blocks of different sizes spread along the genome, including highly conserved regions like the 1BS chromosome arm where the 1BL/1RS wheat/rye translocation is located. Based on GWAS we identified ninety-seven chromosome regions associated with heading date, plant height, thousand grain weight, grain number per spike and fruiting efficiency at harvest (FEh). In particular FEh stands out as a promising trait to raise yield potential in Argentinean wheats; we detected fifteen haplotypes/markers associated with increased FEh values, eleven of which showed significant effects in all three evaluated locations. In the case of adaptation, the Ppd-D1 gene is consolidated as the main determinant of the life cycle of Argentinean wheat cultivars.

CONCLUSION

This work reveals the genetic structure of the Argentinean hexaploid wheat germplasm using a wide set of molecular markers anchored to the Ref Seq v1.0. Additionally GWAS detects chromosomal regions (haplotypes) associated with important yield and adaptation components that will allow improvement of these traits through marker-assisted selection.

Circadian Rhythms in Plants

The circadian oscillator is a complex network of interconnected feedback loops that regulates a wide range of physiological processes. Indeed, variation in clock genes has been implicated in an array of plant environmental adaptations, including growth regulation, photoperiodic control of flowering, and responses to abiotic and biotic stress. Although the clock is buffered against the environment, maintaining roughly 24-h rhythms across a wide range of conditions, it can also be reset by environmental cues such as acute changes in light or temperature. These competing demands may help explain the complexity of the links between the circadian clock network and environmental response pathways. Here, we discuss our current understanding of the clock and its interactions with light and temperature-signaling pathways. We also describe different clock gene alleles that have been implicated in the domestication of important staple crops.

Genome-Wide Analyses Reveal Footprints of Divergent Selection and Drought Adaptive Traits in Synthetic-Derived Wheats

Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (t-test, Tajima’s D, nucleotide diversity (π), Fst, and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 ‘selective sweeps’, out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as TaElf3-D1 (1D) for earliness per se (Eps), TaCKX-D1 (3D), TaGS1a (6D) and TaGS-D1 (7D) for grain size, weight and morphology, TaCwi-D1 (5D) influencing drought tolerance, and Vrn-D3 (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.

From markers to genome-based breeding in wheat

Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050. There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality.

Earliness Per Se by Temperature Interaction on Wheat Development

Differences in time to heading that remain after photoperiod and vernalisation requirements have been saturated are classified as earliness per se (Eps) effects. It has been commonly assumed that Eps genes are purely constitutive and independent of environment, although the likely effect of temperature on Eps effects in hexaploid wheat has never been tested. We grew four near isogenic lines (NILs) for the Eps gene located in chromosome 1D (Eps-D1) at 6, 9, 12, 15, 18, 21 and 24 °C. In line with expectations we found that lines carrying the Eps-late allele were always later than those with Eps-early alleles. But in addition, we reported for the first time that the magnitude of the effect increased with decreasing temperature: an Eps x temperature interaction in hexaploid wheat. Variation in heading time due to Eps x temperature was associated with an increase in sensitivity to temperature mainly during late reproductive phase. Moreover, we showed that Eps alleles exhibited differences in cardinal (base, optimum, maximum) temperatures and that the expression of ELF3, (the likely candidate for Eps-D1) also interacted with temperature.

Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat

BACKGROUND

The extensive adaptability of polyploidy wheat is attributed to its complex genome, and accurately controlling heading stage is a prime target in wheat breeding process. Wheat heading stage is an essential growth and development processes since it starts at a crucial point in the transition from vegetative phase to reproductive phase.

MAIN BODY

Heading stage is mainly decided by vernalization, photoperiod, hormone (like gibberellic acid, GA), and earliness per se (Eps). As a polyploidy species, common wheat possesses the abundant genetic variation, such as allelic variation, copy number variation etc., which have a strong effect on regulation of wheat growth and development. Therefore, understanding genetic manipulation of heading stage is pivotal for controlling the heading stage in wheat. In this review, we summarized the recent advances in the genetic regulatory mechanisms and abundant variation in genetic diversity controlling heading stage in wheat, as well as the interaction mechanism of different signals and the contribution of different genetic variation. We first summarized the genes involved in vernalization, photoperoid and other signals cross-talk with each other to control wheat heading stage, then the abundant genetic variation related to signal components associated with wheat heading stage was also elaborated in detail.

CONCLUSION

Our knowledge of the regulatory network of wheat heading can be used to adjust the duration of the growth phase for the purpose of acclimatizing to different geographical environments.

Genetic modification of spikelet arrangement in wheat increases grain number without significantly affecting grain weight

Crop yield is determined by the acquisition and allocation of photoassimilates in sink organs. Therefore, genetic modification of sink size is essential for understanding the complex signaling network regulating sink strength and source activities. Sink size in wheat depends on the number of spikelets per spike, floret/grain number per spikelet as well as the grain weight or dry matter accumulation. Hence, increasing spikelet number and improving sink size are targets for wheat breeding. The main objective of the present work was to genetically modify the wheat spike architecture, i.e., the sink size by introgressing the 'Miracle wheat' or the bh^t-A1 allele into an elite durum wheat cv. Floradur. After four generations of backcrossing to the recurrent parent, Floradur (FL), we have successfully developed Near Isogenic Lines (NILs) with a modified spikelet arrangement thereby increasing spikelet and grain number per spike. Genotyping of bh^t-A1 NILs using the Genotyping-By-Sequencing approach revealed that the size of the introgressed donor segments carrying bh^t-A1 ranged from 2.3 to 38 cM. The size of the shortest donor segment introgressed into bh^t-A1 NILs was estimated to be 9.8 mega base pairs (Mbp). Phenotypic analysis showed that FL-bh^t-A1-NILs (BC3F2 and BC3F3) carry up to seven additional spikelets per spike, leading to up to 29% increase in spike dry weight at harvest (SDW_h). The increased SDW_h was accompanied by up to 23% more grains per spike. More interestingly, thousand kernel weight (TKW) did not show significant differences between FL-bh^t-A1-NILs and Floradur, suggesting that besides increasing spikelet number, bh^t-A1 could also be targeted for increasing grain yield in wheat. Our study suggests that the genetic modification of spikelet number in wheat can be an entry point for improving grain yield, most interestingly and also unexpectedly without the trade-off effects on TKW. Hence, FL-bh^t-A1-NILs are not only essential for increasing grain number, but also for understanding the molecular and genetic mechanism of the source-sink interaction for a clearer picture of the complex signaling network regulating sink strength and source activities.

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.

Developmental Pathways Are Blueprints for Designing Successful Crops

Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.

Genome-Wide Association Analyses Identify QTL Hotspots for Yield and Component Traits in Durum Wheat Grown under Yield Potential, Drought, and Heat Stress Environments

Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p-values 10-06 to 10-03 and the markers from the whole study explained 7-25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54-70 cM) and 2B (75-82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding.

The identification of new candidate genes Triticum aestivum FLOWERING LOCUS T3-B1 (TaFT3-B1) and TARGET OF EAT1 (TaTOE1-B1) controlling the short-day photoperiod response in bread wheat

Perception of photoperiod changes enables plants to flower under optimum conditions for survival. We used doubled haploid populations of crosses among Avalon × Cadenza, Charger × Badger and Spark × Rialto and identified short-day flowering time response quantitative trait loci (QTL) on wheat chromosomes 1BS and 1BL. We used synteny between Brachypodium distachyon and wheat to identify potential candidates for both QTL. The 1BL QTL peak coincided with TaFT3-B1, a homologue of the barley gene HvFT3, the most likely candidate gene. The 1BS QTL peak coincided with homologues of Arabidopsis thaliana SENSITIVITY TO RED LIGHT REDUCED 1, WUSCHEL-like and RAP2.7, which is also known as Zea mays TARGET OF EAT1, named TaSRR1-B1, TaWUSCHELL-B1 and TaTOE1-B1, respectively. Gene expression assays suggest that TaTOE1-B1 and TaFT3-B1 are expressed more during short days. We identified four alleles of TaFT3-B1 and three alleles of TaTOE1-B1. We studied the effect of these alleles in the Watkins and GEDIFLUX diversity panels by using 936 and 431 accessions, respectively. Loss of TaFT3-B1 by deletion was associated with late flowering. Increased TaFT3-B1 copy number was associated with early flowering, suggesting that TaFT3-B1 promotes flowering. Significant association was observed in the GEDIFLUX collection for TaTOE1-B1, a putative flowering repressor.

Wheat genomics comes of age

Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs. Key functional genomic resources will enable this, including sequenced mutant populations and gene editing technologies which are now available in wheat. Training the next-generation of genomics-enabled researchers will be essential to ensure these advances are quickly translated into farmers' fields.

Genetic and physical mapping of the earliness per se locus Eps-A (m) 1 in Triticum monococcum identifies EARLY FLOWERING 3 (ELF3) as a candidate gene

Wheat cultivars exposed to optimal photoperiod and vernalization treatments still exhibit differences in flowering time, referred to as earliness per se (Eps). We previously identified the Eps-A^m1 locus from Triticum monococcum and showed that the allele from cultivated accession DV92 significantly delays heading time and increases the number of spikelets per spike relative to the allele from wild accession G3116. Here, we expanded a high-density genetic and physical map of the Eps-A^m1 region and identified the wheat ortholog of circadian clock regulator EARLY FLOWERING 3 (ELF3) as a candidate gene. No differences in ELF3 transcript levels were found between near-isogenic lines carrying the DV92 and G3116 Eps-A^m1 alleles, but the encoded ELF3 proteins differed in four amino acids. These differences were associated with altered transcription profiles of PIF-like, PPD1, and FT1, which are known downstream targets of ELF3. Tetraploid wheat lines with combined truncation mutations in the A- and B-genome copies of ELF3 flowered earlier and had less spikelets per spike than the wild-type control under short- and long-day conditions. Both effects were stronger in a photoperiod-sensitive than in a reduced photoperiod-sensitive background, indicating a significant epistatic interaction between PPD1 and ELF3 (P < 0.0001). By contrast, the introgression of the T. monococcum chromosome segment carrying the Eps-A^m1 allele from DV92 into durum wheat delayed flowering and increased the number of spikelets per spike. Taken together, the above results support the hypothesis that ELF3 is Eps-A^m1. The ELF3 alleles identified here provide additional tools to modulate reproductive development in wheat.

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.