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Summary: Although forward‐genetics‐metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co‐mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare‐activity‐exhibiting flavonoid glycosyl‐ and methyl‐transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward‐genetics‐metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics‐assisted wheat crop improvement. [ABSTRACT FROM AUTHOR]

Summary: Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS‐box transcription factor (TF) that usually works by forming hetero‐ or homo‐dimers. We previously identified that TaVRN1 bound to an MADS‐box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1‐like gene TaFPF1‐2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS‐box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1‐2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1‐Hap1 conferred earlier flowering than TaSOC1‐Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement. [ABSTRACT FROM AUTHOR]

Summary: High‐molecular‐weight glutenin subunits (HMW‐GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW‐GS encoded by GLU‐1 loci are mainly controlled at the transcriptional level by interactions between cis‐elements and transcription factors (TFs). We previously identified a conserved cis‐regulatory module CCRM1‐1 as the most essential cis‐element for Glu‐1 endosperm‐specific high expression. However, the TFs targeting CCRM1‐1 remained unknown. Here, we built the first DNA pull‐down plus liquid chromatography‐mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1‐1. TaB3‐2A1 as proof of concept was confirmed to bind to CCRM1‐1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3‐2A1 repressed CCRM1‐1‐driven transcription activity. TaB3‐2A1 overexpression significantly reduced HMW‐GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3‐2A1 down‐regulated SSP genes and up‐regulated starch synthesis‐related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3‐2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3‐2A1 and found that TaB3‐2A1‐Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3‐2A1‐Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high‐efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu‐1 expression, and a useful gene for wheat improvement. [ABSTRACT FROM AUTHOR]

Melatonin (Mel) is a multifunctional biomolecule found in both animals and plants. In plants, the biosynthesis of Mel from tryptophan (Trp) has been delineated to comprise of four consecutive reactions. However, while the genes encoding these enzymes in rice are well characterized no systematic evaluation of the overall pathway has, as yet, been published for wheat. In the current study, the relative contents of six Mel‐pathway‐intermediates including Trp, tryptamine (Trm), serotonin (Ser), 5‐methoxy tryptamine (5M‐Trm), N‐acetyl serotonin (NAS) and Mel, were determined in 24 independent tissues spanning the lifetime of wheat. These studies indicated that Trp was the most abundant among the six metabolites, followed by Trm and Ser. Next, the candidate genes expressing key enzymes involved in the Mel pathway were explored by means of metabolite‐based genome‐wide association study (mGWAS), wherein two TDC genes, a T5H gene and one SNAT gene were identified as being important for the accumulation of Mel pathway metabolites. Moreover, a 463‐bp insertion within the T5H gene was discovered that may be responsible for variation in Ser content. Finally, a ASMT gene was found via sequence alignment against its rice homolog. Validations of these candidate genes were performed by in vitro enzymatic reactions using proteins purified following recombinant expression in Escherichia coli, transient gene expression in tobacco, and transgenic approaches in wheat. Our results thus provide the first comprehensive investigation into the Mel pathway metabolites, and a swift candidate gene identification via forward‐genetics strategies, in common wheat. [ABSTRACT FROM AUTHOR]

Genetic markers can be linked with eco‐physiological crop models to accurately predict genotype performance and individual markers' contributions in target environments, exploring interactions between genotype and environment. Here, wheat (Triticum aestivum L.) yield was dissected into seven traits corresponding to cultivar genetic coefficients in an eco‐physiological model. Loci for these traits were discovered through the genome‐wide association studies (GWAS). The cultivar genetic coefficients were derived from the loci using multiple linear regression or random forest, building a marker‐based eco‐physiological model. It is then applied to simulate wheat yields and design virtual ideotypes. The results indicated that the loci identified through GWAS explained 46%–75% variations in cultivar genetic coefficients. Using the marker‐based model, the normalized root mean square error (nRMSE) between the simulated yield and observed yield was 13.95% by multiple linear regression and 13.62% by random forest. The nRMSE between the simulated and observed maturity dates was 1.24% by multiple linear regression and 1.11% by random forest, respectively. Structural equation modelling indicated that variations in grain yield could be well explained by cultivar genetic coefficients and phenological data. In addition, 24 pleiotropic loci in this study were detected on 15 chromosomes. More significant loci were detected by the model‐based dissection method than considering yield per se. Ideotypes were identified by higher yield and more favourable alleles of cultivar genetic traits. This study proposes a genotype‐to‐phenotype approach and demonstrates novel ideas and tools to support the effective breeding of new cultivars with high yield through pyramiding favourable alleles and designing crop ideotypes. Summary statement: This study developed a novel gene‐based eco‐physiological model by linking genetic markers with cultivar genetic parameters to support effective breeding of new cultivars through pyramiding favourable alleles, designing crop ideotypes and predicting genotype and environment interactions. [ABSTRACT FROM AUTHOR]

Background and Aims Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. Methods Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018–2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. Key Results These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = −0.63, P < 0.01), flag leaf angle (r = −0.49, P < 0.01) and spike number per square metre (r = −0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. Conclusions This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: Wheat (Triticum aestivum L.) radiation use efficiency (RUE) must be raised through crop breeding to further increase the yield potential, as the harvest index is now close to its theoretical limit. Field experiments including 209 wheat cultivars which have been widely cultivated in China since the 1940s were conducted in two growing seasons (2018–2019 and 2019–2020) to evaluate the variations of phenological, physiological, plant architectural, and yield‐related traits and their contributions to RUE and to identify limiting factors for wheat yield potential. The average annual genetic gain in grain yield was 0.60% (or 45.32 kg ha−1 year−1; R2 = 0.44, P < 0.01), mainly attributed to the gain in RUE (r = 0.85, P < 0.01). The net photosynthetic rates were positively and closely correlated with grain RUE and grain yield, suggesting source as a limiting factor to future yield gains. Thirty‐four cultivars were identified, exhibiting not only high RUE, but also traits contributing to high RUE and 11 other critical traits – of known genetic basis – as potential parents for breeding to improve yield and RUE. Our findings reveal wheat traits and the associated loci conferring RUE, which are valuable for facilitating marker‐assisted breeding to improve wheat RUE and yield potential. [ABSTRACT FROM AUTHOR]

Key message: A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F1, 7,325 F2 plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. Bulked segregant RNA-seq (BSR-seq) analyses revealed 13 SNPs in the region 762.50–768.52 Mb on chromosome arm 2AL. By genome mining, we identified SNPs and InDels between the parents and contrasting bulks and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916–764,089,317 bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7–650.5 Mb), Triticum urartu (2A: 750.7–752.3 Mb), Triticum dicoccoides (2A: 771.0–774.5 Mb), Triticum turgidum (2B: 784.7–788.2 Mb), and Triticum aestivum cv. Aikang 58 (2A: 776.3–778.9 Mb) and Jagger (2A: 789.3–791.7 Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32, and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat. [ABSTRACT FROM AUTHOR]

Key message: We fine mapped QTL QTKW.caas-5DL for thousand kernel weight in wheat, predicted candidate genes and developed a breeding-applicable marker. Thousand kernel weight (TKW) is an important yield component trait in wheat, and identification of the underlying genetic loci is helpful for yield improvement. We previously identified a stable quantitative trait locus (QTL) QTKW.caas-5DL for TKW in a Doumai/Shi4185 recombinant inbred line (RIL) population. Here we performed fine mapping of QTKW.caas-5DL using secondary populations derived from 15 heterozygous recombinants and delimited the QTL to an approximate 3.9 Mb physical interval from 409.9 to 413.8 Mb according to the Chinese Spring (CS) reference genome. Analysis of genomic synteny showed that annotated genes in the physical interval had high collinearity among CS and eight other wheat genomes. Seven genes with sequence variation and/or differential expression between parents were predicted as candidates for QTKW.caas-5DL based on whole-genome resequencing and transcriptome assays. A kompetitive allele-specific PCR (KASP) marker for QTKW.caas-5DL was developed, and genotyping confirmed a significant association with TKW but not with other yield component traits in a panel of elite wheat cultivars. The superior allele of QTKW.caas-5DL was frequent in a panel of cultivars, suggesting that it had undergone positive selection. These findings not only lay a foundation for map-based cloning of QTKW.caas-5DL but also provide an efficient tool for marker-assisted selection. [ABSTRACT FROM AUTHOR]

The health benefits of whole wheat grains are partially attributed to their phenolic acid composition, especially that of trans-ferulic acid (TFA), which is a powerful natural antioxidant. Breeders and producers are becoming interested in wheat with enhanced health-promoting effects. This study investigated the effects of different nitrogen (N) application rates (0, 42, 84, 126, and 168 N kg ha−1) on the phenolic acid composition of three wheat varieties in four locations for two years. The results indicate that the different N rates did not affect the TFA concentration but that they significantly affected the concentrations of para-coumaric acid, sinapic acid, and cis-ferulic acid in the wheat grains. A statistical analysis suggested that the wheat phenolic acid composition was predominantly determined by wheat variety, though there existed some interaction effect between the wheat variety and environments. The TFA concentration of the variety Jimai 22 was generally higher (with a mean value of 726.04 µg/g) but was easily affected by the environment, while the TFA concentration of the variety Zhongmai 578 (with a mean value of 618.01 µg/g) was more stable across the different environments. The results also suggest that it is possible to develop new wheat varieties with high yield potential, good end-use properties, and enhanced nutraceutical values. [ABSTRACT FROM AUTHOR]

Root hairs play an important role in absorbing water and nutrients in crop plants. Here we optimized high-throughput root hair length (RHL) and root hair density (RHD) phenotyping in wheat using a portable Dinolite™ microscope. A collection of 24 century wide spring wheat cultivars released between 1911 and 2016 were phenotyped for RHL and RHD. The results revealed significant variations for both traits with five and six-fold variation for RHL and RHD, respectively. RHL ranged from 1.01 mm to 1.77 mm with an average of 1.39 mm, and RHD ranged from 17.08 mm−2 to 20.8 mm−2 with an average of 19.6 mm−2. Agronomic and physiological traits collected from five different environments and their best linear unbiased predictions (BLUPs) were correlated with RHL and RHD, and results revealed that relative-water contents (RWC), biomass and grain per spike (GpS) were positively correlated with RHL in both water-limited and well-watered conditions. While RHD was negatively correlated with grain yield (GY) in four environments and their BLUPs. Both RHL and RHD had positive correlation indicating the possibility of simultaneous selection of both phenotypes during wheat breeding. The expression pattern of TaRSL4 gene involved in regulation of root hair length was determined in all 24 wheat cultivars based on RNA-seq data, which indicated the differentially higher expression of the A- and D- homeologues of the gene in roots, while B-homeologue was consistently expressed in both leaf and roots. The results were validated by qRT-PCR and the expression of TaRSL4 was consistently high in rainfed cultivars such as Chakwal-50, Rawal-87, and Margallah-99. Overall, the new phenotyping method for RHL and RHD along with correlations with morphological and physiological traits in spring wheat cultivars improved our understanding for selection of these phenotypes in wheat breeding. [ABSTRACT FROM AUTHOR]

The health benefits of whole wheat consumption can be partially attributed to wheat's phytochemicals, including phenolic acids, flavonoids, alkylresorcinols, carotenoids, phytosterols, tocopherols, and tocotrienols. It is of increasing interest to produce whole wheat products that are rich in bioactive phytochemicals. This review provides the fundamentals of the chemistry, extraction, and occurrence of wheat phytochemicals and includes critical discussion of several long‐lasting issues: (1) the commonly used nomenclature on distribution of wheat phenolic acids, namely, soluble‐free, soluble‐conjugated, and insoluble‐bound phenolic acids; (2) different extraction protocols for wheat phytochemicals; and (3) the chemistry and application of in vitro antioxidant assays. This review further discusses recent advances on the effects of genotypes, environments, field management, and processing techniques including ultrafine grinding, germination, fermentation, enzymatic treatments, thermal treatments, and food processing. These results need to be interpreted with care due to varied sample preparation protocols and limitations of in vitro assays. The bioaccessibility, bioavailability, metabolism, and potential health benefits of wheat phytochemicals are also reviewed. This comprehensive and critical review will benefit scientific researchers in the field of bioactive compounds of cereal grains and also those in the cereal food industry to produce high‐quality functional foods. [ABSTRACT FROM AUTHOR]

Biofortification is a sustainable strategy to alleviate micronutrient deficiency in humans. It is necessary to improve grain zinc (GZnC) and iron concentrations (GFeC) in wheat based on genetic knowledge. However, the precise dissection of the genetic architecture underlying GZnC and GFeC remains challenging. In this study, high-resolution genome-wide association studies were conducted for GZnC and GFeC by three different models using 166 wheat cultivars and 373,106 polymorphic markers from the wheat 660K and 90K single nucleotide polymorphism (SNP) arrays. Totally, 25 and 16 stable loci were detected for GZnC and GFeC, respectively. Among them, 17 loci for GZnC and 8 for GFeC are likely to be new quantitative trait locus/loci (QTL). Based on gene annotations and expression profiles, 28 promising candidate genes were identified for Zn/Fe uptake (8), transport (11), storage (3), and regulations (6). Of them, 11 genes were putative wheat orthologs of known Arabidopsis and rice genes related to Zn/Fe homeostasis. A brief model, such as genes related to Zn/Fe homeostasis from root uptake, xylem transport to the final seed storage was proposed in wheat. Kompetitive allele-specific PCR (KASP) markers were successfully developed for two major QTL of GZnC on chromosome arms 3AL and 7AL, respectively, which were independent of thousand kernel weight and plant height. The 3AL QTL was further validated in a bi-parental population under multi-environments. A wheat multidrug and toxic compound extrusion (MATE) transporter TraesCS3A01G499300 , the ortholog of rice gene OsPEZ2 , was identified as a potential candidate gene. This study has advanced our knowledge of the genetic basis underlying GZnC and GFeC in wheat and provides valuable markers and candidate genes for wheat biofortification. [ABSTRACT FROM AUTHOR]

Key message: A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene. [ABSTRACT FROM AUTHOR]

Improving canopy photosynthetic light use efficiency and energy conversion efficiency (ε c ) is a major option to increase crop yield potential. However, so far, the diurnal and seasonal variations of canopy light use efficiency (LUE) and ε c are largely unknown due to the lack of an efficient method to estimate ε c in a high temporal resolution. Here we quantified the dynamic changes of crop canopy LUE and ε c during a day and a growing season with the canopy gas exchange method. A response curve of whole-plant carbon dioxide (CO2) flux to incident photosynthetically active radiation (PAR) was further used to calculate ε c and LUE at a high temporal resolution. Results show that the LUE of two wheat cultivars with different canopy architectures at five stages varies between 0.01 to about 0.05 mol CO2 mol–1 photon, with the LUE being higher under medium PAR. Throughout the growing season, the ε c varies from 0.5 to 3.7% (11–80% of the maximal ε c for C3 plants) with incident PAR identified as a major factor controlling variation of ε c . The estimated average ε c from tillering to grain filling stages was about 2.17%, i.e., 47.2% of the theoretical maximal. The estimated season-averaged radiation use efficiency (RUE) was 1.5–1.7 g MJ–1, which was similar to the estimated RUE based on biomass harvesting. The large variations of LUE and ε c imply a great opportunity to improve canopy photosynthesis for greater wheat biomass and yield potential. [ABSTRACT FROM AUTHOR]

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds. [ABSTRACT FROM AUTHOR]

It is important to understand the genetic gain achieved through selection of key yield traits for planning future breeding strategies in developing high yielding wheat (Triticum aestivum L.) cultivars. The aim of this study was to characterize the genetic changes and genotype × environment (G×E) interaction by additive main effect and multiplicative interactions (AMMI) for morphological, physiological, and yield component traits under five environments using 24 wheat cultivars released from 1911 to 2016 in Pakistan. There was a significant increase in grain yield (9.03 kg ha−1 yr−1, 0.37%), and plant height was reduced linearly (−0.26 cm yr−1, −0.33%). The traits waxiness, leaf rolling, harvest index, spike length, and grains per spike significantly increased but the gain was only 0.16–0.2% per year. Analysis of variance revealed that genotype, environment, and G×E interaction were highly significant (P <.01) for all traits except relative chlorophyll content, biomass, days to maturity, and number of spikes. Gene‐specific markers identified the durable resistance gene Lr67/Yr46/Sr55/Pm46 in obsolete cultivars as early as 1911, whereas the photoperiod‐insensitive allele Ppd‐D1a and reduced height alleles Rht‐B1b and Rht‐D1b were present only in the post‐1965 cultivars. Diversity analysis based on a 50K single nucleotide polymorphism genotyping array clearly differentiated temporal patterns in 24 cultivars, which was correlated with the agronomic performance of the cultivars. This dataset provided detailed insight into the performance of historical wheat cultivars and could help in devising wheat breeding strategies to focus on the traits contributing to grain yield and have slower rate of genetic progress. Core Ideas: The genetic gain in morphology of Pakistani bread wheat cultivars over 105 yr areas was assessed.Leaf rolling, waxiness, and grains/spikes associated with genetic gains in grain yield were achieved by breeding.The performance and stability of yield and yield‐related traits was analyzed for the different cultivars. [ABSTRACT FROM AUTHOR]

SUMMARY: High‐molecular‐weight glutenin subunits (HMW‐GS) are major components of seed storage proteins (SSPs) and largely determine the processing properties of wheat (Triticum aestivum) flour. HMW‐GS are encoded by the GLU‐1 loci and regulated at the transcriptional level by interaction between cis‐elements and transcription factors (TFs). We recently validated the function of conserved cis‐regulatory modules (CCRMs) in GLU‐1 promoters, but their interacting TFs remained uncharacterized. Here we identified a CCRM‐binding NAM‐ATAF‐CUC (NAC) protein, TaNAC100, through yeast one‐hybrid (Y1H) library screening. Transactivation assays demonstrated that TaNAC100 could bind to the GLU‐1 promoters and repress their transcription activity in tobacco (Nicotiana benthamiana). Overexpression of TaNAC100 in wheat significantly reduced the contents of HMW‐GS and other SSPs as well as total seed protein. This was confirmed by transcriptome analyses. Conversely, enhanced expression of TaNAC100 increased seed starch contents and expression of key starch synthesis‐related genes, such as TaGBSS1 and TaSUS2. Y1H assays also indicated TaNAC100 binding with the promoters of TaGBSS1 and TaSUS2. These results suggest that TaNAC100 functions as a hub controlling seed protein and starch synthesis. Phenotypic analyses showed that TaNAC100 overexpression repressed plant height, increased heading date, and promoted seed size and thousand kernel weight. We also investigated sequence variations in a panel of cultivars, but did not identify significant association of TaNAC100 haplotypes with agronomic traits. The findings not only uncover a useful gene for wheat breeding but also provide an entry point to reveal the mechanism underlying metabolic balance of seed storage products. Significance Statement: High‐molecular‐weight glutenin subunits (HMW‐GS) have a great effect on wheat (Triticum aestivum) quality. Here we identified a NAC transcription factor, TaNAC100, binding with HMW‐GS promoters. TaNAC100 overexpression in wheat reduced the contents of HMW‐GS and total seed protein, but increased seed starch content. TaNAC100 overproduction also significantly affects agronomic traits. The findings not only uncover a useful gene for wheat breeding but also provide an entry point to reveal the mechanism underlying metabolic balance of seed storage products. [ABSTRACT FROM AUTHOR]

Key message: A major QTL QTgw.caas-5B for thousand grain weight in wheat was fine mapped on chromosome 5B, and TraesCS5B02G044800 was predicted to be the candidate gene. Thousand grain weight (TGW), determined by grain length and width, and is an important yield component in wheat; understanding of the underlying genes and molecular mechanisms remains limited. A stable QTL QTgw.caas-5B for TGW was identified previously in a RIL population developed from a cross between Zhongmai 871 (ZM871) and a sister line Zhongmai 895 (ZM895), and the aim of this study was to perform fine mapping and validate the genetic effect of the QTL. It was delimited to an interval of approximately 2.0 Mb flanked by markers Kasp_5B29 and Kasp_5B31 (49.6–51.6 Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC1F6 line selected from the ZM871/ZM895//ZM871 population. A candidate gene was predicted following sequencing and differential expression analyses. Marker Kasp_5B_Tgw based on a SNP in TraesCS5B02G044800, the QTgw.caas-5B candidate, was developed and validated in a diversity panel of 166 cultivars. The precise mapping of QTgw.caas-5B laid a foundation for cloning of a predicted causal gene and provides a molecular marker for improving grain yield in wheat. [ABSTRACT FROM AUTHOR]

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL , and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D , respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Key message: Two major QTL for tiller angle were identified on chromosomes 1AL and 5DL, and TaTAC-D1 might be the candidate gene for QTA.caas-5DL. An ideal plant architecture is important for achieving high grain yield in crops. Tiller angle (TA) is an important factor influencing yield. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) was used to map TA by extreme pool-genotyping and inclusive composite interval mapping (ICIM). Two quantitative trait loci (QTL) on chromosomes 1AL and 5DL were identified with reduced tiller angle alleles contributed by ZM895. QTA.caas-1AL was detected in six environments, explaining 5.4–11.2% of the phenotypic variances. The major stable QTL, QTA.caas-5DL, was identified in all eight environments, accounting for 13.8–24.8% of the phenotypic variances. The two QTL were further validated using BC1F4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines). Gene TraesCS5D02G322600, located in the 5DL QTL and designated TaTAC-D1, had a SNP in the third exon with 'A' and 'G' in ZM871 and ZM895, respectively, resulting in a Thr169Ala amino acid change. A KASP marker based on this SNP was validated in two sets of germplasm, providing further evidence for the significant effects of TaTAC-D1 on TA. Thus extreme pool-genotyping can be employed to detect QTL for plant architecture traits and KASP markers tightly linked with the QTL can be used in wheat breeding programs targeting improved plant architecture. [ABSTRACT FROM AUTHOR]

Key message: GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding. [ABSTRACT FROM AUTHOR]

Summary: The marriage of metabolomic approaches with genetic design has proven a powerful tool in dissecting diversity in the metabolome and has additionally enhanced our understanding of complex traits. That said, such studies have rarely been carried out in wheat. In this study, we detected 805 metabolites from wheat kernels and profiled their relative contents among 182 wheat accessions, conducting a metabolite‐based genome‐wide association study (mGWAS) utilizing 14 646 previously described polymorphic SNP markers. A total of 1098 mGWAS associations were detected with large effects, within which 26 candidate genes were tentatively designated for 42 loci. Enzymatic assay of two candidates indicated they could catalyse glucosylation and subsequent malonylation of various flavonoids and thereby the major flavonoid decoration pathway of wheat kernel was dissected. Moreover, numerous high‐confidence genes associated with metabolite contents have been provided, as well as more subdivided metabolite networks which are yet to be explored within our data. These combined efforts presented the first step towards realizing metabolomics‐associated breeding of wheat. [ABSTRACT FROM AUTHOR]

Key message: We developed and validated 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for 46 genes of important wheat quality, biotic and abiotic stress resistance, grain yield, and adaptation-related traits for marker-assisted selection in wheat breeding. Development of high-throughput, low-cost, gene-specific molecular markers is important for marker-assisted selection in wheat breeding. In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay design, low operational costs, and platform compatibility. The state-of-the-art assays of this study provide a robust and reliable molecular marker toolkit for wheat breeding programs. [ABSTRACT FROM AUTHOR]

Unmanned aerial vehicle (UAV) based remote sensing is a promising approach for non-destructive and high-throughput assessment of crop water and nitrogen (N) efficiencies. In this study, UAV was used to evaluate two field trials using four water (T0 = 0 mm, T1 = 80 mm, T2 = 120 mm, and T3 = 160 mm), and four N (T0 = 0, T1 = 120 kg ha–1, T2 = 180 kg ha–1, and T3 = 240 kg ha–1) treatments, respectively, conducted on three wheat genotypes at two locations. Ground-based destructive data of water and N indictors such as biomass and N contents were also measured to validate the aerial surveillance results. Multispectral traits including red normalized difference vegetation index (RNDVI), green normalized difference vegetation index (GNDVI), normalized difference red-edge index (NDRE), red-edge chlorophyll index (RECI) and normalized green red difference index (NGRDI) were recorded using UAV as reliable replacement of destructive measurements by showing high r values up to 0.90. NGRDI was identified as the most efficient non-destructive indicator through strong prediction values ranged from R 2 = 0.69 to 0.89 for water use efficiencies (WUE) calculated from biomass (WUE.BM), and R 2 = 0.80 to 0.86 from grain yield (WUE.GY). RNDVI was better in predicting the phenotypic variations for N use efficiency calculated from nitrogen contents of plant samples (NUE.NC) with high R 2 values ranging from 0.72 to 0.94, while NDRE was consistent in predicting both NUE.NC and NUE.GY by 0.73 to 0.84 with low root mean square errors. UAV-based remote sensing demonstrates that treatment T2 in both water 120 mm and N 180 kg ha–1 supply trials was most appropriate dosages for optimum uptake of water and N with high GY. Among three cultivars, Zhongmai 895 was highly efficient in WUE and NUE across the water and N treatments. Conclusively, UAV can be used to predict time-series WUE and NUE across the season for selection of elite genotypes, and to monitor crop efficiency under varying N and water dosages. [ABSTRACT FROM AUTHOR]

Key message: Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield. [ABSTRACT FROM AUTHOR]

The primary cause of time‐dependent discoloration in wheat (Triticum aestivum L.)‐based products is polyphenol oxidase (PPO) activity. A comprehensive genetic characterization of PPO activity in wheat could expedite the development of wheat varieties with low PPO activity. To dissect the genetic architecture of PPO activity in wheat flour, a panel of 166 diverse bread wheat cultivars was phenotyped in four different environments and genotyped by high‐density wheat 90K and 660K arrays. A genome‐wide association study (GWAS) was performed by a mixed linear model that incorporated population structure and relative kinship. Four hundred and sixty‐five stable marker–trait associations representative of 43 quantitative trait loci (QTL) for PPO activity identified in at least two environments were located on all wheat chromosomes except 5A, with each explaining 6.6–32.4% of the phenotypic variance. Based on IWGSC RefSeq v1.0, we found that QPPO2A.3, QPPO2B.1, QPPO2B.2, and QPPO2D.2 were consistent with the previously reported QTL, and 12 QTL located on homoeologous group 1 chromosomes (6 QTL), chromosomes 4B, 4D, and 7A (2 QTL), and chromosome 7B (2 QTL) are likely to be new PPO loci. Based on physical positions of QTL and previous studies, Ppo‐A1, Ppo‐A2, Ppo‐B2, Ppo‐D2, Pinb‐D1, and genes encoding a Cu ion‐binding protein and a Cu‐transporting ATPase RAN1‐like protein were considered as candidates for QPPO2A.3, QPPO2B.1, QPPO2D.2, QPPO5D.1, QPPO4A.2, and QPPO7D.2, respectively. This study provided insights into the molecular basis of wheat PPO activity, and associated markers can be used for selection of low PPO breeding lines as a means of improving the marketing quality of wheat products. [ABSTRACT FROM AUTHOR]

Key message: We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding. [ABSTRACT FROM AUTHOR]

Key message: We identified four chromosome regions harboring QTL for grain yield-related traits, and breeder-friendly KASP markers were developed and validated for marker-assisted selection. Identification of major stable quantitative trait loci (QTL) for grain yield-related traits is important for yield potential improvement in wheat breeding. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) were evaluated for thousand grain weight (TGW), grain length (GL), grain width (GW), and grain number per spike (GNS) in 10 environments and for grain filling rate in six environments. Sixty RILs, with 30 higher and 30 lower TGW, respectively, were genotyped using the wheat 660 K SNP array for preliminary QTL mapping. Four genetic regions on chromosomes 1AL, 2BS, 3AL, and 5B were identified to have a significant effect on TGW-related traits. A set of Kompetitive Allele Specific PCR markers were converted from the SNP markers on the above target chromosomes and used to genotype all 266 RILs. The mapping results confirmed the QTL named Qgw.caas-1AL, Qgl.caas-3AL, Qtgw.caas-5B, and Qgl.caas-5BS on the targeted chromosomes, explaining 5.0–20.6%, 5.7–15.7%, 5.5–17.3%, and 12.5–20.5% of the phenotypic variation for GW, GL, TGW, and GL, respectively. A novel major QTL for GNS on chromosome 5BS, explaining 5.2–15.2% of the phenotypic variation, was identified across eight environments. These QTL were further validated using BC1F4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines) and 186 advanced breeding lines. Collectively, selective genotyping is a simple, economic, and effective approach for rapid QTL mapping and can be generally applied to genetic mapping studies for important agronomic traits. [ABSTRACT FROM AUTHOR]

The increasing severity and prevalence of powdery mildew aided by extensive use of semi-dwarf cultivars and high levels of nitrogenous fertilizers are causing significant yield losses in wheat. Resistant cultivars are the most cost-effective and environmentally friendly approach to manage the disease. The objective of this study was to identify quantitative trait loci (QTL) for powdery mildew resistance in a doubled haploid (DH) population from a cross between leading Chinese cultivars, Yangmai 16 and Zhongmai 895. A high-density genetic map comprising of 14,480 non-redundant markers (equal to 148,179 SNPs) in 21 wheat chromosomes was constructed by genotyping the population with the Wheat 660 K SNP array. The DH population was phenotyped for powdery mildew resistance at the adult plant stage in multiple field trials, including four environments in the 2016–2017 cropping season and two environments in 2017–2018. Composite interval mapping detected six stable QTL explaining 3.8–23.6% of the phenotypic variance across environments. QPmyz.caas-5DS, QPmyz.caas-6BL and QPmyz.caas-7BS, are probably new QTL for powdery mildew resistance. One SNP marker closely linked to QPmyz.caas-6BL, the most stable QTL, was converted into a Kompetitive Allele-Specific PCR marker (K_AX-94973433) and validated on 103 commercial wheat cultivars. Significantly lower maximum disease severities of cultivars with the resistance-associated allele than those with the susceptibility-associated allele at QPmyz.caas-6BL in some environments indicated partial effectiveness of the marker. The novel QTL and their closely linked markers identified in the present study should facilitate development of cultivars with improved powdery mildew resistance. [ABSTRACT FROM AUTHOR]

Background: Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential. Results: Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78–18.17%, 16.61–21.83% and 19.08–28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0. Conclusions: Three major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat. [ABSTRACT FROM AUTHOR]

Key message: Genetic dissection uncovered a major QTL QTKW.caas-4BS corresponding with a 483 kb deletion that included genes ZnF, EamA and Rht-B1. This deletion was associated with increased grain weight and semi-dwarf phenotype. Previous studies identified quantitative trait loci (QTL) for thousand kernel weight (TKW) in the region spanning the Rht-B1 locus in wheat (Triticum aestivum L.). We recently mapped a major QTL QTKW.caas-4BS for TKW spanning the Rht-B1 locus in a recombinant inbred line (RIL) population derived from Doumai/Shi 4185 using the wheat 90K array. The allele from Doumai at QTKW.caas-4BS significantly increased TKW and kernel number per spike, and conferred semi-dwarf trait, which was beneficial to improve grain yield without a penalty to lodging. To further dissect QTKW.caas-4BS, we firstly re-investigated the genotypes and phenotypes of the RILs and confirmed the QTL using cleaved amplified polymorphic sequence (CAPS) markers developed from flanking SNP markers IWA102 and IWB54814. The target sequences of the CAPS markers were used as queries to BLAST the wheat reference genome RefSeq v1.0 and hit an approximate 10.4 Mb genomic region. Based on genomic mining and SNP loci from the wheat 660K SNP array in the above genomic region, we developed eight new markers and narrowed QTKW.caas-4BS to a genetic interval of 1.5 cM. A 483 kb deletion in Doumai corresponded with QTKW.caas-4BS genetically, including three genes ZnF, EamA and Rht-B1. The other 15 genes with either differential expressions and/or sequence variations between parents were also potential candidate genes for QTKW.caas-4BS. The findings not only provide a toolkit for marker-assisted selection of QTKW.caas-4BS but also defined candidate genes for further functional analysis. [ABSTRACT FROM AUTHOR]

Key message: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued. [ABSTRACT FROM AUTHOR]

Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B , and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1 , and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding. [ABSTRACT FROM AUTHOR]

Trehalose 6-phosphate phosphatase ( TPP) dephosphorylates trehalose 6-phosphate to trehalose, an important growth regulator, and is involved in starch accumulation and grain yield. In this study, wheat TPP homologs were isolated from chromosomes 6AL, 6BL, and 6DL, designated as TaTPP- 6AL1, TaTPP- 6BL1, and TaTPP-6DL1, respectively. Sequence alignment showed a single-nucleotide polymorphism (SNP) at TaTPP- 6AL1 locus between cultivars with contrasting thousand grain weight (TGW), forming alleles TaTPP- 6AL1a and TaTPP- 6AL1b, respectively. A cleaved amplified polymorphic sequence (CAPS) marker, TaTPP- 6AL1-CAPS, was developed to differentiate the two alleles. TaTPP- 6AL1 was mapped within the interval of IWB65749 and IWB60449 in a recombinant inbred line (RIL) population derived from Zhou8425B/Chinese Spring using the wheat 90K SNP assay. A QTL for TGW identified in the interval explained 12.1 -19.1% of the phenotypic variance across five environments. Association analysis on 141 Chinese wheat cultivars also indicated a significant correlation of TaTPP- 6AL1 with TGW. In conclusion, TaTPP- 6AL1 and its functional marker are valuable to improve grain yield in wheat breeding. [ABSTRACT FROM AUTHOR]

Key message : Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Abstract: Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas- 2AL, QBp.caas- 2BL, QBp.caas- 3AL, QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 6A, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS, respectively. All resistance alleles, except for QBp.caas- 7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas- 3BL, QBp.caas- 5AS, QBp.caas- 7AL.1, QBp.caas- 7AL.2 and QBp.caas- 7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance. [ABSTRACT FROM AUTHOR]

Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content) and unfavorable alleles (decreasing WSC), indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars. [ABSTRACT FROM AUTHOR]

We investigated alleles at 31 loci associated with adaptability, yield, and end-use quality in 107 wheat (Triticum aestivum L.) landraces (WLRs) and 121 improved historical wheat cultivars (HWCs) from Pakistan. The WLRs were categorized into two further subgroups: 36 pre-Green-Revolution landraces released as cultivars and 71 geographically spread landraces from all over Pakistan. Alleles VrnA1a, TaGW2-6A-A, TaCKX6-D1b, Pinb-D1b, Psy-A1b, and Wx-D1b were absent in WLRs, whereas ample diversity was observed at all other loci. In HWCs, only Wx-D1b and Glu-A3e were absent among the alleles tested, whereas the alleles Ppd-D1a (90%), Rht-B1b or Rht-D1b (83.4%), TaCwi-A1a (95%), TaGW2-6A-G (76%), TaCKX6-D1a (77.3%), Glu-A1b (66.1%), Glu-D1d (61.3%), Pina-D1b (88.2%), Pinb-D1a (90%), Psy-A1a (66.1%), Psy-B1b (81.8%), Psy-D1a (86.5%), Ppo-A1a (70%), TaZds-D1b (73.9%), TaLox-B1b (80.1%), and Wx-D1a (100%) predominated, indicating significant improvement in adaptability, yield potential, and end-use quality and unconscious selection for favored alleles. Higher frequencies of favored alleles at the TaCwi-A1 and TaCKX6-D1 loci influencing 1000-kernel weight (TKW) in HWCs indicated that selection pressure on these alleles during breeding successfully contributed to cultivar improvement. Wright's pairwise fixation index (Fst) statistics indicated greater genetic divergence between HWC and WLR collections (0.16) than HWC and WLR cultivars (0.14). Population structure based on functional markers (FMs) using principal component analysis partitioned the germplasm into two distinct groups. High genetic divergence and low admixture between HWCs and WLRs indicated limited use of landraces in wheat breeding in Pakistan. Our results suggested these collections as rich reservoirs of alleles and haplotype combinations that may be useful in future breeding programs. [ABSTRACT FROM AUTHOR]

The OsGS3 gene plays a principal role in controlling grain weight and grain length in rice. However, the function of an orthologous gene TaGS in wheat has not been analyzed to date. In the present study, we cloned the gDNA of TaGS gene, designated TaGS- D1, with four exons and three introns on chromosome 7DS by a comparative genomics approach. The cDNA of TaGS- D1 is 255 bp, and it encodes 85 amino acids. We also found a plant-specific organ size regulation domain in the deduced polypeptide, indicating that TaGS- D1, like OsGS3, does not belong to the PEBP family. DNA sequencing of the TaGS- D1 locus revealed no diversity in the coding sequence of exons, but there was a single nucleotide polymorphism (SNP) in the first intron, and 30 SNPs, a 40-bp InDel and a 3-bp InDel were found in the second intron between genotypes with higher and lower thousand grain weights (TGW). Based on the 40-bp InDel, a co-dominant STS marker, designated GS7D, was developed to discriminate the two alleles. GS7D was 8.0 cM from Xbarc184 located on chromosome 7DS by linkage mapping. A QTL for TGW and grain length at GS7D locus explained up to 16.3 and 7.7 %, respectively, of the phenotypic variances in a RIL population derived from Doumai/Shi 4185 grown in Shijiazhuang and Beijing. One hundred and seventy-five Chinese wheat cultivars were genotyped with GS7D, indicating that TaGS- D1 was significantly associated with grain weight. The allelic distribution at the TaGS- D1 locus showed that the frequencies of TaGS- D1a were high in cultivars from Serbia, Japan, Australia, Canada, and the Northeastern Spring Wheat and Northern Winter Wheat Regions of China. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst), is a serious yield-limiting factor for wheat production worldwide. The objective of this study was to identify and map a stripe rust resistance gene in wheat line Shaannong 104 using SSR markers. F1, F2 and F3 populations from Shaannong 104/Mingxian 169 were inoculated with Chinese Pst race CYR32 in a greenhouse. Shaannong 104 carried a single dominant gene, YrSN104. Six potential polymorphic SSR markers identified in bulk segregant analysis were used to genotype F2 and F3 families. YrSN104 was closely linked with all six SSR markers on chromosome 1BS with genetic distances of 2.0 cM ( Xgwm18, Xgwm273, Xbarc187), 2.6 cM ( Xgwm11, Xbarc137) and 5.9 cM ( Xbarc240). Pedigree analysis, pathogenicity tests using 26 Pst races, haplotyping of associated markers on isogenic lines carrying known stripe rust resistance genes, and associations with markers suggested that YrSN104 was a new resistance gene or an allele at the Yr24/Yr26 locus on chromosome 1BS. Deployment of YrSN104 singly or in combination to elite genotypes could play an effective role to lessen yield losses caused by stripe rust. [ABSTRACT FROM AUTHOR]

Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs. [ABSTRACT FROM AUTHOR]

Cell wall invertase (CWI) is a critical enzyme for sink tissue development and carbon partition, and has a high association with kernel weight. Characterization of Cwi genes and development of functional markers are of importance for marker-assisted selection in wheat breeding. In the present study, the full-length genomic DNA sequence of a Cwi gene located on wheat chromosome 2A, designated TaCwi- A1, was characterized by in silico cloning and experimental validation. TaCwi- A1 comprises seven exons and six introns, with 3,676 bp in total, and an open reading frame (ORF) of 1,767 bp. A pair of complementary dominant markers, CWI21 and CWI22, was developed based on allelic variations at the TaCwi- A1 locus. A 404-bp PCR fragment was amplified by CWI21 in varieties with lower kernel weights, whereas a 402-bp fragment was generated by CWI22 in the varieties with higher kernel weights. The markers CWI21 and CWI22 were located on chromosome 2AL using a F population from a cross Doumai/Shi 4185, and a set of Chinese Spring nullisomic-tetrasomic lines. They were linked to the SSR locus Xbarc15- 2AL with a genetic distance of 10.9 cM. QTL analysis indicated that TaCwi- A1 could explain 4.8% of phenotypic variance for kernel weight over 2 years. Two sets of Chinese landraces and two sets of commercial wheat varieties were used to validate the association of CWI21 and CWI22 with kernel weight. The results indicated that the functional markers CWI21 and CWI22 were closely related to kernel weight and could be used in wheat breeding for improving grain yield. [ABSTRACT FROM AUTHOR]

Polyphenol oxidase (PPO) plays a crucial role in browning reactions in fresh and processed fruits and vegetables, as well as products made from cereal grains. Common wheat ( Triticum aestivum L.) has a large genome, representing an interesting system to advance our understanding of plant PPO gene expression, regulation and function. In the present study, we characterized the expression of Ppo-A1, a major PPO gene located on wheat chromosome 2A, using DNA sequencing, semi-quantitative RT-PCR, PPO activity assays and whole-grain staining methods during grain development. The results indicated that the expression of the Ppo-A1b allele was regulated by alternative splicing of pre-mRNAs, resulting from a 191-bp insertion in intron 1 and one C/G SNP in exon 2. Eight mRNA isoforms were identified in developing grains based on alignments between cDNA and genomic DNA sequences. Only the constitutively spliced isoform b encodes a putative full-length PPO protein based on its coding sequence whereas the other seven spliced isoforms, a, c, d, e, f, g and h, have premature termination codons resulting in potential nonsense-mediated mRNA decay. The differences in expression of Ppo-A1a and Ppo-A1b were confirmed by PPO activity assays and whole grain staining, providing direct evidence for the influence of alternative splicing in the coding region of Ppo-A1 on polyphenol oxidase activity in common wheat grains. [ABSTRACT FROM AUTHOR]

Abstract: Chinese wheat (Triticum aestivum) production has developed rapidly during the last 57 years, largely due to improved crop management technologies and new varieties. The history of wheat planting technologies in China was reviewed, and the physiological mechanisms that allow wheat to attain high yield under these planting systems were analyzed. The use of leaf number and stage of development to indicate the optimum timing for applications of fertilizers and irrigation water, and uniform seeding at reduced seeding rates to control lodging contributed significantly to the substantial progress in wheat productivity. However, flood irrigation and tillage-based practices also resulted in serious problems, including a decline in soil fertility and quality, environmental pollution, and inefficient use of water resources. The major future challenges facing wheat production are to improve water and nutrient use efficiency. Conservation agriculture-based resource conservation technologies such as zero or reduced tillage, flat or raised bed-planting systems, and rational management of crop residues to eliminate burning in the field are among the strategies we strongly recommend for improving agricultural environments and stabilizing/increasing wheat production in China. [Copyright &y& Elsevier]

Abstract: Thirty-three cultivars and advanced lines originated from China, Mexico, and Australia were sown in four environments in Chinese spring wheat regions to investigate the association between gluten protein fractions determined by reversed-phase high-performance liquid chromatography (RP-HPLC), and dough properties and northern-style Chinese steamed bread (CSB) quality. The genotypes were divided into two groups of 10 and 23 entries with and without the 1B/1R translocation, respectively. 1B/1R translocation lines had significantly high amounts of ω-gliadins, and low levels of glutenin and low molecular weight glutenin subunits (LMW-GS), but no significant difference in dough properties and CSB quality from non-translocation lines. The association between protein fractions and dough properties, and CSB quality largely depended upon the presence of 1B/1R translocation. Gliadin contributed more in quantity to flour protein content (FPC) than glutenin, while glutenin and its fractions contributed more to dough strength and CSB quality. Among non-translocation lines, moderate to high correlation coefficients between quantified glutenin and its fractions, and farinograph development time (DT, –0.92) and stability (ST, –0.93), extensograph maximum resistance (R max, –0.93), CSB stress relaxation (SR, –0.61) and CSB score (–0.62), were observed. Gliadin:glutenin ratios showed significant and negative associations with dough properties and CSB quality. Correlation coefficients between gliadin:glutenin, gliadin:HMW-GS, gliadin:LMW-GS ratios, and CSB score were −0.79, −0.73, and −0.79 among non-translocation lines, respectively. HMW-GS and LMW-GS, x-type HMW-GS and y-type HMW-GS contributed similarly to dough properties and CSB quality for non-translocation lines. Weak correlations between protein fractions and dough properties, and CSB quality were observed among translocation lines. This information should be useful for improvement of dough properties and CSB quality. [Copyright &y& Elsevier]