Climate change-driven heat and drought stresses during reproductive stages significantly threaten wheat productivity. To investigate the genetic and physiological basis of combined heat-drought (HD) tolerance, we evaluated 345 wheat genotypes under three environments of HD stresses, non-stress glasshouse conditions and a late-sowing field trial. HD stresses caused significant reductions in chlorophyll content, flag leaf area, biomass, seed-setting rate and grain weight-related traits. Notably, HD-tolerant lines maintained higher grain weight, grain number and chlorophyll retention, with less than half the reductions observed in sensitive genotypes. A genome-wide association study using a 40K single-nucleotide polymorphism (SNP) array identified 124 candidate SNPs (cSNPs) associated with 51 traits across three environments with 78 cSNPs associated with HD tolerance. In total, 24 cSNP blocks exhibited pleiotropic associations with multiple traits under those three environments. Tight genomic co-localisations were detected between chlorophyll content (SPAD or CCM200 values), flag leaf width, seed-setting rate and grain yield components (thousand grain weight, grain number per spike), with superior haplotypes identified, supporting their utility in selections. Stay-green traits appeared to contribute significantly to yield stability under HD stresses. Those results provide valuable genomic and physiological insights into wheat HD tolerance for future targeted wheat breeding.

The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide, with remarkable progress in China. Drawing on two sets of data, production yield from the National Bureau of Statistics of China and experimental yield from literature, this study aims to (1) illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China, (2) explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China, and (3) compare the yield gap between experimental yield and production yield. The results show that both the production and experimental yields significantly increased along with the variety replacement. The national annual yield increase ratio for the production yield was 1.67% from 1978 to 2018, varying from 0.96% in Sichuan Province to 2.78% in Hebei Province; such ratio for the experimental yield was 1.13% from 1937 to 2016. The yield gap between experimental and production yields decreased from the 1970s to the 2010s. This study reveals significant increases in some yield components consequent to variety replacement, including thousand-grain weight, kernel number per spike, and grain number per square meter; however, no change is shown in spike number per square meter. The biomass and harvest index consistently and significantly increased, whereas the plant height decreased significantly.

To improve the yield and quality of wheat is of great importance for food security worldwide. One of the most effective and significant approaches to achieve this goal is to enhance the nitrogen use efficiency (NUE) in wheat. In this review, a comprehensive understanding of the factors involved in the process of the wheat nitrogen uptake, assimilation and remobilization of nitrogen in wheat were introduced. An appropriate definition of NUE is vital prior to its precise evaluation for the following gene identification and breeding process. Apart from grain yield (GY) and grain protein content (GPC), the commonly recognized major indicators of NUE, grain protein deviation (GPD) could also be considered as a potential trait for NUE evaluation. As a complex quantitative trait, NUE is affected by transporter proteins, kinases, transcription factors (TFs) and micro RNAs (miRNAs), which participate in the nitrogen uptake process, as well as key enzymes, circadian regulators, cross-talks between carbon metabolism, which are associated with nitrogen assimilation and remobilization. A series of quantitative genetic loci (QTLs) and linking markers were compiled in the hope to help discover more efficient and useful genetic resources for breeding program. For future NUE improvement, an exploration for other criteria during selection process that incorporates morphological, physiological and biochemical traits is needed. Applying new technologies from phenomics will allow high-throughput NUE phenotyping and accelerate the breeding process. A combination of multi-omics techniques and the previously verified QTLs and molecular markers will facilitate the NUE QTL-mapping and novel gene identification.

Polyphenol oxidase (PPO) activity is a major cause of the undesirable brown color of wheat-based products. Ppo1, a major gene for PPO activity, was cloned based on sequence homology in previous studies; however, its function and regulation mechanism remain unclear. In this study, the function and genetic regulation of Ppo1 were analyzed using RNA interference (RNAi) and Targeting Induced Local Lesions IN Genomes (TILLING) technology, and superior mutants were identified. Compared with the control, the level of Ppo1 transcript in RNAi transgenic lines was drastically decreased by 15.5%–60.9% during grain development, and PPO activity was significantly reduced by 12.9%–20.4%, confirming the role of Ppo1 in PPO activity. Thirty-two Ppo1 mutants were identified in the ethyl methanesulfonate (EMS)-mutagenized population, including eight missense mutations, 16 synonymous mutations, and eight intron mutations. The expression of Ppo1 was reduced significantly by 6.7%–37.1% and 10.1%–54.4% in mutants M092141 (G311S) and M091098 (G299R), respectively, in which PPO activity was decreased by 29.7% and 28.8%, respectively, indicating that mutation sites of two mutants have important effects on PPO1 function. Sequence and structure analysis revealed that the two sites were highly conserved among 74 plant species, where the frequency of glycine was 94.6% and 100%, respectively, and adjacent to the entrance of the hydrophobic pocket of the active site. The M092141 and M091098 mutants can be used as important germplasms to develop wheat cultivars with low grain PPO activity. This study provided important insights into the molecular mechanism of Ppo1 and the genetic improvement of wheat PPO activity.

Phenotypic plasticity is the ability of an individual genotype to express phenotype variably in different environments. This study investigated the plasticity of yield-related traits of bread wheat by utilising 225 doubled haploid (DH) lines developed from cv. Westonia and cv. Kauz, through two field trials in Western Australia. Plasticity was quantified via two previously published methods: responsiveness to varying ecological conditions and slopes of reaction norms. The spikelets/spike was the most plastic trait, with an overall plasticity of 1.62. The least plastic trait was grain protein content, with an overall plasticity of 0.79. The trait hierarchy based on phenotypic plasticity was spikelets/spike > thousand kernel weight > seed number > seed length > grain yield > grain protein content. An increase in yield plasticity of 0.1 was associated with an increase in maximum yield of 4.45 kg ha−1. The plasticity of seed number and grain protein content were significantly associated with yield plasticity. The maximal yield was positively associated with spikelets/spike and grain yield, whereas it negatively associated with grain protein content. In contrast, the minimal yield was found to be negatively related to the plasticity of spikelets/spike and the plasticity of grain yield, whereas it was not related to grain protein content plasticity. Seed number and seed length exhibited plastic responses at the higher fertilisation state while remaining relatively stable at the lower fertilisation state for the wheat DH population. The finding of the current study will play a key role in wheat improvement under the changing climate. Seed length and seed number should be the breeding target for achieving stable yield in adverse environmental conditions.

The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of ‘Westonia’ × ‘Kauz’. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat ‘Westonia’. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed.

Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding.

Wild emmer wheat (WEW) played a central role in wheat evolution. During the long process of evolution, rapid alteration and sporadic genomic changes occurred in wheat resulting gene modifications and loss to some extent. WEW contains numerous genes that are absent in modern wheat gene pool, which might be useful for improving wheat. But, there is a lack of investigation in exploring genotype to phenotype associations in WEW. This study conducted genome wide association study (GWAS) on 19 shoot morphological traits and identified the genetic loci associated with several phenotypes from a collection of 263 WEW accessions using 90K SNP (single nucleotide polymorphism). A total of 11,393 SNP markers which passed the data quality screening, were used to conduct the GWAS analysis using a mixed linear model in TASSEL (Trait Analysis by Association, Evolution, and Linkage) software. A total of 857 significant MTAs (marker-trait association) were identified harbouring on all fourteen chromosomes, among which 81 were highly significant. On average, each significant MTA explained approximately 7% of phenotypic variance. The most significant MTAs were for tiller number, biomass, and some of yield related traits such as yield/plant and seed size. Putative candidate genes were also predicted for highly significant MTAs using the bioinformatics platform. The majority of the selected MTAs showed significant differences between alternative alleles for the corresponding phenotypes indicating their potential to be used in the breeding program. The genetic loci, contributing significantly to phenotypic variation, identified from this study will be useful in improving wheat morphological traits.

Wheat grain yield is generally sink-limited during grain filling. The grain-filling rate (GFR) plays a vital role but is poorly studied due to the difficulty of phenotype surveys. This study explored the grain-filling traits in a recombinant inbred population and wheat collection using two highly saturated genetic maps for linkage analysis and genome-wide association study (GWAS). Seventeen stable additive quantitative trait loci (QTLs) were identified on chromosomes 1B, 4B, and 5A. The linkage interval between IWB19555 and IWB56078 showed pleiotropic effects on GFR(1), GFR(max), kernel length (KL), kernel width (KW), kernel thickness (KT), and thousand kernel weight (TKW), with the phenotypic variation explained (PVE) ranging from 13.38% (KW) to 33.69% (TKW). 198 significant marker-trait associations (MTAs) were distributed across most chromosomes except for 3D and 4D. The major associated sites for GFR included IWB44469 (11.27%), IWB8156 (12.56%) and IWB24812 (14.46%). Linkage analysis suggested that IWB35850, identified through GWAS, was located in approximately the same region as QGFRmax2B.3-11, where two high-confidence candidate genes were present. Two important grain weight (GW)-related QTLs colocalized with grain-filling QTLs. The findings contribute to understanding the genetic architecture of the GFR and provide a basic approach to predict candidate genes for grain yield trait QTLs.

Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.

Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.

Reproductive stage frost poses a major constraint for wheat production in countries such as Australia. However, little progress has been made in identifying key genes to overcome the constraint. In the present study, a severe frost event hit two large-scale field trials consisting of six doubled haploid (DH) wheat populations at reproductive stage (young microspore stage) in Western Australia, leading to the identification of 30 robust frost QTL on 17 chromosomes. The major 18 QTL with the phenotype variation over 9.5% were located on 13 chromosomes including 2A, 2B, 2D, 3A, 4A, 4B, 4D, 5A, 5D, 6D, 7A, 7B and 7D. Most frost QTL were closely linked to the QTL of anthesis, maturity, Zadok stages as well as linked to anthesis related genes. Out of those, six QTL were repetitively detected on the homologous regions on 2B, 4B, 4D, 5A, 5D, 7A in more than two populations. Results showed that the frost damage is associated with alleles of Vrn-A1a, Vrn-D1a, Rht-B1b, Rht-D1b, and the high copy number of Ppd-B1. However, anthesis QTL and anthesis related genes of Vrn-B1a and TaFT3-1B on chromosomes 5B and 1B did not lead to frost damage, indicating that these early-flowering phenotype related genes are compatible with frost tolerance and thus can be utilised in breeding. Our results also indicate that wild-type alleles Rht-B1a and Rht-D1a can be used when breeding for frost-tolerant varieties without delaying flowering time.

The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSeq v1.0) were analyzed based on the Spearman rank correlation coefficients. As results, the three constructed genetic maps of Sp7A, G7A and Sp7A_G7A showed high collinearity with the Con_map_Wang2014 and the physical map, and importantly, the collinearity level between our constructed maps and the wheat physical map is higher than that between the Con_map_Wang2014 and the physical map. The seed coat color QTL detected in both populations under multiple environments were on the region (745.73–760.14 Mbp) of the seed color gene R-B1/Tamyb10-B1 (TraesCS3B02G515900, 3B: 757,918,264–757,920,082 bp). The validated consensus map will be beneficial for QTL mapping, positional cloning, meta-QTL analysis and wheat breading.

For improving lodging resistance and increasing grain yield in wheat in the Yellow-Huai River Basin in China, different sowing modes have been investigated. Conventionally, the small-flat-plot sowing mode has been adopted in wheat cultivation. However, this sowing mode leads to heavy lodging and low land use efficiency. In this study, a new sowing mode, high-low-plot sowing mode with two more rows sowed on the high plot, was investigated. Two cultivars, Hengguan 35 and Jimai 44 were used for two seasonal field experiments from 2018 to 2020. The results showed that grain yield improved with the high-low sowing mode by as much as 25% since more spikes per unit area were observed concomitant with reduced stem lodging. The grain yield increase was mainly due to the enhanced spike number per m(2), while the lodging resistance was improved through the lowered plant height and the center of gravity height. This research proves that the high-low-plot sowing mode is an improved sowing mode for producing greater grain yield with better lodging resistance in the wheat production area in northern China.

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.

Introgression of a high-molecular-weight glutenin subunit (HMW-GS) allele, 1Ay21∗, into commercial wheat cultivars increased overall grain protein content and bread-making quality, but the role of proteins beyond this HMW-GS itself was unknown. In addition to increased abundance of 1Ay HMW-GS, 115 differentially accumulated proteins (DAPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines. Functional category analysis showed that the DAPs were predominantly other storage proteins and proteins involved in protein synthesis, protein folding, protein degradation, stress response, and grain development. Nearly half the genes encoding the DAPs showed strong coexpression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21∗ improves grain protein content but also directs selection of protein candidates for future wheat quality breeding programs.

Two challenges that the global wheat industry is facing are a lowering nitrogen-use efficiency (NUE) and an increase in the reporting of wheat-protein related health issues. Sulphur deficiencies in soil has also been reported as a global issue. The current study used large-scale field and glasshouse experiments to investigate the sulphur fertilization impacts on sulphur deficient soil. Here we show that sulphur addition increased NUE by more than 20% through regulating glutamine synthetase. Alleviating the soil sulphur deficiency highly significantly reduced the amount of gliadin proteins indicating that soil sulphur levels may be related to the biosynthesis of proteins involved in wheat-induced human pathologies. The sulphur-dependent wheat gluten biosynthesis network was studied using transcriptome analysis and amino acid metabolomic pathway studies. The study concluded that sulphur deficiency in modern farming systems is not only having a profound negative impact on productivity but is also impacting on population health.

The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.