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Key message: A new stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou was mapped to a 943.6-kb interval on chromosome arm 6DS and co-segregated with a marker CAPS3 developed from candidate gene TraesCS6D03G0027300. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease of wheat. Chinese landrace wheat Baidatou has shown high resistance to a broad spectrum of Pst races at both the seedling and adult-plant stages for decades in the Longnan region of Gansu province, a hot spot for stripe rust epidemics. Here, we report fine mapping and candidate gene analysis of stripe rust resistance gene YrBDT in Baidatou. Analysis of F1, F2 plants and F2:3 lines indicated that resistance in Baidatou to Pst race CYR31 was conferred by a single dominant gene, temporarily designated YrBDT. Bulked segregant exome capture sequencing (BSE-seq) analysis revealed 61 high-confidence polymorphic SNPs concentrated in a 5.4-Mb interval at the distal of chromosome arm 6DS. Several SNPs and InDels were also identified by genome mining of DNA sampled from the parents and contrasting bulks. The YrBDT locus was mapped to a 943.6-kb (4,658,322–5,601,880 bp) genomic region spanned by markers STS2 and STS3 based on IWGSC RefSeq v2.1, including five putative disease resistance genes. There was high collinearity of the target interval among Chinese Spring RefSeq v2.1, Ae. tauschii AL8/78 and Fielder genomes. The expression level of TraesCS6D03G0027300 showed significant association with Pst infection, and a gene-specific marker CAPS3 developed from TraesCS6D03G0027300 co-segregated with YrBDT suggesting this gene as a candidate of YrBDT. The resistance gene and flanking markers can be used in marker-assisted selection for improvement of stripe rust resistance. [ABSTRACT FROM AUTHOR]

Drought is one of the most adverse factors affecting plant growth and productivity. Identifying elite genotypes and their ideotypic traits conferring high yield potential and drought tolerance is critical in selecting and breeding drought‐tolerant wheat cultivars. In this study, we conducted field experiments at the Xinxiang Agricultural Comprehensive Experimental station in the North China Plain from 2018 to 2020 and assessed 209 wheat cultivars released since the 1940s under irrigated and nonirrigated conditions. Then, we selected drought‐tolerant cultivars by classifying them into four groups based on yield response to drought stress and several drought indices. Finally, the key ideotypic traits associated with high yield potential and drought tolerance were identified. Results indicated that the grain yield of the 209 cultivars decreased on average by 10.4% and 9.4% under nonirrigated treatment in 2018–2019 and 2019–2020, respectively, relative to full irrigation. The high‐yielding cultivars under both irrigation treatments are characterised by a compact plant type, larger thousand‐grain weight, larger chlorophyll content, higher leaf photosynthesis, shorter plant height and stay‐green traits. The stomatal and nonstomatal limitations are strongly associated with genotype yield performance, elucidating a potential mechanism underlying drought tolerance. Drought tolerance and yield stability of wheat cultivars have been improved through breeding over the past 70 years. Our findings enhance understanding of drought tolerance and identify genotypes and traits beneficial for breeding high‐yielding and drought‐tolerant cultivars. [ABSTRACT FROM AUTHOR]

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]

Key message: Three stable QTL for grain zinc concentration were identified in wheat landrace Chinese Spring. Favorable alleles were more frequent in landraces than in modern wheat cultivars. Wheat is a major source of dietary energy for the growing world population. Developing cultivars with enriched zinc and iron can potentially alleviate human micronutrient deficiency. In this study, a recombinant inbred line (RIL) population with 245 lines derived from cross Zhou 8425B/Chinese Spring was used to detect quantitative trait loci (QTL) for grain zinc concentration (GZnC) and grain iron concentration (GFeC) across four environments. Three stable QTL for GZnC with all favorable alleles from Chinese Spring were identified on chromosomes 3BL, 5AL, and 5BL. These QTL explaining maxima of 8.7%, 5.8%, and 7.1% of phenotypic variances were validated in 125 resequenced wheat accessions encompassing both landraces and modern cultivars using six kompetitive allele specific PCR (KASP) assays. The frequencies of favorable alleles for QGZnCzc.caas-3BL, QGZnCzc.caas-5AL and QGZnCzc.caas-5BL were higher in landraces (90.4%, 68.0%, and 100.0%, respectively) compared to modern cultivars (45.9%, 35.4%, and 40.9%), suggesting they were not selected in breeding programs. Candidate gene association studies on GZnC in the cultivar panel further delimited the QTL into 8.5 Mb, 4.1 Mb, and 47.8 Mb regions containing 46, 4, and 199 candidate genes, respectively. The 5BL QTL located in a region where recombination was suppressed. Two stable and three less stable QTL for GFeC with favorable alleles also from Chinese Spring were identified on chromosomes 4BS (Rht-B1a), 4DS (Rht-D1a), 1DS, 3AS, and 6DS. This study sheds light on the genetic basis of GZnC and GFeC in Chinese Spring and provides useful molecular markers for wheat biofortification. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease, leading to huge yield losses in wheat production. Identification of resistance genes and closely linked molecular markers can greatly facilitate breeding resistant wheat cultivars. Shaannong69 conferred high resistance to stripe rust both at the seedling and adult-plant stages. The Pst race CYR31 was used to infect Shaannong69, Huixianhong, F1 and F2 plants and F2:3 lines at the seedling stage in the greenhouse. Genetic analysis identified a single dominant gene, designated as YrSN69, conferring resistance to Pst race CYR31 in Shaannong69. Seventy-four of 176 SNPs with the absolute value of ∆SNP-index more than 0.85 were identified in 753.33–766.18 Mb on chromosome 2BL based on bulked segregant RNA sequencing. Fifteen kompetitive allele-specific PCR markers were developed to genotype susceptible F2 plants derived from the Shaannong69/Huixianhong cross. YrSN69 was mapped on chromosome arm 2BL in a 2.0 cM genetic interval, with genetic distances of 0.2 cM and 1.8 cM to markers 2BC17 and 2BA20, respectively, corresponding to a 3.16 Mb physical region based on the IWGSC RefSeq v1.1 with 44 high-confidence annotated genes. The YrSN69 is likely to be a new allele of Yr72 in comparison with known Yr genes on chromosome 2BL. These results provide a solid foundation for map-based cloning of YrSN69 and marker-assisted selection for pyramiding stripe rust resistance genes. [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]

Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield–quality trade‐off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed. [ABSTRACT FROM AUTHOR]

Key message: We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4–8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP−390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Introduction: This study aimed to evaluate the impact of Lugol‐unstained lesion (LUL) location on the detection yield, which may help the endoscopist select targets for biopsy. Methods: We enrolled 1064 subjects who had LULs at the baseline screening of a population‐based randomized controlled trial. There were 1166 LULs with recorded location and pathologic diagnosis, and these were used for analysis. The detection rate of severe dysplasia and above (SDA) was calculated as the number of LULs identified as SDA divided by the number of LULs biopsied. Logistic regression with a generalized estimating equation was applied to evaluate the association between the location of a given LUL and the risk of the LUL being SDA. Results: The detection rate of SDA for LULs located in the lower, middle, and upper esophagus increased from 5.9% and 10.9% to 16.7%. LUL location was significantly associated with having SDA (adjusted odds ratio (OR)upper vs. lower = 2.88, 95% confidential interval (CI) = 1.48–5.60; adjusted ORmiddle vs. lower = 1.63, 95% CI = 0.96–2.76), and the association was stronger in subgroups with a family history of esophageal squamous cell carcinoma (ESCC) (adjusted ORupper vs. lower = 9.72, 95% CI = 2.57–36.69; adjusted ORmiddle vs. lower = 3.76, 95% CI = 0.93–15.21). Conclusions: Our results suggest that more attention should be paid by endoscopists to LULs in the upper and middle esophagus, particularly for individuals with a family history of ESCC. [ABSTRACT FROM AUTHOR]

Key message: Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0–89.6 Mb) and 1.7 cM and 4.9 Mb (659.9–664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR. [ABSTRACT FROM AUTHOR]

Sustainable wheat production is challenged by climate change events such as drought, salinity, and heat stress. Senescence is a gradual programmed cell death trait occurring post anthesis in wheat (Triticum aestivum), with significant affecting stability of yield and quality‐related traits under climate severities. Phenotyping of complex traits is increasingly perceived as a bottleneck due to elevated labor costs and time in large field conditions. Unmanned aerial vehicle (UAV)‐based platforms using RGB imagery and ground phenotyping–based novel traits can facilitate the repeated nondestructive measurements of crop canopy traits cost‐effectively. Here, we described combined application of UAV‐based RGB imaging and ground measurements based novel trait to quantify canopy senescence in wheat. We reported senescence related traits with high heritability in a recombinant inbred line population derived from the cross Zhongmai 175/Lunxuan 987. Our results showed that the selection of slow senescence genotypes using UAV‐based vegetation indices (VIs) was equally effective as ground‐based traits and illustrated significant variations among the genotypes. We also identified five quantitative trait loci (QTL) for canopy senescence in both UAV and ground‐based datasets using a 50K single‐nucleotide polymorphism array. QTL for UAV‐based VIs from RGB imaging and ground measurements based traits were mapped on chromosomes 1B, 2B, 3A, and 4B. The integration of both datasets with genetic analysis identified an important slow senescence/stay‐green related locus on chromosome 4B that explained phenotypic variation up to 23.07% for both UAV and ground traits at late grain‐ filling stage. Three QTL (QTL‐caas.1B, QTL‐caas.3A, and QTL‐caas.4B2) on chromosomes 1B, 3A, and 4B were also validated for slow senescence with high chlorophyll level and cool canopy temperature in a natural population of 160 lines by developing kompetitive allele‐specific PCR markers. QTL‐caas.4B1 was validated not only for senescence but also for plant height. Our findings suggest that UAV‐based RGB imagery is advantageous for precise and rapid assessment of senescence related traits and genetic studies of senescence in wheat. Core Ideas: Unmanned aerial vehicle (UAV)‐based phenotyping platforms using RGB imagery can facilitate the repeated nondestructive measurements of canopy greenness and senescence cost‐effectively.We have integrated vegetation indices derived from UAV‐based RGB pixels and ground measurements with quantitative genetic analysis to identify loci controlling canopy senescence in wheat.We have developed kompetitive allele‐specific PCR (KASP) markers based on identified loci that contribute to variations in wheat senescence. [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]

Key message: Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat. [ABSTRACT FROM AUTHOR]

Background: Current guidelines recommend only severe dysplasia and above (SDA) lesions of the esophageal squamous epithelium for clinical intervention. However, the histopathologic diagnosis derived from tissue biopsies may be subject to underestimation of severity. Methods: 1073 participants from whom biopsies were taken at baseline chromoendoscopic examination in a population‐based screening trial were enrolled in this study. The size of the Lugol‐unstained lesions (LULs) was mainly analyzed. The outcome was defined as SDA lesions either identified at baseline screening, or during follow‐up, collectively referred to as the cumulative risk of SDA. Multivariable logistic regression models were used to evaluate the cumulative risk of SDA. Results: One hundred and forty‐six SDA cases were identified in the study period. Participants with large LULs had a high cumulative incidence of SDA (cumulative incidence16–20mm: 55.88%; cumulative incidence>20mm: 76.92%) in the median of 7‐year duration. LULs of large size were significantly associated with a higher cumulative risk of SDA, regardless of the pathologic diagnosis (adjusted OR16–20mmvs.≤5mm = 21.02, 95% CI: 7.56–58.47; adjusted OR>20mmvs.≤5mm = 33.62, 95% CI: 11.79–95.87). Conclusions: Results from this study suggest physician–patient shared decision‐making regarding clinical treatment or intensive surveillance should be carried out for LULs >20 mm in the esophagus, regardless of the histologic diagnosis. For those with LULs of 16–20 mm, intensive surveillance would also best be considered. [ABSTRACT FROM AUTHOR]

Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2–42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Powdery mildew is a very destructive disease that threatens yield and quality of wheat. In the present study, 262 recombinant inbred lines derived from a cross between Zhongmai 578 (ZM578) with moderate resistance to powdery mildew and Jimai 22 (JM22) with high resistance to powdery mildew in the field were used to map powdery mildew resistance loci using the high‐density Illumina iSelect 50K single‐nucleotide polymorphism array. Three quantitative trait loci (QTLs) on chromosomes 2B, 5B, and 5D were identified by inclusive composite interval mapping, designated as QPm.caas‐2BL.1, QPm.caas‐5BL, and QPm.caas‐5DL, respectively, explaining 5.0%–37.0% of the phenotypic variances. The resistance allele of QPm.caas‐5BL was contributed by ZM578, whereas alleles of QPm.caas‐2BL.1 and QPm.caas‐5DL were from JM22. QPm.caas‐2BL.1, detected in all the six experimental environments, was a major and stable QTL. QPm.caas‐5DL was detected in five of the six environments and is likely to be a new QTL for powdery mildew resistance. The kompetitive allele‐specific PCR (KASP) markers Kpm‐2BL and Kpm‐5DL for QPm.caas‐2BL.1 and QPm.caas‐5DL, respectively, were validated in a diverse panel of 287 cultivars. These KASP markers, tightly linked with the QTLs, can be used for marker‐assisted breeding targeting the improvement of powdery mildew resistance in wheat. Core Ideas: Three major quantitative trait loci (QTLs) for powdery mildew resistance were identified in the Zhongmai 578/Jimai 22 population.QPm.caas‐5DL is likely a new QTL, with the resistance allele from Jimai 22.Two kompetitive allele‐specific PCR (KASP) markers for QPm.caas‐2BL.1 and QPm.caas‐5DL were validated in a panel of 287 wheat cultivars. [ABSTRACT FROM AUTHOR]

The colorectal cancer (CRC) and polyps incidentally found in autopsies represent the lesions that have not actually caused problems throughout the lifetime and thus may not need to be removed during screening. This study aimed to investigate the prevalence of incidental CRC (iCRC) and polyps in autopsies of different populations. A systematic search was performed on 19 August 2022 to identify autopsy studies that provided data on prevalence of iCRC, adenomatous polyps, hyperplastic polyps, and/or all polyps combined. The prevalence was pooled with the random-effects model. Subgroup and multivariable meta-regression analyses were conducted to investigate the heterogeneity. Forty-three eligible studies including 59,656 autopsies were identified, with 94% conducted before 1990 when CRC screening was uncommon or not available. The pooled prevalence was 0.7% (95% confidence interval [CI], 0.3–1.2%) for iCRC, 18.4% (95% CI, 13.3–24.1%) for adenomatous polyps, 16.4% (95% CI, 8.7–25.9%) for hyperplastic polyps, 26.3% (95% CI, 15.4–38.8%) for all polyps combined, and 29.9% (95% CI, 14.8–47.6%) for iCRC plus polyps. The prevalence of iCRC was higher (1.2%) in white-predominant populations but lower (0.4%) after excluding low-quality studies. Multivariable analyses showed that the prevalence of polyps was higher in white-predominant populations and higher-quality studies, increased with age, and showed a downward trend from "before 1975" through "after 1985". In conclusion, the prevalence of iCRC in autopsies was not low, considering the average lifetime risk of CRC, while incidental polyps were common. Both varied greatly in different populations. These findings may have implications when weighing the benefits and harms of screening. [ABSTRACT FROM AUTHOR]

Key message: We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars. Plant height is an important agronomic trait, and appropriately reduced height can improve yield potential and stability in wheat, usually combined with sufficient water and fertilizer. We previously detected a stable major-effect quantitative trait locus QPH.caas-5AL for plant height on chromosome 5A in a recombinant inbred line population of the cross ‘Doumai × Shi 4185’ using the wheat 90 K SNP assay. Here , QPH.caas-5AL was confirmed using new phenotypic data in additional environment and new-developed markers. We identified nine heterozygous recombinant plants for fine mapping of QPH.caas-5AL and developed 14 breeder-friendly kompetitive allele-specific PCR markers in the region of QPH.caas-5AL based on the genome re-sequencing data of parents. Phenotyping and genotyping analyses of secondary populations derived from the self-pollinated heterozygous recombinant plants delimited QPH.caas-5AL into an approximate 3.0 Mb physical region (521.0–524.0 Mb) according to the Chinese Spring reference genome. This region contains 45 annotated genes, and six of them were predicted as the candidates of QPH.caas-5AL based on genome and transcriptome sequencing analyses. We further validated that QPH.caas-5AL has significant effects on plant height but not yield component traits in a diverse panel of wheat cultivars; its dwarfing allele is frequently used in modern wheat cultivars. These findings lay a solid foundation for the map-based cloning of QPH.caas-5AL and also provide a breeding-applicable tool for its marker-assisted selection. Keymessage We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars. [ABSTRACT FROM AUTHOR]

Key message: Adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895 was mapped to the physical interval 710.2–713.2 Mb on the long arm of chromosome 2A. Adult-plant resistance to stripe rust is generally more durable than all-stage resistance. Chinese wheat cultivar Zhongmai 895 showed stable stripe rust resistance at the adult-plant stage. To map the genetic loci underlying its resistance, 171 doubled haploid (DH) lines from a Yangmai 16/Zhongmai 895 cross were genotyped with the wheat 660 K SNP chip. Disease severities of the DH population and parents were assessed in four environments. A major QTL designated QYryz.caas-2AL was mapped to interval 703.7–715.3 Mb on the long arm of chromosome 2A using both chip-based and KASP (kompetitive allele-specific PCR) marker-based methods, explaining 31.5 to 54.1% of the phenotypic variances. The QTL was further validated in an F2 population of cross Emai 580/Zhongmai 895 with 459 plants and a panel of 240 wheat cultivars using KASP markers. Three reliable KASP markers predicted a low frequency (7.2–10.5%) of QYryz.caas-2AL in the test panel and remapped the gene to the physical interval 710.2–713.2 Mb. Based on different physical positions or genetic effects from known genes or QTL on chromosome arm 2AL, the gene was predicted to be a new one for adult-plant stripe rust resistance and was named Yr86. Twenty KASP markers linked to Yr86 were developed in this study based on wheat 660 K SNP array and genome re-sequencing. Three of them are significantly associated with stripe rust resistance in natural population. These markers should be useful for marker-assisted selection and also provide a starting point for fine mapping and map-based cloning of the new resistance gene. [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]

Key message: We fine mapped RHT26 for plant height in wheat, confirmed its genetic effects in a panel of wheat cultivars and predicted candidate genes. Development of wheat cultivars with appropriate plant height (PH) is an important goal in breeding. Utilization of semi-dwarfing genes Rht-B1b and Rht-D1b triggered wheat Green Resolution in the 1960s. Since these genes also bring unfavorable features, such as reduced coleoptile length and grain weight, it is necessary to identify alternative reduced height genes without yield penalty. Here we constructed a high-density genetic map of a recombinant inbred line population derived from the cross of Zhongmai175 and Lunxuan987 and detected a stable genetic locus for PH, designated RHT26, on chromosome arm 3DL in all of six environments, accounting for 6.8–14.0% of the phenotypic variances. RHT26 was delimited to an approximate 1.4 Mb physical interval (517.1–518.5 Mb) using secondary mapping populations derived from 22 heterozygous recombinant plants and 24 kompetitive allele-specific PCR markers. Eleven high-confidence genes were annotated in the physical interval according to the Chinese Spring reference genome, and four of them were predicted as candidates for RHT26 based on genome and transcriptome sequencing analyses. We also confirmed that RHT26 had significant effects on PH, but not grain yield in a panel of wheat cultivars; its dwarfing allele has been frequently used in wheat breeding. These findings lay a sound foundation for map-based cloning of RHT26 and provide a breeding-applicable tool for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Background and Aim: The impact of the presence of multiple Lugol‐unstained lesions (LULs) in the esophagus on the risk of having severe dysplasia and above (SDA) lesions among asymptomatic individuals is unknown. Methods: We collected demographic factors, behavioral variables, and features of LULs from 1073 participants who were biopsied at baseline endoscopic screening in a population‐based screening trial, and these individuals were followed over a median time of 7 years. Outcome events were defined as SDA identified at screening, at reexamination, or during follow‐up. "Multiple LULs" were defined as ≥ 2 LULs found in the entirety of the esophagus. Multivariable logistic regression models were fitted to assess the effect of "multiple LULs" on the cumulative risk of SDA. Results: There were 147 SDA cases in the current study. After adjustment for potential risk factors and endoscopic features of LULs, the presence of "multiple LULs" slightly increased the cumulative risk of having SDA with no statistical significance (adjusted odds ratio [OR] = 1.26; 95% confidence interval [CI] [0.85, 1.88]). Further stratified analysis showed that this association was strong among subjects with small LULs (≤ 5 mm) (adjusted OR = 3.29; 95% CI [1.39, 7.79]). However, no such association was observed in subjects with larger LULs (adjusted OR = 0.99; 95% CI [0.63, 1.55], Pinteraction = 0.022). Conclusions: The presence of "multiple small LULs (≤ 5 mm)" in chromoendoscopy indicates a higher cumulative risk of having SDA in the esophagus. We recommend biopsies be taken and surveillance be maintained at a more active level in individuals with relatively small but multiple LULs. [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]

We evaluated root system architecture (RSA) of a set of 58 historical spring wheat cultivars from Pakistan representing 105 years of selection breeding. The evaluations were carried out under control and water-limited conditions using a high-throughput phenotyping system coupled with RhizoVision Explorer software. The cultivars were classified into three groups based on release year as cultivars released pre-1965, released between 1965 and 2000, and cultivars released post-2000. Under water-limited conditions a decline in 20 out of 25 RSA component traits was observed in pre-1965 cultivars group. Whereas cultivars released after the 1965, so-called green revolution period, showed a decline in 17 traits with significant increments in root length, depth, and steep angle frequency which are important root traits for resource-uptake under water-limited conditions. Similarly, cultivars released after 2000 indicated an increase in the number of roots, depth, diameter, surface area, and steep angle frequency. The coefficient of correlation analysis showed a positive correlation between root depth and yield-related traits under water-limited conditions. We also investigated the effects of green-revolution genes (Rht1) and some phenology-related genes such as DRO1, TaMOR, TaLTPs, TaSus-2B on RSA and identified significant associations of these genes with important root traits. There was strong selection pressure on DRO1 gene in cultivated wheat indicating the allele fixed in modern wheat cultivars is different from landraces. The expression of DRO1, and TaMOR were retrieved from an RNAseq experiment, and results were validated using qRT-PCR. The highest expression of DRO1 and TaMOR was found in Chakwal-50, a rainfed cultivar released in 2008, and MaxiPak-65 released in 1965. We conclude that there is a positive historic change in RSA after 1965 that might be attributed to genetic factors associated with favored RSA traits. Furthermore, we suggest root depth and steep angle as promising traits to withstand water-limited environments and may have implications in selection for breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple and effective risk stratification tools which allow prediction of the risk of malignant esophageal lesions are needed for the practice of opportunistic screening. The aim of the current study was to develop an improved version of the diagnostic model based on a large-scale outpatient cohort and assess the robustness and generalizability of the model through external validations. The improved diagnostic model had seven predictors and generated an area under the receiver operating characteristic curve of 0.860 in the development set. Validation of the model in two external populations also showed high discrimination power and was able to increase the detection rate of malignant esophageal lesions. This questionnaire-based diagnostic model provides an easy-to-use tool to identify high-risk individuals and will be useful for the promotion of the opportunistic screening of esophageal cancer. We aimed to develop an improved version of the diagnostic model predicting the risk of malignant esophageal lesions in opportunistic screening and validate it in external populations. The development set involved 10,595 outpatients receiving endoscopy from a hospital in Hua County, a high-risk region for esophageal squamous cell carcinoma in northern China. Validation set A enrolled 9453 outpatients receiving endoscopy in a non-high-risk region in southern China. Validation set B involved 17,511 residents in Hua County. The improved diagnostic model consisted of seven predictors including age, gender, family history of esophageal squamous cell carcinoma, smoking, body mass index, dysphagia, and retrosternal pain, with an area under the receiver operating characteristic curve (AUC) of 0.860 (95% confidence interval: 0.835–0.886) in the development set. Ideal discrimination ability was achieved in external validations (AUC validation set A: 0.892, 95% confidence interval: 0.858–0.926; AUC validation set B: 0.799, 95% confidence interval: 0.705–0.894). This improved model also markedly increased the detection rate of malignant esophageal lesions compared with universal screening, demonstrating great potential for use in opportunistic screening of malignant esophageal lesions in heterogeneous populations. [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]

Currently, surveillance for esophageal squamous cell carcinoma (ESCC) runs a risk of underestimation of early lesions which show absence of iodine staining, with no or only mild histologic changes. The development of molecular markers that indicate risk of progression is thus warranted. We performed whole‐exome sequencing on biopsies from two sequential endoscopies of a single esophageal lesion and matching blood samples. There were 27 pairs of age‐, gender‐, pathologic stage‐, and sampling interval‐matched progressors and non‐progressors identified in a prospective community‐based ESCC screening trial. Putative molecular progression markers for ESCC were first evaluated by comparing somatic mutation, copy number alteration (CNA), and mutational signature information among progressors and non‐progressors. These markers were then validated with another 24 pairs of matched progressors and non‐progressors from the same population using gene alteration status identified by target sequencing and quantitative PCR. Progressors had more somatic mutation and CNA burden, as well as apolipoprotein B mRNA editing catalytic polypeptide‐like and age‐related signature weights compared with non‐progressors. A gene score consisting of somatic NOTCH1 mutation and CDKN2A deletion is predictive of risk of progression in lesions which show absence of iodine staining under endoscopy but have no or only mild dysplasia. This gene score was also validated in an external cohort of matched progressors and non‐progressors. Absence of NOTCH1 mutation and presence of CDKN2A deletion are markers of progression in squamous lesions of the esophagus. This gene score would be an ideal indicator for assisting the pathologist in the identification of high‐risk individuals who could be potentially 'missed' or subject to a risk underestimation by histologic analysis, and might improve the performance of ESCC surveillance. © 2022 The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Background: The aim was to systematically select blood markers routinely tested in clinical settings, which are independently associated with overall survival (OS) and are able to stratify prognosis of esophageal squamous cell carcinoma (ESCC) patients undergoing esophagectomy. Methods: We selected optimal blood markers for prognostic stratification from 60 candidates in a clinical cohort of 1819 consecutive patients with resectable ESCC in China. Selection was carried out using two-step multivariable Cox proportional hazards regression adjusted for multifaceted confounders. A composite index was developed by multiplying risk factors and dividing them by protective factors. Results: With a median follow-up of 48.07 months, 641 deaths occurred in the 1819 patients and the 5-year OS was 56.30%. Two risk factors (mean corpuscular hemoglobin, fibrinogen) and a protective factor (albumin), all dichotomized and assigned values 1 and 2, were used to construct the composite index marker "MF-A". Three risk groups were created based on the MF-A score including low- (0.5), moderate- (1), and high-risk groups (2 and 4). Compared with patients in the low-risk group (1184/1778, 66.59%), those in the moderate- (488, 27.45%), and high-risk (106, 5.96%) groups were at elevated risk of death (adjusted HR: 1.32, 95% CI: 1.11–1.57; adjusted HR: 2.08, 95% CI: 1.56–2.75; Ptrend < 10-7). Within each TNM stage grouping, OS also trended to be significantly worse as the MF-A score increased. Conclusions: "MF-A" is a novel independent predictor which may be used to estimate and stratify prognosis for ESCC patients undergoing esophagectomy. [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]

Key Message: A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat. [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]

Grain yield (GY) prediction for wheat based on canopy spectral reflectance can improve selection efficiency in breeding programs. Time-series spectral information from different growth stages such as flowering to maturity is considered to have high accuracy in predicting GY and combining this information from multiple growth stages could effectively improve prediction accuracy. For this, 207 wheat cultivars and breeding lines were grown in full and limited irrigation treatments, and their canopy spectral reflectance was measured at the flowering, early, middle, and late grain fill stages. The potential of temporal spectral information at multiple growth stages for GY prediction was evaluated by a new method based on stacking the multiple growth stages data. Twenty VIs derived from spectral reflectance were used as the input feature of a support vector regression (SVR) to predict GY at each growth stage. The predicted GY values at multiple growth stages were trained by multiple linear regression (MLR) to establish a second-level prediction model. Results suggested that the prediction accuracy (R2) of VIs data from single growth stages ranged from 0.60 to 0.66 and 0.35 to 0.42 in the full and limited irrigation treatments, respectively. The prediction accuracy was increased by an average of 0.06, 0.07, and 0.07 after stacking the VIs of two, three, and four growth stages, respectively, under full irrigation. Similarly, under limited irrigation, the prediction accuracy was increased by 0.03, 0.04, and 0.04 by stacking the VIs of two, three, and four growth stages, respectively. Stacking of VIs of multiple important growth stages can increase the accuracy of GY prediction and application of a stable stacking model could increase the usefulness of data obtained from different phenotyping platforms. [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]

SUMMARY: Roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this 'hidden half' provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image‐based approaches for high‐throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non‐invasive methods like X‐ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root‐based cereal breeding. The integrated use of pan‐genome resources, now available in most cereals, coupled with new in‐field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA. Significance Statement: We reviewed the current status of genetics underpinning root system architecture in cereals and presented a comprehensive genetic framework. We further provided a comparative analysis of the phenotyping methods, different root phenes and their interaction with the environment, and breeding applications. [ABSTRACT FROM AUTHOR]

Objectives: Upper gastrointestinal (G.I.) cancer screening has been conducted in China for decades. However, the economic burden for treatment "intensively" occurred in advance due to screening in resource-limited communities remain unclear. Methods: We compared the treatment costs for upper G.I. cancers from the screening and control arms of a population-based randomized trial in a high-risk area for esophageal cancer (EC) in China based on claims data from the health insurance system in the local area which included whole population coverage. Results: The average out-of-pocket cost per treatment of EC in the screening arm was lower than that in the control arm ($5,972 vs. $7,557). This difference was a consequence of down-staging from screening which resulted in lower cost therapy for earlier stage cancers. Moreover, this result is similar for cardial and non-cardial gastric cancer in the two study arms ($7,933 vs. $10,605). However, three times as many (103 vs. 36) families in the screening arm suffered catastrophic health expenditure for all cancer types. The overall treatment cost for all EC patients in the screening arm ($1,045,119) was 2.44 times that in the control arm ($428,292), and the ratio for cardial and non-cardial gastric cancer was 1.12 ($393,261 vs. $351,557). Conclusion: Cancer treatment secondary to screening may triple the likelihood of catastrophic patient medical expenditure, and sharply increase the economic pressure on the local community, particularly for cancer types which are of high prevalence. Financial support for patients and the health insurance system should be taken into consideration when planning budgets for cancer screening programs in communities which are resource-limited. [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]

Summary: Rht‐B1b and Rht‐D1b, the 'Green Revolution' (GR) genes, greatly improved yield potential of wheat under nitrogen fertilizer application, but reduced coleoptile length, seedling vigor and grain weight. Thus, mining alternative reduced plant height genes without adverse effects is urgently needed.We isolated the causal gene of Rht24 through map‐based cloning and characterized its function using transgenic, physiobiochemical and transcriptome assays. We confirmed genetic effects of the dwarfing allele Rht24b with an association analysis and also traced its origin and distribution.Rht24 encodes a gibberellin (GA) 2‐oxidase, TaGA2ox‐A9. Rht24b conferred higher expression of TaGA2ox‐A9 in stems, leading to a reduction of bioactive GA in stems but an elevation in leaves at the jointing stage. Strikingly, Rht24b reduced plant height, but had no yield penalty; it significantly increased nitrogen use efficiency, photosynthetic rate and the expression of related genes. Evolutionary analysis demonstrated that Rht24b first appeared in wild emmer and was detected in more than half of wild emmer and wheat accessions, suggesting that it underwent both natural and artificial selection.These findings uncover an important genetic resource for wheat breeding and also provide clues for dissecting the regulatory mechanisms underlying GA‐mediated morphogenesis and yield formation. [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]

Background: The association of early-life undernutrition and dyslipidemia found in previous studies may be confounded by the uncontrolled age difference between exposed and unexposed participants. The study aimed to investigate the association of early-life undernutrition and the risk of dyslipidemia in adulthood with good control of the age variable.Methods: We took the Great Chinese Famine (1959-1961) as a natural experiment of severe undernutrition. This study was based on the baseline investigation of a population-based cohort in rural China. Undernutrition in early life was defined as being exposed to famine at younger than 3 years of age. Three approaches including Adjustment, Restriction, and Matching were applied to control the confounding effect of age. Logistic regression models were applied to evaluate the association between early-life famine and the presence of dyslipidemia. Stratified analysis by gender was also performed, and potential effect modification was tested by adding the interaction term of the famine exposure variable and gender into the model.Results: Undernutrition in early life was associated with increased risk of borderline high and above (BHA) levels of total cholesterol (TC, ORAdjustment = 1.61; ORRestriction = 1.56; ORMatching = 1.87), triglycerides (TG, ORAdjustment = 1.33; ORRestriction = 1.30; ORMatching = 1.34), low-density lipoprotein cholesterol (LDL-C, ORAdjustment = 1.75; ORRestriction = 1.53; ORMatching = 1.77) and dyslipidemia (ORAdjustment = 1.52; ORRestriction = 1.45; ORMatching = 1.60), as well as high levels of TC, TG, LDL-C and dyslipidemia. An inverse association of undernutrition and risk of low high-density lipoprotein cholesterol (HDL-C) was found. Female participants with undernutrition experience had an increased risk of BHA TG and LDL-C (TG: ORAdjustment, female = 1.45; ORRestriction, female = 1.39; ORMatching, female = 1.51; LDL-C: ORAdjustment, female = 2.11; ORRestriction, female = 1.80; ORMatching, female = 2.15), but this association was not found in males.Conclusion: Early-life undernutrition increased the risk of TC, TG, LDL-C, and dyslipidemia. Gender would significantly modify this effect for TG and LDL-C. These results emphasize the importance of nutritional conditions in the early stages of life to long-term health consequences. [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]