Search

Genetic recombination produces new allelic combinations, thereby introducing variation for domestication. Allopolyploidization has increased the evolutionary potential of hexaploid common wheat by conferring the advantages of heterosis and gene redundancy, but whether a relationship exists between allopolyploidization and genetic recombination is currently unknown. To study the impact of allopolyploidization on genetic recombination in the ancestral D genome of wheat, we generated new synthetic hexaploid wheats by crossing tetraploid Triticum turgidum with multiple diploid Aegilops tauschii accessions, with subsequent chromosome doubling, to simulate the evolutionary hexaploidization process. Using the DArT-Seq approach, we determined the genotypes of two new synthetic hexaploid wheats with their parents, F2 plants in a diploid population (2x, D1D1 × D2D2) and its new synthetic hexaploid wheat-derived population (6x, AABBD1D1 × AABBD2D2). About 11% of detected SNP loci spanning the D genome of Ae. tauschii were eliminated after allohexaploidization, and the degree of segregation distortion was increased in their hexaploid offspring from the F2 generation. Based on codominant genotypes, the mean genetic interval length and recombination frequency between pairs of adjacent and linked SNPs on D genome of the hexaploid F2 population were 2.3 fold greater than those in the diploid F2 population, and the recombination frequency of Ae. tauschii was increased by their hexaploidization with T. turgidum. In conclusion, allopolyploidization increases genetic recombination of the ancestral diploid D genome of wheat, and DNA elimination and increased segregation distortion also occur after allopolyploidization. Increased genetic recombination could have produced more new allelic combinations subject to natural or artificial selection, helping wheat to spread rapidly to become a major global crop and thereby accelerating the evolution of wheat via hexaploidization.

Key message Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. Abstract A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.

Rye (Secale cereale L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a common wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent (Chuanmai 42) from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome breakage was detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting germplasm to enhance wheat-breeding founder parents or to breed new varieties.

Six major QTLs for wheat grain size and weight were identified on chromosomes 4A, 4B, 5A and 6A across multiple environments, and were validated in different genetic backgrounds. Grain size and weight are crucial components of wheat yield. Dissection of their genetic control is thus essential for the improvement of yield potential in wheat breeding. We used a doubled haploid (DH) population to detect quantitative trait loci (QTLs) for grain width (GW), grain length (GL), and thousand grain weight (TGW) in five environments. Six major QTLs, QGw.cib-4B.2, QGl.cib-4A, QGl.cib-5A.1, QGl.cib-6A, QTgw.cib-4B, and QTgw.cib-5A, were consistently identified in at least three individual environments and in best linear unbiased prediction (BLUP) datasets, and explained 5.65–34.06% of phenotypic variation. QGw.cib-4B.2, QTgw.cib-4B, QGl.cib-5A.1 and QGl.cib-6A had no effect on grain number per spike (GNS). In addition to QGl.cib-4A, the other major QTLs were further validated by using Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. Moreover, significant interactions between the three major GL QTLs and two major TGW QTLs were observed. Comparison analysis showed that QGl.cib-5A.1 and QGl.cib-6A are likely new loci. Notably, QGw.cib-4B.2 and QTgw.cib-4B were co-located on chromosome 4B and improved TGW by increasing only GW, unlike nearby or overlapped loci reported previously. Three genes associated with grain development within the QGw.cib-4B.2/QTgw.cib-4B interval were identified by searches on sequence similarity, spatial expression patterns, and orthologs. The major QTLs and KASP markers reported here will be useful for elucidating the genetic architecture of grain size and weight and for developing new wheat cultivars with high and stable yield.

Two major and stable QTLs for spike compactness and length were detected and validated in multiple genetic backgrounds and environments, and their pleiotropic effects on yield-related traits were analyzed. Spike compactness (SC) and length (SL) are greatly associated with wheat (Triticum aestivum L.) grain yield. To detect quantitative trait loci (QTL) associated with SC and SL, two biparental populations derived from crosses of Chuanmai42/Kechengmai1 and Chuanmai42/Chuannong16 were employed to perform QTL mapping in five environments. A total of 34 QTLs were identified, in which six major QTLs were repeatedly detected in more than four environments and the best linear unbiased prediction datasets, explaining 7.13–33.6% of phenotypic variation. These major QTLs were co-located in two genomic regions on chromosome 5A and 6A, namely QSc/Sl.cib-5A and QSc/Sl.cib-6A, respectively. By developing kompetitive allele-specific PCR (KASP) markers that linked to them, the two loci were validated in different genetic backgrounds, and their interactions were also analyzed. Comparison analysis showed that QSc/Sl.cib-5A was not Vrn-A1 and Q, and QSc/Sl.cib-6A was likely a new locus for SC and SL. Both QSc/Sl.cib-5A and QSc/Sl.cib-6A had pleiotropic effects on other yield-related traits including plant height, thousand grain weight and grain length. Therefore, the two loci combined with the developed KASP markers might be potentially applicable in wheat breeding. Furthermore, based on the spatiotemporal expression patterns, gene annotation, orthologous search and sequence differences, TraesCS5A01G301400 and TraesCS6A01G090300 were considered as potential candidates for QSc/Sl.cib-5A and QSc/Sl.cib-6A, respectively. These results provided valuable information for fine mapping and cloning of the two loci in the future.

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

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a serious disease in bread wheat (Triticum aestivum L.). Identification and use of adult plant resistance (APR) resources are important for stripe rust resistance breeding. Bread wheat line C33 is an exotic germplasm that has shown stable APR to stripe rust for more than 10 years in Sichuan Province of China. Here, 183 recombinant inbred lines (RILs) derived from the cross between C33 and a susceptible line X440 were genotyped with diversity arrays technology (DArT) markers to identify resistance quantitative trait locus (QTL). Field trials were conducted in five years at Chengdu and Xindu of Sichuan Province, using maximum disease severity (MDS) as stripe rust reaction phenotypes. A total of four quantitative trait loci (QTLs) were detected, respectively designed as QYr.saas-3AS, QYr.saas-5AL, QYr.saas-5BL, and QYr.saas-7DS, explaining 4.14–15.21% of the phenotypic variances. QYr.saas-5BL and QYr.saas-7DS were contributed by C33. However, the level for stripe rust resistance contributed by them was not strong as C33, suggesting the presence of other unidentified QTLs in C33. QYr.saas-7DS corresponded to Yr18 and QYr.saas-5BL remains to be formally named. The RIL lines carrying combinations QYr.saas-5AL, QYr.saas-5BL, and QYr.saas-7DS showed comparability resistance with C33. The present study provides resources to pyramid diverse genes into locally adapted elite germplasm to improve the stripe rust resistance of bread wheat.

Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.

Background: Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with wheat (Triticum aestivum L.) grain yield. To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six or eight environments. Results: A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multiple environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked to five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. Conclusions: Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grian yield and developing new wheat varieties with high and stable yield in wheat.

Six major QTLs for wheat grain size and weight were identified on chromosomes 4A, 4B, 5A and 6A across multiple environments, and were validated in different genetic backgrounds. Grain size and weight are crucial components of wheat yield. Dissection of their genetic control is thus essential for the improvement of yield potential in wheat breeding. We used a doubled haploid (DH) population to detect quantitative trait loci (QTLs) for grain width (GW), grain length (GL), and thousand grain weight (TGW) in five environments. Six major QTLs, QGw.cib-4B.2, QGl.cib-4A, QGl.cib-5A.1, QGl.cib-6A, QTgw.cib-4B, and QTgw.cib-5A, were consistently identified in at least three individual environments and in best linear unbiased prediction (BLUP) datasets, and explained 5.65-34.06% of phenotypic variation. QGw.cib-4B.2, QTgw.cib-4B, QGl.cib-5A.1 and QGl.cib-6A had no effect on grain number per spike (GNS). In addition to QGl.cib-4A, the other major QTLs were further validated by using Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. Moreover, significant interactions between the three major GL QTLs and two major TGW QTLs were observed. Comparison analysis showed that QGl.cib-5A.1 and QGl.cib-6A are likely new loci. Notably, QGw.cib-4B.2 and QTgw.cib-4B were co-located on chromosome 4B and improved TGW by increasing only GW, unlike nearby or overlapped loci reported previously. Three genes associated with grain development within the QGw.cib-4B.2/QTgw.cib-4B interval were identified by searches on sequence similarity, spatial expression patterns, and orthologs. The major QTLs and KASP markers reported here will be useful for elucidating the genetic architecture of grain size and weight and for developing new wheat cultivars with high and stable yield.

Two major and stable QTLs for spike compactness and length were detected and validated in multiple genetic backgrounds and environments, and their pleiotropic effects on yield-related traits were analyzed. Spike compactness (SC) and length (SL) are greatly associated with wheat (Triticum aestivum L.) grain yield. To detect quantitative trait loci (QTL) associated with SC and SL, two biparental populations derived from crosses of Chuanmai42/Kechengmai1 and Chuanmai42/Chuannong16 were employed to perform QTL mapping in five environments. A total of 34 QTLs were identified, in which six major QTLs were repeatedly detected in more than four environments and the best linear unbiased prediction datasets, explaining 7.13-33.6% of phenotypic variation. These major QTLs were co-located in two genomic regions on chromosome 5A and 6A, namely QSc/Sl.cib-5A and QSc/Sl.cib-6A, respectively. By developing kompetitive allele-specific PCR (KASP) markers that linked to them, the two loci were validated in different genetic backgrounds, and their interactions were also analyzed. Comparison analysis showed that QSc/Sl.cib-5A was not Vrn-A1 and Q, and QSc/Sl.cib-6A was likely a new locus for SC and SL. Both QSc/Sl.cib-5A and QSc/Sl.cib-6A had pleiotropic effects on other yield-related traits including plant height, thousand grain weight and grain length. Therefore, the two loci combined with the developed KASP markers might be potentially applicable in wheat breeding. Furthermore, based on the spatiotemporal expression patterns, gene annotation, orthologous search and sequence differences, TraesCS5A01G301400 and TraesCS6A01G090300 were considered as potential candidates for QSc/Sl.cib-5A and QSc/Sl.cib-6A, respectively. These results provided valuable information for fine mapping and cloning of the two loci in the future.

Introgressing one-eighth of synthetic hexaploid wheat genome through a double top-cross plus a two-phase selection is an effective strategy to develop high-yielding wheat varieties. The continued expansion of the world population and the likely onset of climate change combine to form a major crop breeding challenge. Genetic advances in most crop species to date have largely relied on recombination and reassortment within a relatively narrow gene pool. Here, we demonstrate an efficient wheat breeding strategy for improving yield potentials by introgression of multiple genomic regions of de novo synthesized wheat. The method relies on an initial double top-cross (DTC), in which one parent is synthetic hexaploid wheat (SHW), followed by a two-phase selection procedure. A genotypic analysis of three varieties (Shumai 580, Shumai 969 and Shumai 830) released from this program showed that each harbors a unique set of genomic regions inherited from the SHW parent. The first two varieties were generated from very small populations, whereas the third used a more conventional scale of selection since one of bread wheat parents was a pre-breeding material. The three varieties had remarkably enhanced yield potential compared to those developed by conventional breeding. A widely accepted consensus among crop breeders holds that introducing unadapted germplasm, such as landraces, as parents into a breeding program is a risky proposition, since the size of the breeding population required to overcome linkage drag becomes too daunting. However, the success of the proposed DTC strategy has demonstrated that novel variation harbored by SHWs can be accessed in a straightforward, effective manner. The strategy is in principle generalizable to any allopolyploid crop species where the identity of the progenitor species is known.

Background: Genetic recombination produces different allelic combinations potentially, providing new variations to the selection pools for domestication. Allopolyploidization increases evolutionary potential of the hexaploid common wheat by taking its advantages of heterosis and gene redundancy. May there be any relationship between allopolyploidization and genetic recombination? To study the impact of allopolyploidization on genetic recombination in different ancestral genomes of wheat, we generated synthetic hexaploid wheat by crossed tetraploid Triticum turgidum with diploid Aegilops tauschii to simulate its evolutionary hexaploidization process. Results: Using Wheat Breeder’s Genotyping Array, the genotypes of F2 individuals were investigated in both tetraploid (A1A1B1B1 x A2A2B2B2) and their synthetic hexaploid wheat derived populations (A1A1B1B1DD x A2A2B2B2DD). And the genotypes of the diploid population (D1D1 x D2D2) and their synthetic hexaploid wheat derived population (AABBD1D1 x AABBD2D2) were obtained with DArT-Seq™ technology. Based on genotypes of F2 populations, the genetic recombination frequency of homologous chromosome were consequently calculated in ancestral tetraploid AABB (4x), diploid DD (2x) and their synthetic hexaploid AABBDD (6x) plants, respectively. The recombination frequency of the ancestral diploid genome DD from Aegilops tauschii was found enhanced significantly more than 2 folds after their hexaploidization, while no significant changes was found in their ancestral tetraploid genome AABB via hexaploidization.Conclusions: Allopolyploidization enhancing genetic recombination of the ancestral diploid genome is found to increase the evolutionary potential of wheat, which is beneficial for wheat to conquer their narrow origination of D genome, quickly spread and make it a major crop of the world.

Allopolyploidy increases its evolutionary potential by fixing heterosis and the advantage of gene redundancy. Allelic combinations generated from genetic recombination potentially provide many variations to the selection pools for evolution. May there be any relationship between allopolyploidization and genetic recombination? To study the impact of polyploidy on genetic recombination, we selected wheat as a model and simulated its evolution pathway of allopolyploidy by developing synthetic hexaploid wheat. The change of homologous chromosome recombination were investigated on their diploid DD and tetraploid AABB genomes after their allohexaploidization, respectively. The genetic recombination of the ancestral diploid genome ofAegilops tauschiiwas enhanced significantly more than 2 folds after their hexaploidization. Hexaploidization enhancing genetic recombination of the ancestral diploid D genome was firstly reported to be a new way to increase evolutionary potential of wheat, which is beneficial for wheat to conquer their narrow origination of D genome, quickly spread and make it a major crop of the world. Finally, re-synthetizing hexaploid wheat using diverseAe. tauschiispecies with tetraploid wheat can be considered as a pleiotropic strategy to speed adaptive evolution of bread wheat in breeding processes by increasing both gene allele types and genetic recombination variations.

Strong early vigour plays a crucial role in wheat yield improvement by enhancing resource utilization efficiency. Synthetic hexaploid wheat (SHW) combines the elite genes of tetraploid wheat with Aegilops tauschii and has been widely used in wheat genetic improvement for its abundant genetic variation. The two SHWs Syn79 and Syn80 were derived from the crossing of the same tetraploid wheat DOY1 with two different Ae. tauschii accessions, AT333 and AT428, respectively. The Syn80 possessed better early vigour traits than Syn79, theretically caused by their D genome from Ae. tauschii. To dissect their genetic basis in a hexaploid background, 203 recombinant inbred lines (RILs) derived from the cross of Syn79 x Syn80 were developed to detect quantitative trait loci (QTL) for four early biomass related traits: plant height (PH), tiller number (TN), shoot fresh weight (SFW) and shoot dry weight (SDW) per plant, under five different environmental conditions. Determined from the data of SNP markers, two genome regions on 1DS and 7D were stably associated with the four early biomass related traits showing pleiotropic effects. Four stable QTLs QPh.saas-1DS, QTn.saas-1DS, QSfw.saas-1DS and QSdw.saas-1DS explaining 7.92, 15.34, 9.64 and 10.15% of the phenotypic variation, respectively, were clustered in the region of 1DS from AX-94812958 to AX-110910133. Meanwhile, QPh.saas-7D, QTn.saas-7D, QSfw.saas-7D and QSdw.saas-7D were flanked by AX-109917900 and AX-110605376 on 7D, explaining 16.12, 24.35, 15.25 and 13.37% of the phenotypic variation on average, respectively. Moreover, these genomic QTLs on 1DS and 7D enhancing biomass in the parent Syn80 were from Ae. tauschii AT428. These findings suggest that these two QTLs from Ae. tauschii can be expressed stably in a hexaploid background at the jointing stage and be used for wheat improvement.

Novel fluorescent sequence-related amplified polymorphism (FSRAP) markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL.) recombinant inbred line population derived from a Chuanmai 42?Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B, Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24&ndash, 34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.

High molecular weight (HMW) glutenin, one of the important storage proteins of wheat, mainly confers end-use quality of wheat grain. Among the loci of HMW-GS, the locus D1 determines the breaking quality of bread wheat dough mostly. Synthetic hexaploid wheat (SHW) inherits vast genetic diversity in the D genome of Aegilops tauschii and has gradually been used as a bridge-tool for wheat improvement. Therefore, more and more HMW-GS subunit types of Ae. tauschii have been introgressed into the common wheat with irresistible application of SHW in wheat breeding. However, the traditional SDS-PAGE couldn’t distinguish Dtx5 of Ae. tauschii from Dx5 of common wheat. In this study, we developed two AS-PCR markers based on three SNPs in the HMW-GS D1 sequences of Ae. tauschii and common wheat. The sharp and stable fragments amplified by designed AS-PCR primers indicated their availability and convenience in Dtx5 and Dx5 identification. And Dx5 of common wheat obtained the amplified fragments by AS-PCR primers, while no fragment was amplified for Dtx5 of Ae. tauschii. And the amplified results were consistent in both pairs of AS-PCR primers. Moreover, Dtx5 is more highly homologous with Dx2 than Dx5 from their protein sequences.

Aegilops tauschii, the diploid D genome progenitor of the hexaploid wheat, has been used to improve modern common wheat by creating synthetic hexaploid wheat (SHW) as a bridging mechanism for wheat breeding. Most Ae. tauschii accessions have hairiness on the leaf sheath, whereas the hexaploid common wheat is usually glabrous. In this study a major QTL for leaf sheath hairiness (LSH) was detected on the long arm of chromosome 4D in two recombinant inbred line (RIL) populations produced from SHW-derived cultivar Chuanmai 42. The QTL peak was flanked by markers Xbarc48 and Xbarc1183/D_GB5Y7FA01AGCKH_224, and explained more than 75 % of the phenotypic variation. The QTL allele for LSH was contributed by Chuanmai 42, and originated from Ae. tauschii. In both RIL populations the QTL allele producing hairy leaf sheath was significantly and positively associated with increased grain yield, grain weight and grain weight per spike. Moreover, most Chuanmai 42-derived cultivars have inherited the hairy leaf sheath character. These findings suggest that the hairy leaf sheath gene in Chuanmai 42 can be applied in marker-assisted selection (MAS) as a morphologically selectable marker in breeding for high yield.

Wheat stripe rust, caused byPuccinia striiformisf. sp.tritici(Pst), is a devastating disease that can cause severe yield losses. Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease. Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailingPstraces in China. A set of 200 F6:7recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation. Genetic analysis indicated that the stripe rust resistance of TZ-2 toPstrace CYR34 was controlled by a single dominant gene, temporarily designatedYrTZ2. Through bulked segregant analysis (BSA) and SSR mapping,YrTZ2was located on chromosome arm 1BS and flanked by SSR markersXwmc230andXgwm413with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively. By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consist of 250 SNP markers) closely linked withYrTZ2were identified.YrTZ2was further delimited into a 0.8 cM genetic interval between SNP markerIWB19368and SSR markerXgwm413, and co-segregated with SNP markerIWB28744(attached with 28 SNP markers). Comparative genomics analyses revealed high level of collinearity between theYrTZ2genomic region and the orthologous region ofAegilops tauschii1DS. The genomic region between lociIWB19368andIWB31649harboringYrTZ2is orthologous to a 24.5 Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS. The genetic and comparative maps ofYrTZ2provide framework for map-based cloning and marker-assisted selection (MAS) ofYrTZ2.

A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F5:6 and F6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.

Stripe rust, a major disease in areas where cool temperatures prevail, can strongly influence grain yield. To control this disease, breeders have incorporated seedling resistance genes from a variety of sources outside the primary wheat gene pool. The wheat line C51, introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA), Syria, confers resistance to all races of Puccinia striiformis f. sp. tritici (PST) in China. To map the resistant gene(s) against stripe rust in wheat line C51, 212 F8 recombinant inbred lines (RILs) derived from the cross X440 x C51 were inoculated with Chinese PST race CYR33 (Chinese yellow rust, CYR) in the greenhouse. The result showed that C51 carried a single dominant gene for resistance (designated YrC51) to CYR33. Simple sequence repeat (SSR) and resistance gene-analogue polymorphism (RGAP) markers that were polymorphic between the parents were used for genotyping the 212 F8 RILs. YrC51 was closely linked to two SSR loci on chromosome 2BS with genetic distances of 5.1 cM (Xgwm429) and 7.2 cM (Xwmc770), and to three RGAP markers C51R1 (XLRR For / NLRR For), C51R2 (CLRR Rev / Cre3LR-F) and C51R3 (Pto kin4 / NLRRINV2) with genetic distances of 5.6, 1.6 and 9.2 cM, respectively. These RGAP-linked markers were then converted into STS markers.Among them, one STS marker, C51STS-4, was located at a genetic distance of 1.4 cM to YrC51 and was closely associated with resistance when validated in several populations derived from crosses between C51 and Sichuan cultivars. The results indicated that C51STS-4 can be used for marker assisted selection (MAS) and would facilitate the pyramiding of YrC51 with other genes for stripe rust resistance.

The objective of this research was to characterize the high level of resistance to stripe that has been observed in the released wheat cultivar, Chuanmai45. A combination of classic genetic analysis, molecular and cytogenetic methods were used to characterize resistance in an F2 population derived from Chuanmai45 and the susceptible Chuanmai42. Inheritance of resistance was shown to be conferred by two genes in Chuanmai45. Fluorescence in situ hybridization (FISH) was used along with segregation studies to show that one gene was located on a 1RS.1BL translocation. Molecular markers were employed to show that the other locus was located on chromosome 4B. The defeated gene, Yr24/26, on chromosome 1BL was present in the susceptible parent and lines that recombined this gene with the 1RS.1BL translocation were identified. The germplasm, loci, and associated markers identified in this study will be useful for application in breeding programs utilizing marker-assisted selection.

Synthetic hexaploid wheat (SHW) represents a valuable source of new resistances to a range of biotic and abiotic stresses. A recombinant inbred line (RIL) population with 127 recombinant inbred lines derived from a SHW-derived variety Chuanmai 42 crossing with a Chinese spring wheat variety Chuannong 16 was used to map QTLs for agronomic traits including grain yield, grains per square meter, thousand-kernel weight, spikes per square meter, grain number per spike, grains weight per spike, and biomass yield. The population was genotyped using 184 simple-sequence repeat (SSR) markers and 34 sequence-related amplified polymorphism (SRAP) markers. Of 76 QTLs (LOD>2.5) identified, 42 were found to have a positive effect from Chuanmai 42. The QTL QGy.saas-4D.2 associated with grain yield on chromosome 4D was detected in four of the six environments and the combined analysis, and the mean yield, across six environments, of individuals carrying the Chuanmai 42 allele at this locus was 8.9% higher than that of those lines carrying the Chuannong 16 allele. Seven clusters of the yield-coincident QTLs were detected on 1A, 4A, 3B, 5B, 4D, and 7D.

Synthetic hexaploid wheat (SHW), a carrier of multiple elite genes, is an important genetic resource in improvement of common wheat (Triticum aestivum L.). Chuanmai 42 is a wheat cultivar with high-yield potential and resistance to strip rust (Puccinia striiformis f. sp. tritici), which was developed by crossing and backcrossing Syn769 (an elite synthetic hexaploid wheat) with Sichuan commercial wheat cultivars. For understanding the genetic effects of the introgression loci from SHW in Chuanmai 42, a total of 78 introgression loci of SHW were tested in Chuanmai 42 using 1029 simple sequence repeat (SSR) markers. Using 127 recombinant inbred lines (RILs, F8) in Chuanmai 42 (introgression loci) and Chuannong 16 (Chuannong 16 loci) backgrounds, the genetic effects of the introgression loci were evaluated across 6 environments in Sichuan Province, China from 2006 to 2009. One locus from the SHW parent, Barc1183, was detected in Chuanmai 42. It was located on the long arm of chromosome 4D after idenfication using the 4DS and 4DL telosomic lines of Chinese Spring and the 4D(4A) and 4D(4B) substitution lines of Longdon (T. turgidum subsp. durum). This locus had positive effects on increasing tiller number per plant, number of effective spikes, grains per square meter, harvest index, and grain production rate. The average yield of the 6 growing environments was increased by 8.9% when comparing locus Barc1183 in Chuanmai 42 to that in Chuannong 16. Therefore, Barc1183 from SHW is a candidate locus in high-yield breeding of wheat.

Vernalization, the process of a long exposure to low temperature to induce flowering in plants, is essential for plants to adapt to cold winters. The presence of vernalization genes Vrn-A1 , -B1 , and -D1 in four cornerstone breeding parents of wheat in China (Funo, Mentana, Yanda 1817, and Bima 4) and 322 derivative varieties (mostly winter wheat) from these parents were determined using PCR based molecular method. The frequencies of the VRN−1 genes in these derivative varieties were in order of Vrn-D1 (67.1%) > Vrn-B1 (19.6%) > Vrn-A1 (5.3%), which are similar as the former conclusion that Vrn-D1 is associated with the latest heading time, Vrn-A1 the earliest, and Vrn-B1 intermediate values. The frequencies of Vrn-A1 and Vrn-B1 loci in the derivative varieties from winter wheat zones were higher than that from spring winter zones. Based on the wheat breeding history in China and the fact of non-random distribution of Vrn-A1 and Vrn-B1 in the derivative varieties from the four parents, there could be a strong selective effect on VRN−1 genes in different regions where the derivative varieties were cultivated.

With 3 figures and 3 tables Abstract Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating diseases in common wheat (Triticum aestivum L.). With the objective of identifying and tagging a new gene for resistance to stripe rust in wheat line P81, F1, F2 and F2:3 populations from the cross ‘Chuanmai 28’/P81 were inoculated with Chinese PST race CYR32 in greenhouse and field trials. P81 carried a single dominant gene for resistance (designated YrP81) to CYR32. Tests of allelism showed that YrP81 was different from Yr5, Yr10, Yr15 and Yr26. Simple sequence repeat (SSR) and resistance gene-analogue polymorphism (RGAP) between the parents were used for genotyping the F2 populations. YrP81 was closely linked to four SSR loci on chromosome 2BS with genetic distances of 18.3 cM (Xwmc25), 1.8 cM (Xgwm429), 4.1 cM (Xwmc770) and 5.3 cM (Xgwm148). Two RGAP markers RGA1 (NLRR/XLRR) and RGA2 (Pto kin4/NLRR-INV2) were also closely linked to YrP81 with genetic distances of 4.7 and 6.3 cM, respectively. The linkage map of YrP81 and molecular markers was established in the order Xwmc25-RGA2-RGA1-Xgwm429-YrP81-Xwmc770-Xgwm148. Pedigree analysis, response patterns with Chinese PST races and associations with markers suggested that YrP81 is a novel stripe rust resistance gene. The PCR-based microsatellite and RGAP markers identified here could be applied in selection of YrP81 in wheat breeding.

Genetic diversity and relationships of wild goat grass ( Aegilops tauschii Cosson) from Iran and Xinjiang, west China, as well as its weedy type from the Yellow River region of Shaanxi and Henan provinces in China were analyzed by simple sequence repeat (SSR) fingerprints. A high level of genetic diversity in Aegilops tauschii accessions from Iran was observed, and the richness of genetic diversity was followed by accessions from Shaanxi, Henan, and Xinjiang. The weedy type of Aegilops tauschii showed a close genetic relationship with the wild type from different regions in Iran. The results indicated that the weedy Aegilops tauschii found in the Yellow River region was most likely introduced from Iran—the diversity center of Aegilops tauschii . The weedy Aegilops tauschii populations found in the Yellow River region may be brought into the central part of China as a weed species together with common wheat ( Triticum aestivum L.) from the West during various periods of time in history. This finding has provided strong evidence for the introduction of common wheat from the West into China via the Silk Road, and also demonstrated the important role of the Silk Road in the exchange of agriculture and other relevant technologies between China and the West.

Photoperiod response is of great importance for optimal adaptation of bread wheat cultivars to specific environments, and variation is commonly associated with allelic differences at the Ppd-D1 locus on chromosome 2D. A total of 926 Chinese wheat landraces and improved cultivars collected from nine wheat growing zones were tested for their genotypes at the Ppd-D1 locus using allele-specific markers. The average frequency of the photoperiod-insensitive Ppd-D1a allele was 66.0%, with the frequencies of 38.6 and 90.6% in landraces and improved cultivars, respectively. However, the Ppd-D1a allele was present in all improved cultivars released after 1970 except for spring wheats in high latitude northwestern China, and winter wheats in Gansu and Xinjiang. The presence of the Ppd-D1a allele in landraces and improved cultivars increased gradually from north to south, illustrating the relationship between photoperiod response and environment. Ppd-D1a in Chinese wheats is derived from three sources, Japanese landrace Akagomughi and Chinese landraces Mazhamai and Youzimai. The current information is important for understanding the broad adaptation of improved Chinese wheat cultivars.

Common wheat is one of the most important crops in China, which is the largest producer in the world. A set of 230 cultivars was used to identify yield-related loci by association mapping. This set was tested for seven yield-related traits, viz. plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), thousand-kernel weight (TKW), kernel weight per spike (KWPS), and sterile spikelet number (SSN) per plant in four environments. A total of 106 simple sequence repeat (SSR) markers distributed on all 21 chromosomes were used to screen the set. Twenty-one and 19 of them were associated with KNPS and TKW, respectively. Association mapping detected 73 significant associations across 50 SSRs, and the phenotypic variation explained (R2) by the associations ranged from 1.54 to 23.93%. The associated loci were distributed on all chromosomes except 4A, 7A, and 7D. Significant and potentially new alleles were present on 8 chromosomes, namely 1A, 1D, 2A, 2D, 3D, 4B, 5B, and 6B. Further analysis showed that genetic effects of associated loci were greatly influenced by association panels, and the R2 of crucial loci were lower in modern cultivars than in the mini core collection, probably caused by strong selection in wheat breeding. In order to confirm the results of association analysis, yield-related favorable alleles Xgwm135-1A138, Xgwm337-1D186, Xgwm102-2D144, and Xgwm132-6B128 were evaluated in a double haploid (DH) population derived from Hanxuan10 xLumai14.These favorable alleles that were validated in various populations might be valuable in breeding for high-yield.