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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

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 (r

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.

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.

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.

Environmental stresses from climate change can alter source–sink relations during plant maturation, leading to premature senescence and decreased yields. Elucidating the genetic control of natural variations for senescence in wheat (Triticum aestivum) can be accelerated using recent developments in unmanned aerial vehicle (UAV)-based imaging techniques. Here, we describe the use of UAVs to quantify senescence in wheat using vegetative indices (VIs) derived from multispectral images. We detected senescence with high heritability, as well as its impact on grain yield (GY), in a doubled-haploid population and parent cultivars at various growth time points (TPs) after anthesis in the field. Selecting for slow senescence using a combination of different UAV-based VIs was more effective than using a single ground-based vegetation index. We identified 28 quantitative trait loci (QTL) for vegetative growth, senescence, and GY using a 660K single-nucleotide polymorphism array. Seventeen of these new QTL for VIs from UAV-based multispectral imaging were mapped on chromosomes 2B, 3A, 3D, 5A, 5D, 5B, and 6D; these QTL have not been reported previously using conventional phenotyping methods. This integrated approach allowed us to identify an important, previously unreported, senescence-related locus on chromosome 5D that showed high phenotypic variation (up to 18.1%) for all UAV-based VIs at all TPs during grain filling. This QTL was validated for slow senescence by developing kompetitive allele-specific PCR markers in a natural population. Our results suggest that UAV-based high-throughput phenotyping is advantageous for temporal assessment of the genetics underlying for senescence in wheat., Temporal multispectral imaging from unmanned aerial vehicles can be used to quantify senescence and identify underlying quantitative trait loci in wheat (Triticum aestivum).

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Stripe rust and leaf rust cause wheat yield losses of up to 70% worldwide. The employment of resistant cultivars is the major method to reduce losses from these diseases. The objective of this study was to detect quantitative trait loci (QTL) for stripe rust and leaf rust resistance in 150 F6 recombinant inbred lines (RIL) derived from a cross between Mianyang351-15 and Zhengzhou 5389. Both parents and the RIL population were genotyped with the Wheat55K single nucleotide polymorphism (SNP) array and simple sequence repeat markers, and phenotyped for stripe rust severity at Mianyang in Sichuan Province and Baoding in Hebei Province, and for leaf rust severity at Zhoukou in Henan Province and at Baoding in 2014 to 2017 cropping seasons. Seven and four QTL all contributed from Mianyang351-15 were identified for resistance to stripe rust and leaf rust, respectively. Four of these QTL on chromosomes 1BL, 2AS, 2DS, and 7BL conferred resistance to both stripe rust and leaf rust. The QTL on 1BL, 2AS, and 7BL were identified as Lr46/Yr29, Lr37/Yr17, and Lr68, respectively. QYr.hbau-2DS/QLr.hbau-2DS was detected at similar positions to previously reported loci. QYr.hbau-1DL, QYr.hbau-3AS, and QYr.hbau-3DL are likely to be new. Combined effects of QTL in the RIL population indicated RIL combining all QTL had the highest resistance level compared with those of lower numbers or no QTL. These QTL, with their closely linked SNP markers, are applicable for marker-assisted breeding and candidate gene discovery.

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.

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. 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 T. 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.

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.

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

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.

Wheat leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) cause large production losses in many regions of the world. The objective of this study was to identify quantitative trait loci (QTL) for resistance to leaf rust and stripe rust in a recombinant inbred line population derived from a cross between wheat cultivars SW 8588 and Thatcher. The population and parents were genotyped with the Wheat 55K SNP Array and SSR markers and phenotyped for leaf rust severity at Zhoukou in Henan Province and Baoding in Hebei Province. Stripe rust responses were also evaluated at Chengdu in Sichuan Province, and at Baoding. Seven and six QTL were detected for resistance to leaf rust and stripe rust, respectively. Four QTL on chromosomes 1BL, 2AS, 5AL, and 7BL conferred resistance to both rusts. The QTL on 1BL and 2AS were identified as Lr46/Yr29 and Lr37/Yr17, respectively. QLr.hebau-2DS from Thatcher, identified as Lr22b that was previously thought to be ineffective in China, contributed a large effect for leaf rust resistance. QLr.hebau-5AL/QYr.hebau-5AL, QLr.hebau-3BL, QLr.hebau-6DS, QYr.hebau-4BS, and QYr.hebau-6DS are likely to be new QTL, but require further validation. Kompetitive allele-specific PCR (KASP) markers for QLr.hebau-2DS and QLr.hebau-5AL/QYr.hebau-5AL were successfully developed and validated in a diverse wheat panel from Sichuan Province, indicating their usefulness under different genetic backgrounds. These QTL and their closely linked SNP and SSR markers will be useful for fine mapping, candidate gene discovery, and marker-assisted selection in breeding for durable resistance to both leaf and stripe rusts.

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.

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

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.

Thousand grain weight (TGW), determined by grain length and width, 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 Mb to 51.6 Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC1F4 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.

Wheat black point, which occurs in most wheat growing regions of the world, is detrimental to grain appearance, processing and nutrient quality. Mining and characterization of genetic loci for black point resistance is helpful for breeding resistant wheat cultivars. We previously identified a major QTL QBp.caas-3BL in a recombinant inbred line (RIL) population of Linmai 2/Zhong 892 across five environments. Here we confirmed the QTL in two additional environments. The genetic region of QBp.caas-3BL was enriched with newly developed markers. Using four sets of near isogenic lines QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five annotated genes according to IWGSC reference genome. TraesCS3B02G404300, TraesCS3B02G404600 and TraesCS3B02G404700 were predicted as candidate genes based on the analyses of sequence polymorphisms and differential expression. We also converted a SNP of TraesCS3B02G404700 into a breeding-applicable KASP marker and verified its efficacy for marker-assisted breeding in a panel of germplasm. The findings not only lay a foundation for map-based cloning of QBp.caas-3BL but also provide a useful marker for selection of resistant cultivars genotypes in wheat breeding.

Background Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map. Results All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895. Conclusions This study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

Fusarium head blight (FHB) is a destructive disease of wheat worldwide, particularly in China. To map genetic loci underlying FHB resistance, a doubled haploid (DH) population consisting of 174 lines was developed from a cross between widely grown Chinese cultivars Yangmai 16 and Zhongmai 895. The DH population and parents were evaluated in field nurseries at Wuhan in 2016 to 2017 and 2017 to 2018 crop seasons with both spray inoculation and natural infection, and at Jingzhou in 2017 to 2018 crop season with grain-spawn inoculation. The DH lines were genotyped with a wheat 660K SNP array. The FHB index, plant height, anther extrusion, and days to anthesis were recorded and used for quantitative trait loci (QTL) analysis. Seven QTL for FHB resistance were mapped to chromosome arms 3BL, 4AS, 4BS, 4DS, 5AL, 6AL, and 6BS in at least two environments. QFhb.caas-4BS and QFhb.caas-4DS co-located with semi-dwarfing alleles Rht-B1b and Rht-D1b, respectively, and were associated with anther extrusion. The other five QTL were genetically independent of the agronomic traits, indicating their potential value when breeding for FHB resistance. Based on correlations between FHB indices and agronomic traits in this population, we concluded that increasing plant height to some extent would enhance FHB resistance, that anther extrusion had a more important role in environments with less severe FHB, and that days to anthesis were independent of the FHB response when viewed across years. PCR-based markers were developed for the 3BL and 5AL QTL, which were detected in more than three environments. The InDel marker InDel_AX-89588684 for QFhb.caas-5AL was also validated on a wheat panel, confirming its effectiveness for marker-assisted breeding for improvements in FHB resistance.

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.

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.

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, is an economically devastating disease of wheat worldwide. Fhb1, a widely used genetic source of FHB resistance, originated in East Asia. The recent cloning of Fhb1 opens a new avenue to improve FHB resistance in wheat and potentially other crops.

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

Background Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. Results Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction. Conclusion SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction. Electronic supplementary material The online version of this article (10.1186/s12870-017-1167-3) contains supplementary material, which is available to authorized users.

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.

The content and composition of seed storage proteins is largely responsible for wheat end-use quality. They mainly consist of polymeric glutenins and monomeric gliadins. According to their electrophoretic mobility, gliadins and glutenins are subdivided into several fractions. Glutenins are classified as high molecular weight or low molecular weight glutenin subunits (HMW-GSs and LMW-GSs, respectively). LMW-GSs are encoded by multigene families located at the orthologous Glu-3 loci. We designed a set of 16 single-nucleotide polymorphism (SNP) markers that are able to detect SDS-PAGE alleles at the Glu-A3 and Glu-B3 loci. The SNP markers captured the diversity of alleles in 88 international reference lines and 27 Mexican cultivars, when compared to SDS-PAGE and STS markers, however, showed a slightly larger percent of multiple alleles, mainly for Glu-B3. SNP markers were then used to determine the Glu-1 and Glu-3 allele composition in 54 CIMMYT historical lines and demonstrated to be useful tool for breeding programs to improve wheat end product properties.

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.

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.

BackgroundWheat 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.ResultsHere 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.2andQDek.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.ConclusionsThree 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.

Background Identification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits. Results A total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90 K and 660 K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8 Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4–725.8 Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS. Conclusions The loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY. Electronic supplementary material The online version of this article (10.1186/s12870-019-1781-3) contains supplementary material, which is available to authorized users.

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 BC

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. 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.

We cloned TaSST genes, developed a gene-specific marker for TaSST - D1 , and identified three QTL in the Doumai/Shi 4185 RIL population. TaSST - D1 is within one of the three QTL. Sucrose:sucrose-1-fructosyltransferase (1-SST), a critical enzyme in the fructan biosynthetic pathway, is significantly and positively associated with water soluble carbohydrate (WSC) content in bread wheat stems. In the present study, wheat 1-SST genes (TaSST) were isolated and located on chromosomes 4A, 7A and 7D. Sequence analysis of TaSST-D1 revealed 15 single nucleotide polymorphisms (SNP) in the third exon between cultivars with higher and lower WSC content. A cleaved amplified polymorphism sequence (CAPS) marker, WSC7D, based on the polymorphism at position 1216 (C-G) was developed to discriminate the two alleles. WSC7D was located on chromosome 7DS using a recombinant inbred line (RIL) population from a Doumai/Shi 4185 cross, and a set of Chinese Spring nullisomic-tetrasomic lines. TaSST-D1 co-segregated with the CAPS marker WSC7D and was linked to SNP marker BS00108793_51 on chromosome 7DS at a genetic distance of 6.1 cM. It explained 8.8, 10.9, and 11.3 % of the phenotypic variances in trials at Beijing and Shijiazhuang as well as the averaged data from those environments, respectively. Two additional QTL (QWSC.caas-4BS and QWSC.caas-7AS) besides TaSST-D1 were mapped in the RIL population. One hundred and forty-nine Chinese wheat cultivars and advanced lines tested in four environments were used to validate a highly significant (P

The recently published reference genome of Aegilops tauschii provides new insights into the originator of the D genome donor of hexaploid wheat. This will be a foundation for exploring the genomic diversity underpinning adaptive traits in wheat, and ultimately advance wheat improvement efforts.

Three novel QTL for peroxidase activity were mapped, and gene-specific markers for TaPod-A1 were developed and validated using RILs derived from the Doumai/Shi 4185 cross and 281 wheat cultivars. TaPod-A1 is within one of the three QTL. Peroxidase (POD) activity in grain is an important factor determining the color of flour and end-use products of wheat, such as noodles and steamed bread. Mapping QTL for POD activity, characterization of POD genes and development of gene-specific markers are important for molecular marker-assisted selection in wheat breeding. Quantitative trait loci (QTL) for POD activity in common wheat were mapped using a recombinant inbred line (RIL) population derived from a Doumai/Shi 4185 cross grown in four environments and genotyped using the wheat 90 K iSelect assay. Three novel QTL for POD activity, QPod.caas-3AL, QPod.caas-4BS and QPod.caas-5AS, were identified on chromosomes 3AL, 4BS and 5AS, explaining 5.3–21.2 % of phenotypic variance across environments. The full-length genomic DNA (gDNA) sequence of a POD gene, designated TaPod-A1, on chromosome 3A was characterized by homolog cloning and PCR verification. Two complementary dominant sequence-tagged site (STS) markers, POD-3A1 and POD-3A2, were developed based on single nucleotide polymorphisms (SNPs) between two alleles at the TaPod-A1 locus, amplifying 291- and 766-bp fragments in cultivars with lower and higher POD activities, respectively. The two gene-specific markers were mapped on chromosome 3AL using a set of Chinese Spring (CS) nulli-tetrasomic lines, and ditelosomic lines 3AL and 3AS. QTL analysis indicated that QPod.caas-3AL co-segregated with the gene-specific markers POD-3A1 and POD-3A2. POD-3A1 and POD-3A2 were verified on 281 wheat cultivars and advanced lines, and showed significant (P

Background Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges. Perspectives and conclusion Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes.

Wheat improvement programs require rapid assessment of large numbers of individual plots across multiple environments. Vegetation indices (VIs) that are mainly associated with yield and yield-related physiological traits, and rapid evaluation of canopy normalized difference vegetation index (NDVI) can assist in-season selection. Multi-spectral imagery using unmanned aerial vehicles (UAV) can readily assess the VIs traits at various crop growth stages. Thirty-two wheat cultivars and breeding lines grown in limited irrigation and full irrigation treatments were investigated to monitor NDVI across the growth cycle using a Sequoia sensor mounted on a UAV. Significant correlations ranging from R2 = 0.38 to 0.90 were observed between NDVI detected from UAV and Greenseeker (GS) during stem elongation (SE) to late grain gilling (LGF) across the treatments. UAV-NDVI also had high heritabilities at SE (h2 = 0.91), flowering (F)(h2 = 0.95), EGF (h2 = 0.79) and mid grain filling (MGF) (h2 = 0.71) under the full irrigation treatment, and at booting (B) (h2 = 0.89), EGF (h2 = 0.75) in the limited irrigation treatment. UAV-NDVI explained significant variation in grain yield (GY) at EGF (R2 = 0.86), MGF (R2 = 0.83) and LGF (R2 = 0.89) stages, and results were consistent with GS-NDVI. Higher correlations between UAV-NDVI and GY were observed under full irrigation at three different grain-filling stages (R2 = 0.40, 0.49 and 0.45) than the limited irrigation treatment (R2 = 0.08, 0.12 and 0.14) and GY was calculated to be 24.4% lower under limited irrigation conditions. Pearson correlations between UAV-NDVI and GY were also low ranging from r = 0.29 to 0.37 during grain-filling under limited irrigation but higher than GS-NDVI data. A similar pattern was observed for normalized difference red-edge (NDRE) and normalized green red difference index (NGRDI) when correlated with GY. Fresh biomass estimated at late flowering stage had significant correlations of r = 0.30 to 0.51 with UAV-NDVI at EGF. Some genotypes Nongda 211, Nongda 5181, Zhongmai 175 and Zhongmai 12 were identified as high yielding genotypes using NDVI during grain-filling. In conclusion, a multispectral sensor mounted on a UAV is a reliable high-throughput platform for NDVI measurement to predict biomass and GY and grain-filling stage seems the best period for selection.

Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

Neijiang 977671 and 19 near-isogenic lines with known leaf rust resistance genes were inoculated with 12 pathotypes of Puccinia triticina for postulation of leaf rust resistance genes effective at the seedling stage. The reaction pattern of Neijiang 977671 differed from those of the lines with known leaf rust resistance genes used in the test, indicating that Neijiang 977671 may carry a new leaf rust resistance gene(s). With the objective of identifying and mapping the new gene for resistance to leaf rust, F1 and F2 plants, and F2:3 families, from Neijiang 977671 × Zhengzhou 5389 (susceptible) were inoculated with Chinese P. triticina pathotype FHNQ in the greenhouse. Results from the F2 and F2:3 populations indicated that a single dominant gene, temporarily designated LrNJ97, conferred resistance. In order to identify other possible genes in Neijiang 977671 other eight P. triticina pathotypes avirulent on Neijiang 977671 were used to inoculate 25 F2:3 families. The results showed that at least three leaf rust resistance genes were deduced in Neijiang 977671. Bulked segregant analysis was performed on equal amounts of genomic DNA from 20 resistant and 20 susceptible F2 plants. SSR markers polymorphic between the resistant and susceptible bulks were used to analyze the F2:3 families. LrNJ97 was linked to five SSR loci on chromosome 2BL. The two closest flanking SSR loci were Xwmc317 and Xbarc159 at genetic distances of 4.2 and 2.2 cM, respectively. At present two designated genes (Lr50 and Lr58) are located on chromosome 2BL. In the seedling tests, the reaction pattern of LrNJ97 was different from that of Lr50. Lr50 and Lr58 were derived from T. armeniacum and Ae. triuncialis, respectively, whereas according to the pedigree of Neijiang 977671 LrNJ97 is from common wheat. Although seeds of lines with Lr58 were not available, it was concluded that LrNJ97 is likely to be a new leaf rust resistance gene.

About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker's flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.

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.

Background Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches. Results Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54–76 % and yellow pigment content (YPC) was reduced by 26–35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development. Conclusion The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0916-z) contains supplementary material, which is available to authorized users.

The wheat avenin-like proteins (ALP) are considered atypical gluten constituents and have shown positive effects on dough properties revealed using a transgenic approach. However, to date the genetic architecture of ALP genes is unclear, making it impossible to be utilized in wheat breeding. In the current study, three genes of type-b ALPs were identified and mapped to chromosomes 7AS, 4AL and 7DS. The coding gene sequence of both TaALP-7A and TaALP-7D was 855 bp long, encoding two identical homologous 284 amino acid long proteins. TaALP-4A was 858 bp long, encoding a 285 amino acid protein variant. Three alleles were identified for TaALP-7A and four for TaALP-4A. TaALP-7A alleles were of two types: type-1, which includes TaALP-7A1 andTaALP-7A2, encodes mature proteins, while type-2, represented byTaALP-7A3, contains a stop codon in the coding region and thus does not encode a mature protein. Dough quality testing of 102 wheat cultivars established a highly significant association of the type-1 TaALP-7A allele with better wheat processing quality. This allelic effects were confirmed among a range of commercial wheat cultivars. Our research makes the ALP be the first of such genetic variation source that can be readily utilized in wheat breeding.

We cloned TaSdr - A1 gene, and developed a gene-specific marker for TaSdr - A1 . A QTL for germination index at the TaSdr - A1 locus was identified in the Yangxiaomai/Zhongyou 9507 RIL population. Pre-harvest sprouting (PHS) affects yield and end-use quality in bread wheat (Triticum aestivum L.). In the present study we found an association between the TaSdr-A1 gene and PHS tolerance in bread wheat. TaSdr-A1 on chromosome 2A was cloned using a homologous cloning approach. Sequence analysis of TaSdr-A1 revealed an SNP at position 643, with the G allele being present in genotypes with lower germination index (GI) values and A in those with higher GI. These alleles were designated as TaSdr-A1a and TaSdr-A1b, respectively. A cleaved amplified polymorphism sequence (CAPS) marker Sdr2A based on the SNP was developed, and linkage mapping and QTL analysis were conducted to confirm the association between TaSdr-A1 and seed dormancy. Sdr2A was located in a 2.9 cM interval between SSR markers Xgwm95 and Xgwm372. A QTL for GI at the TaSdr-A1 locus explained 6.6, 7.3, and 8.2 % of the phenotypic variances in a Yangxiaomai/Zhongyou 9507 RIL population grown at Beijing, Shijiazhuang, and the averaged data from the two environments, respectively. Two sets of Chinese wheat cultivars used for validating the TaSdr-A1 polymorphism and the corresponding gene-specific marker Sdr2A showed that TaSdr-A1 was significantly associated with GI. Among 29 accessions with TaSdr-A1a, 24 (82.8 %) were landraces, indicating the importance of Chinese wheat landraces as sources of PHS tolerance. This study identified a novel PHS resistance allele TaSdr-A1a mainly presented in Chinese landraces and it is likely to be the causal gene for QPhs.ccsu-2A.3, providing new information for an understanding of seed dormancy.

Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus and have potential applications for wheat quality improvement through marker-assisted selection.

Kernel texture is a major factor influencing the classification and end use properties of wheat (Triticum aestivum L.), and is mainly controlled by the Puroindoline a (Pina) and Puroindoline b (Pinb) genes. Recently, a new puroindoline gene, Puroindoline b-2 (Pin b-2), was identified. In this study, 388 wheat cultivars and advanced breeding lines from the U.S. Pacific Northwest were investigated for frequencies of Puroindoline D1 alleles and Pinb-2 variants 2 and 3. Results indicated that Pinb-D1b (74.0%) was the predominant genotype among hard wheats (N = 196), the only other hard allele encountered was Pina-D1b (26.0%). Across all varieties, Pinb-2v3 was the predominant genotype (84.5%) compared with Pinb-2v2 (15.5%). However, among 240 winter wheat varieties (124 soft white, 15 club, 68 hard red and 33 hard white varieties), all carried Pinb-2v3. Among spring wheats, Pinb-2v2 and Pinb-2v3 frequencies were more variable (soft white 25.0:75.0, hard red 58.2:41.8 and hard white 40.0:60.0, respectively). Kernel texture variation was analyzed using 247 of the 388 wheat varieties grown in multi-location factorial trials in up to 7 crop years. The range of variety means among the four groups, soft winter, soft spring, hard winter and hard spring, was on the order of 15-25 single kernel characterization system (SKCS) Hardness Index. The least significant difference for each of these trials ranged from 2.8 to 5.6 SKCS Hardness Index. Observations lead to the conclusion that Pinb-2 variants do not exert a prominent effect on kernel texture, however, Pinb-2 variants do identify features of wheat germ plasm structure in the U.S. Pacific Northwest.