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Protein- and starch-related quality traits, which are quantitatively inherited and significantly influenced by the environment, are critical determinants of the end-use quality of wheat. We constructed a high-density genetic map containing 10,739 loci (5,399 unique loci) using a set of 184 recombinant inbred lines (RILs) derived from a cross of 'Tainong 18 × Linmai 6' (TL-RILs). In this study, a quantitative trait loci (QTLs) analysis was used to examine the genetic control of grain protein content, sedimentation value, farinograph parameters, falling number and the performance of the starch pasting properties using TL-RILs grown in a field for three years. A total of 106 QTLs for 13 quality traits were detected, distributed on the 21 chromosomes. Of these, 38 and 68 QTLs for protein- and starch-related traits, respectively, were detected in three environments and their average values (AV). Twenty-six relatively high-frequency QTLs (RHF-QTLs) that were detected in more than two environments. Twelve stable QTL clusters containing at least one RHF-QTL were detected and classified into three types: detected only for protein-related traits (type I), detected only for starch-related traits (type II), and detected for both protein- and starch-related traits (type III). A total of 339 markers flanked with 11 QTL clusters (all except C6), were found to be highly homologous with 282 high confidence (HC) and 57 low confidence (LC) candidate genes based on IWGSC RefSeq v 1.0. These stable QTLs and RHF-QTLs, especially those grouped into clusters, are credible and should be given priority for QTL fine-mapping and identification of candidate genes with which to explain the molecular mechanisms of quality development and inform marker-assisted breeding in the future.

Phosphorus (P) efficiency (PE), which comprises phosphorus uptake (PupE) and utilization efficiency (PutE), is considered as one of the most important factors for crop yield. In the present study, 11 seedling traits and 13 maturity traits related to wheat PE and morphology were investigated using a set of recombinant inbred lines (RILs) derived from the cross of \"TN 18 × LM 6,\" under hydroponic culture trials and field trials at low P (LP) and normal P (NP) levels in two different years, respectively. The LP input reduced of biomass, yield and PupE traits, but increased PutE traits. A total of 163 QTLs for seedling and maturity traits under different P levels and their AV, and 15 QTLs for relative traits were detected on 21 chromosomes. Of these, 49 and 63 QTLs for were detected specially in LP and NP treatments, respectively. We found 11 relatively high-frequency QTLs (RHF-QTLs) and four important QTL clusters, which may be the potential targets for marker-assisted selection (MAS) in wheat breeding programs for PE. Favorable relationships for breeding programs were found in the four important QTL clusters, which allow the possibility of improving the morphological traits and PutE simultaneously. A total of 29 markers which associated with 51 QTLs were found highly homologous with EST sequences, which suggested that they were potential functional loci. We suggested that the four biomass traits (SDW, RDW, TDW, and RSDW), five yield traits (SN, PH, TGW, GWP, and StWP) and two relative traits (Rstwp and Rgwp) can be considered as the primary indexes for the evaluation of PE for they are easy to identify on a large-scale.

Plant height (PH) in wheat is a complex trait; its components include spike length (SL) and internode lengths. To precisely analyze the factors affecting PH, two F 8:9 recombinant inbred line (RIL) populations comprising 485 and 229 lines were generated. Crosses were performed between Weimai 8 and Jimai 20 (WJ) and between Weimai 8 and Yannong 19 (WY). Possible genetic relationships between PH and PH components (PHC) were evaluated at the quantitative trait locus (QTL) level. PH and PHC (including SL and internode lengths from the first to the fourth counted from the top, abbreviated as FIITL, SITL, TITL, and FOITL, respectively) were measured in four environments. Individual and the pooled values from four trials were used in the present analysis. A QTL for PH was mapped using data on PH and on PH conditioned by PHC using IciMapping V2.2. All 21 chromosomes in wheat were shown to harbor factors affecting PH in two populations, by both conditional and unconditional QTL mapping methods. At least 11 pairwise congruent QTL were identified in the two populations. In total, ten unconditional QTL and five conditional QTL that could be detected in the conditional analysis only have been verified in no less than three trials in WJ and WY. In addition, three QTL on the short arms of chromosomes 4B, 4D, and 7B were mapped to positions similar to those of the semi-dwarfing genes Rht - B1 , Rht - D1 and Rht13 , respectively. Conditional QTL mapping analysis in WJ and WY proved that, at the QTL level, SL contributed the least to PH, followed by FIITL; TITL had the strongest influence on PH, followed by SITL and FOITL. The results above indicated that the conditional QTL mapping method can be used to evaluate possible genetic relationships between PH and PHC, and it can efficiently and precisely reveal counteracting QTL, which will enhance the understanding of the genetic basis of PH in wheat. The combination of two related populations with a large/moderate population size made the results authentic and accurate.

The wheat dough quality is of great significance for the end-use of flour. Some genes have been cloned for controlling the protein fractions, grain protein content, starch synthase, grain hardness, etc. Using a unigene map of the recombinant inbred lines (RILs) for “TN 18 × LM 6,” we mapped a quantitative trait locus (QTL) for dough stability time (ST) and SDS-sedimentation values (SV) on chromosome 6A ( QSt/Sv-6A-2851 ). The peak position of the QTL covered two candidate unigenes, and we speculated that TraesCS6A02G077000 (a xylanase inhibitor protein) was the primary candidate gene (named the TaXip gene). The target loci containing the three homologous genes TaXip-6A , TaXip-6B , and TaXip-6D were edited in the variety “Fielder” by clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR/Cas9). Two mutant types in the T 2:3 generation were obtained ( aaBBDD and AAbbdd ) with about 120 plants per type. The SVs of aaBBDD , AAbbdd , and WT were 31.77, 27.30, and 20.08 ml, respectively. The SVs of the aaBBDD and AAbbdd were all significantly higher than those of the wild type (WT), and the aaBBDD was significantly higher than the AAbbdd . The STs of aaBBDD , AAbbdd , and WT were 2.60, 2.24, and 2.25 min, respectively. The ST for the aaBBDD was significantly higher than that for WT and was not significantly different between WT and AAbbdd . The above results indicated that XIP in vivo can significantly affect wheat dough quality. The selection of TaXip gene should be a new strategy for developing high-quality varieties in wheat breeding programs.

Reducing plant height (PH) is one of the core contents of the “Green Revolution”, which began in the 1960s in wheat. A number of 27 reduced-height ( Rht ) genes have been identified and a great number of quantitative trait loci (QTLs) for PH have been mapped on all 21 chromosomes. Nonetheless, only several genes regulated PH have been cloned. In this study, we found the interval of QTL QPh-1B included an EST-SSR marker swes1079 . According to the sequence of swes1079 , we cloned the TaOSCA1.4 gene. We developed a CAPS marker to analyze the variation across a natural population. The result showed that the PH was significantly different between the two haplotypes of TaOSCA1.4–1B under most of the 12 environments and the average values of irrigation and rainfed conditions. This result further demonstrated that TaOSCA1.4 was associated with PH. Then, we validated the TaOSCA1.4 via RNAi technology. The average PHs of the wild-type (WT), RNAi lines 1 (Ri-1) and 2 (Ri-2) were 94.6, 83.6 and 79.2 cm, respectively, with significant differences between the WT and Ri-1 and Ri-2. This result indicated that the TaOSCA1.4 gene controls PH. TaOSCA1.4 is a constitutively expressed gene and its protein localizes to the cell membrane. TaOSCA1.4 gene is a member of the OSCA gene family, which regulates intracellular Ca 2+ concentration. We hypothesized that knock down mutants of TaOSCA1.4 gene reduced regulatory ability of Ca 2+ , thus reducing the PH. Furthermore, the cell lengths of the knock down mutants are not significantly different than that of WT. We speculate that TaOSCA1.4 gene is not directly associated with gibberellin (GA), which should be a novel mechanism for a wheat Rht gene.

A new genetic linkage map was constructed based on recombinant inbred lines (RILs) derived from the cross between the Chinese winter wheat (Triticum aestivum L.) varieties, Chuang 35050 and Shannong 483 (ChSh). The map included 381 loci on all the wheat chromosomes, which were composed of 167 SSR, 94 EST-SSR, 76 ISSR, 26 SRAP, 15 TRAP, and 3 Glu loci. This map covered 3636.7 cM with 1327.7 cM (36.5%), 1485.5 cM (40.9%), and 823.5 cM (22.6%) for A, B, and D genome, respectively, and contained 13 linkage gaps. Using the RILs and the map, we detected 46 putative QTLs on 12 chromosomes for grain yield (GY) per m2, thousand-kernel weight (TKW), spike number (SN) per m2, kernel number per spike (KNS), sterile spikelet number per spike (SSS), fertile spikelet number per spike (FSS), and total spikelet number per spike (TSS) in four environments. Each QTL explained 4.42–70.25% phenotypic variation. Four QTL cluster regions were detected on chromosomes 1D, 2A, 6B, and 7D. The most important QTL cluster was located on chromosome 7D near the markers of Xwmc31, Xgdm67, and Xgwm428, in which 8 QTLs for TKW, SN, SSS and FSS were observed with very high contributions (27.53–67.63%).

The English grain aphid (EGA) (Sitobion avenae F.) is one of the most destructive species of aphids in wheat- (Triticum aestivum L.) planting areas worldwide. Large quantities of insecticides are usually used to control aphid damage. The identification of new EGA-resistant genes is necessary for sustainable wheat production. The objective of this study was to identify candidate genes for EGA resistance from stable quantitative trait loci (QTLs). We previously constructed a genetic map of unigenes (UG-Map) with 31,445 polymorphic sub-unigenes via the RNA sequencing of ‘TN18 × LM6’ recombinant inbred lines (TL-RILs). The relative aphid index (RAI) for the TL-RILs was investigated for two growing seasons, with three measured times (MTs) in each season. Using the UG-Map, 43 candidate genes were identified from 22 stable QTLs, with an average of 1.95 candidate genes per QTL. Among the 34 candidate genes annotated in the reference genome Chinese Spring (CS) RefSeq v1.1, the homologous genes of seven candidate genes, TraesCS1A02G-319900, TraesCS1B02G397300, TraesCS2D02G460800, TraesCS4A02G015600LC, TraesCS5B02G329200, TraesCS-6A02G000600 and TraesCS6A02G418600LC have been previously reported to play roles in aphid resistance. This suggests that these genes are strongly associated with EGA resistance in wheat. The candidate genes in this study should facilitate the cloning of EGA-resistant genes and genetic improvement in wheat breeding programs.

Antioxidant enzymes played an important role in seed germination. In this study, Quantitative trait locus (QTLs) for activity of antioxidant enzymes (AEAs) and malondialdehyde (MDA) content in different time of seed germination were first identified, and antioxidant enzymes investigated included superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT). QTL analysis was conducted both in unconditional and conditional methods., which demonstrated the “static” and “dynamic” expression of QTLs controlling AEAs and MDA content during wheat germination, respectively. Twenty-two unconditional QTLs were detected on 1A, 1B, 1D, 2B, 2D, 3A, 4A, 6B, 7A, 7B, and the contributions ranged from 8 % of CAT3 to 28.46 % of MDA3. Fifteen conditional QTLs were detected on 1A, 1B, 1D, 2B, 2D, 4A, 5B, 6B, 7A, 7D, and the contributions ranged from 8.59 % of CAT5|3 to 30.18 % of MDA3|1.

Soil-borne wheat mosaic virus (SBWMV) is considered to be one of the most important diseases in winter wheat regions of the central and southeastern United States. Utilization of resistant cultivars is the most efficient and environmentally friendly means of control. To identify potential quantitative trait loci (QTL) or effective gene(s) for SBWMV resistance, two independent recombinant inbred line populations, Pioneer 26R61/AGS 2000 (PR61/A2000, 178 lines) and AGS 2020/LA 95135 (A2020/LA, 130 lines), were developed. Pioneer 26R61 and AGS 2020 were resistant to SBWMV, and AGS 2000 and LA 95135 were susceptible. Based on the whole genome genotyping for the PR61/A2000 population and targeted mapping of chromosome 5D for the A2020/LA, the same major QTL QSbm.uga-5DL was identified in all environments with highly significant LOD values, explaining up to 62 and 65 % of the total phenotypic variation in the PR61/A2000 and A2020/LA populations, respectively. The location of the resistance QTL coincided with previously published SBCMV resistance genes Sbm1, Sbm Claire and Sbm Tremie on the long arm of chromosome 5D. A conserved locus was therefore proposed for conditioning SBWMV/SBCMV resistance in common wheat. Validation of the QTL using the flanking markers Xbarc177 and Xbarc161 in three cultivars and three elite lines with Pioneer 26R61 in their pedigrees indicated that the markers were suitable for marker-assisted selection.

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of ‘TN18 × LM6’ (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3–10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.Key MessageWe identified a number of 36 candidate genes for FHB resistance from 19 stable QTLs. Of these, 12 candidate genes should be highly associated with FHB resistance in wheat.