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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 F 1 , F 2 plants and F 2:3 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., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2024 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

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., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Competing Interests: Conflict of interest The authors declare no competing interests.

Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

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., (© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

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., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The utilization of reduced plant height genes Rht-B1b and Rht-D1b, encoding homeologous DELLA proteins, led to the wheat Green Revolution (GR). However, the specific functions of GR genes in yield determination and the underlying regulatory mechanisms remained unknown. Here, we validated that Rht-B1b, as a representative of GR genes, affects plant architecture and yield component traits. Upregulation of Rht-B1b reduced plant height, leaf size and grain weight, but increased tiller number, tiller angle, spike number per unit area, and grain number per spike. Dynamic investigations showed that Rht-B1b increased spike number by improving tillering initiation rather than outgrowth, and enhanced grain number by promoting floret fertility. Rht-B1b reduced plant height by reducing cell size in the internodes, and reduced grain size or weight by decreasing cell number in the pericarp. Transcriptome analyses uncovered that Rht-B1b regulates many homologs of previously reported key genes for given traits and several putative integrators for different traits. These findings specify the pleiotropic functions of Rht-B1b in improving yield and provide new insights into the regulatory mechanisms underlying plant morphogenesis and yield formation., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2023. Published by The Company of Biologists Ltd.)

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., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Powdery mildew caused by Blumeria graminis f. sp. tritici is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of B. graminis f. sp. tritici isolates, named #Bgt-HB and #Bgt-BJ . Using genotypic data obtained from the Wheat TraitBreed 50K single-nucleotide polymorphism array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1, and 6BL.2. The QTL on 2AL conferred all-stage resistance to B. graminis f. sp. tritici race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB . The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL , QPmja.caas-4DL , and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both B. graminis f. sp. tritici mixtures, indicating their probable broad-spectrum resistance. A Kompetitive allele-specific PCR marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Because both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders., Competing Interests: The author(s) declare no conflict of interest.

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., (© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Background: Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments., Results: We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection., Conclusion: Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat., (© 2023. BioMed Central Ltd., part of Springer Nature.)

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., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits., Results: Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions., Conclusion: This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding., (© 2023. The Author(s).)

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., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2022 John Wiley & Sons Ltd.)

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., (© 2022. The Author(s).)

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 F 1 , 7,325 F 2 plants and 117 F 2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F 2:3 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., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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 ; R 2  = 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., (© 2022 Society for Experimental Biology and John Wiley & Sons Ltd.)

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 (r 2 ) ranged between 0.57 and 0.74. The r 2 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., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2022. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2022 The Authors. Comprehensive Reviews in Food Science and Food Safety published by Wiley Periodicals LLC on behalf of Institute of Food Technologists.)

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&#95;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., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

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., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

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., (© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)

Key Message: A major QTL QTgw.caas-5B for thousand grain weight in wheat was fine mapped on chromosome 5B, and TraesCS5B02G044800 was predicted to be the candidate gene. Thousand grain weight (TGW), determined by grain length and width, and is an important yield component in wheat; understanding of the underlying genes and molecular mechanisms remains limited. A stable QTL QTgw.caas-5B for TGW was identified previously in a RIL population developed from a cross between Zhongmai 871 (ZM871) and a sister line Zhongmai 895 (ZM895), and the aim of this study was to perform fine mapping and validate the genetic effect of the QTL. It was delimited to an interval of approximately 2.0 Mb flanked by markers Kasp&#95;5B29 and Kasp&#95;5B31 (49.6-51.6 Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC 1 F 6 line selected from the ZM871/ZM895//ZM871 population. A candidate gene was predicted following sequencing and differential expression analyses. Marker Kasp&#95;5B&#95;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., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Key Message: We fine-mapped QBp.caas-3BL for black point resistance in an interval of 1.7 Mb containing five high-confidence annotated genes and developed a KASP marker suitable for selection of QBp.caas-3BL. 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 are 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., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: A genome-wide association analysis identified diverse loci for seedling and adult plant resistance to leaf rust and stripe rust. KASP markers were developed and validated for marker-assisted selection. Wheat leaf rust and stripe rust cause significant losses in many wheat producing regions worldwide. The objective of this study was to identify chromosome regions conferring resistance to both leaf rust and stripe rust at the seedling and adult plant stages. A diversity panel of 268 wheat lines, including 207 accessions from different wheat growing regions in China, and 61 accessions from foreign countries, were evaluated for leaf rust response at seedling stage using eight Chinese Puccinia triticina pathotypes, and also tested for leaf rust and stripe rust at adult plant stage in multiple field environments. The panel was genotyped with the Wheat 90 K Illumina iSelect SNP array. Genome-wide association mapping (GWAS) was performed using the mixed linear model (MLM). Twenty-two resistance loci including the known Lr genes, Lr1, Lr26, Lr3ka, LrZH22, and 18 potentially new loci were identified associated with seedling resistance, explaining 4.6 to 25.2% of the phenotypic variance. Twenty-two and 23 adult plant resistance (APR) QTL associated with leaf and stripe rust, respectively, were identified at adult stage, explaining 4.2-11.5% and 4.4-9.7% of the phenotypic variance. Among them, QLr-2BS was the potentially most valuable all-stage resistance gene. Seven and six consistent APR QTL were identified in multiple environments including best linear unbiased prediction (BLUP) data, respectively. Comparison with previously mapped resistance loci indicated that three of the seven leaf rust resistance APR QTL, and two of the six stripe rust resistance APR QTL were new. Four potentially pleiotropic APR QTL, including Lr46/Yr29, QLr-2AL.1/QYr-2AL.1, QLr-2AL.2/QYr-2AL.2, and QLr-5BL/QYr-5BL.1, were identified. Twelve associated SNPs were converted into kompetitive allele-specific PCR (KASP) markers and verified in bi-parental populations. The study reports genetic loci conferring resistance to both diseases, and the closely linked markers should be applicable for marker-assisted 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.

Key Message: Two major QTL for tiller angle were identified on chromosomes 1AL and 5DL, and TaTAC-D1 might be the candidate gene for QTA.caas-5DL. An ideal plant architecture is important for achieving high grain yield in crops. Tiller angle (TA) is an important factor influencing yield. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) was used to map TA by extreme pool-genotyping and inclusive composite interval mapping (ICIM). Two quantitative trait loci (QTL) on chromosomes 1AL and 5DL were identified with reduced tiller angle alleles contributed by ZM895. QTA.caas-1AL was detected in six environments, explaining 5.4-11.2% of the phenotypic variances. The major stable QTL, QTA.caas-5DL, was identified in all eight environments, accounting for 13.8-24.8% of the phenotypic variances. The two QTL were further validated using BC 1 F 4 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.

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

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., (© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Stripe rust, caused by Puccinia striiformis f. sp. tritici , is a globally devastating disease of common wheat ( Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

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

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

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., Competing Interests: The authors declare no conflict of interest.

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 F 6 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.

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

Key Message: We identified four chromosome regions harboring QTL for grain yield-related traits, and breeder-friendly KASP markers were developed and validated for marker-assisted selection. Identification of major stable quantitative trait loci (QTL) for grain yield-related traits is important for yield potential improvement in wheat breeding. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) were evaluated for thousand grain weight (TGW), grain length (GL), grain width (GW), and grain number per spike (GNS) in 10 environments and for grain filling rate in six environments. Sixty RILs, with 30 higher and 30 lower TGW, respectively, were genotyped using the wheat 660 K SNP array for preliminary QTL mapping. Four genetic regions on chromosomes 1AL, 2BS, 3AL, and 5B were identified to have a significant effect on TGW-related traits. A set of Kompetitive Allele Specific PCR markers were converted from the SNP markers on the above target chromosomes and used to genotype all 266 RILs. The mapping results confirmed the QTL named Qgw.caas-1AL, Qgl.caas-3AL, Qtgw.caas-5B, and Qgl.caas-5BS on the targeted chromosomes, explaining 5.0-20.6%, 5.7-15.7%, 5.5-17.3%, and 12.5-20.5% of the phenotypic variation for GW, GL, TGW, and GL, respectively. A novel major QTL for GNS on chromosome 5BS, explaining 5.2-15.2% of the phenotypic variation, was identified across eight environments. These QTL were further validated using BC 1 F 4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines) and 186 advanced breeding lines. Collectively, selective genotyping is a simple, economic, and effective approach for rapid QTL mapping and can be generally applied to genetic mapping studies for important agronomic traits.

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.

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

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

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

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., (Copyright © 2019 Afzal et al.)

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 R 2  = 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 (h 2  = 0.91), flowering (F)(h 2  = 0.95), EGF (h 2  = 0.79) and mid grain filling (MGF) (h 2  = 0.71) under the full irrigation treatment, and at booting (B) (h 2  = 0.89), EGF (h 2  = 0.75) in the limited irrigation treatment. UAV-NDVI explained significant variation in grain yield (GY) at EGF (R 2  = 0.86), MGF (R 2  = 0.83) and LGF (R 2  = 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 (R 2  = 0.40, 0.49 and 0.45) than the limited irrigation treatment (R 2  = 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., (Copyright © 2018 Elsevier B.V. All rights reserved.)

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.

Key Message: 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.