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Increasing wheat yield is a long-term goal for wheat breeders around the world. Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat breeding. This study evaluated nine crucial agronomic traits found in a natural population of 156 wheat varieties and 77 landraces from Sichuan, China in seven environments over two years. The results of this investigation of agronomic traits showed that the landraces had more tillers and higher kernel numbers per spike (KNS), while the breeding varieties had higher thousand-kernel weight (TKW) and kernel weight per spike (KWS). The generalized heritability (H2) values of the nine agronomic traits varied from 0.74 to 0.95. Structure analysis suggested that the natural population could be divided into three groups using 43 198 single nucleotide polymorphism (SNP) markers from the wheat 55K SNP chip. A total of 67 quantitative trait loci (QTLs) were identified by the genome-wide association study (GWAS) analysis based on the Q+K method of a mixed linear model. Three important QTLs were analyzed in this study. Four haplotypes of QFTN.sicau-7BL.1 for fertile tillers number (FTN), three haplotypes of QKNS.sicau-1AL.2 for KNS, and four haplotypes of QTKW.sicau-3BS.1 for TKW were detected. FTN-Hap2, KNS-Hap1, and TKW-Hap2 were excellent haplotypes for each QTL based on the yield performance of 42 varieties in regional trials from 2002 to 2013. The varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one haplotype. In addition, the KASP-AX-108866053 marker of QTL QKNS.sicau-1AL.2 was successfully distinguished between three haplotypes (or alleles) in 63 varieties based on the number of kernels per spike in regional trials between 2018 and 2021. These genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield.

High-molecular-weight glutenin subunits (HMW-GSs) are the most critical grain storage proteins that determine the unique processing qualities of wheat. Although it is a part of the superior HMW-GS pair (Dx5+Dy10), the contribution of the Dy10 subunit to wheat processing quality remains unclear. In this study, we elucidated the effect of Dy10 on wheat processing quality by generating and analyzing a deletion mutant (with the Dy10-null allele), and by elucidating the changes to wheat flour following the incorporation of purified Dy10. The Dy10-null allele was transcribed normally, but the Dy10 subunit was lacking. These findings implied that the Dy10-null allele reduced the glutenin:gliadin ratio and negatively affected dough strength (i.e., Zeleny sedimentation value, gluten index, and dough development and stability times) and the bread-making quality; however, it positively affected the biscuit-making quality. The incorporation of various amounts of purified Dy10 into wheat flour had a detrimental effect on biscuit-making quality. The results of this study demonstrate that the Dy10 subunit is essential for maintaining wheat dough strength. Furthermore, the Dy10-null allele may be exploited by soft wheat breeding programs.

The spikelet number per spike (SNS) contributes greatly to grain yield in wheat. Identifying various genes that control wheat SNS is vital for yield improvement. This study used a recombinant inbred line population genotyped by the Wheat55K single-nucleotide polymorphism array to identify two major and stably expressed quantitative trait loci (QTLs) for SNS. One of them (QSns.sau-2SY-2D.1) was reported previously, while the other (QSns.sau-2SY-7A) was newly detected and further analyzed in this study. QSns.sau-2SY-7A had a high LOD value ranging from 4.46 to 16.00 and explained 10.21–40.78% of the phenotypic variances. QSns.sau-2SY-7A was flanked by the markers AX-110518554 and AX-110094527 in a 4.75-cM interval on chromosome arm 7AL. The contributions and interactions of both major QTLs were further analyzed and discussed. The effect of QSns.sau-2SY-7A was successfully validated by developing a tightly linked kompetitive allele specific PCR marker in an F2:3 population and a panel of 101 high-generation breeding wheat lines. Furthermore, several genes including the previously reported WHEAT ORTHOLOG OF APO1 (WAPO1), an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1) related to SNS, were predicted in the interval of QSns.sau-2SY-7A. In summary, these results revealed the genetic basis of the multi-spikelet genotype of wheat line 20828 and will facilitate subsequent fine mapping and breeding utilization of the major QTLs.

Understanding the genetic basis of quality-related traits contributes to the improvement of grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) in wheat. In this study, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed on 236 wheat accessions, including 160 cultivars and 76 landraces, using a 55K single nucleotide polymorphism (SNP) array in multiple environments. A total of 12 stable QTL/SNPs that control different quality traits in this populations in at least two environments under stripe rust stress were identified. Among these 12, three, seven and two QTLs associated with GPC, GSC and WGC were characterized, respectively, and they were located on chromosomes (chr) 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D with the phenotypic variation explained (PVE) ranging from 4.2 to 10.7%. Compared with the previously reported QTLs/genes, five QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, and QWgc.sicau-5DL) were potentially novel. KASP markers for the SNPs AX-108770574 and AX-108791420 on chr5D associated with wet gluten concentration were successfully developed. The phenotypes of the cultivars containing the A-allele in AX-108770574 and the T-allele in AX-108791420 were extremely significantly (P

Uppermost-internode diameter (UID) is a key morphological trait associated with spike development and yield potential in wheat. Our understanding of its genetic basis remains largely unknown. Here, quantitative trait loci (QTLs) for UID with high-density genetic maps were identified in five wheat recombinant inbred line (RIL) populations. In total, 25 QTLs for UID were detected in five RIL populations, and they were located on chromosomes 1A, 1D (3 QTL), 2B (2), 2D (3), 3B, 3D, 4A, 4B (3), 4D, 5A (5), 5B (2), 6B, and 7D. Of them, five major and stable QTLs (QUid.sau-2CN-1D.1, QUid.sau-2SY-1D, QUid.sau-QZ-2D, QUid.sau-SC-3D, and QUid.sau-AS-4B) were identified from each of the five RIL populations in multiple environments. QUid.sau-2CN-1D.1, QUid.sau-2SY-1D and QUid.sau-SC-3D are novel QTLs. Kompetitive Allele Specific PCR (KASP) markers tightly linked to them were further investigated for developing near-isogenic lines (NILs) carrying the major loci. Furthermore, candidate genes at these intervals harboring major and stable QTLs were predicted, and they were associated with plant development and water transportation in most cases. Comparison of physical locations of the identified QTL on the ‘Chinese Spring’ reference genome showed that several QTLs including two major ones, QUid.sau-2CN-1D.1 and QUid.sau-2SY-1D, are likely allelic confirming their validity and effectiveness. The significant relationships detected between UID and other agronomic traits and a proper UID were discussed. Collectively, our results dissected the underlying genetic basis for UID in wheat and laid a foundation for further fine mapping and map-based cloning of these QTLs.

Synthetic hexaploid wheat (SHW), possesses numerous genes for drought that can help breeding for drought-tolerant wheat varieties. We evaluated 10 root traits at seedling stage in 111 F9 recombinant inbred lines derived from a F2 population of a SHW line (SHW-L1) and a common wheat line, under normal (NC) and polyethylene glycol-simulated drought stress conditions (DC). We mapped quantitative trait loci (QTLs) for root traits using an enriched high-density genetic map containing 120370 single nucleotide polymorphisms (SNPs), 733 diversity arrays technology markers (DArT) and 119 simple sequence repeats (SSRs). With four replicates per treatment, we identified 19 QTLs for root traits under NC and DC, and 12 of them could be consistently detected with three or four replicates. Two novel QTLs for root fresh weight and root diameter under NC explained 9 and 15.7% of the phenotypic variation respectively, and six novel QTLs for root fresh weight, the ratio of root water loss, total root surface area, number of root tips, and number of root forks under DC explained 8.5–14% of the phenotypic variation. Here seven of eight novel QTLs could be consistently detected with more than three replicates. Results provide essential information for fine-mapping QTLs related to drought tolerance that will facilitate breeding drought-tolerant wheat cultivars.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most damaging diseases of wheat. Chinese wheat cultivar Mianmai 41 showed high resistance against most of the prevailing Pst races in China. Genetic analysis of the F1, F2 and F2:3 populations from a cross between Mianmai 41 and a susceptible line Mingxian 169 indicated that resistance to Pst race CYR32 was conferred by a single dominant gene, temporarily designated as YrMY41. Molecular marker analysis placed the gene on chromosome 1B near the centromere. Six co-dominant genomic SSR markers Xwmc329, Xwmc406, Xgwm18, Xgwm131, Xgwm413, and Xbarc312, and one STS marker Xwe173 linked with the resistance gene. The two closest flanking SSR markers were Xgwm18 and Xwmc406, with genetic distances of 2.0 and 4.9 cM, respectively. A seedling test with 29 Pst isolates indicated the reaction patterns of Mianmai 41 were different from those of lines carrying Yr3, Yr9, Yr10, Yr15, Yr26, and YrCH42 on chromosome 1B. Allelic tests indicated that YrMY41 is likely a new allele at Yr26 locus.

Starch is the major carbohydrate in oat (Avena sativa L.) and starch formation requires the coordinated actions of several synthesis enzymes. In this study, the granule morphology, composition and physicochemical properties of oat starch, as well as the expressions of starch synthesis genes were investigated during oat endosperm development. Under the scanning electron microscopy (SEM), we observed that the unique compound granules were developed in oat endosperms at 10 days post anthesis (DPA) and then fragmented into irregular or polygonal simple granules from 12 DPA until seed maturity. The amylose content, branch chain length of degree of polymerization (DP=13–24), gelatinization temperature and percentage of retrogradation were gradually increased during the endosperm development; whereas the distribution of short chains (DP=6–12) were gradually decreased. The relative expressions of 4 classes of 13 starch synthesis genes characterized in this study indicated that three expression pattern groups were significantly different among gene classes as well as among varied isoforms, in which the first group of starch synthesis genes may play a key role on the initiation of starch synthesis in oat endosperms.

Micronutrient malnutrition affects over three billion people worldwide, especially women and children in developing countries. Increasing the bioavailable concentrations of essential elements in the edible portions of crops is an effective resolution to address this issue. To determine the genetic factors controlling micronutrient concentration in wheat, the quantitative trait locus (QTL) analysis for iron, zinc, copper, manganese, and selenium concentrations in two recombinant inbred line populations was performed. In all, 39 QTLs for five micronutrient concentrations were identified in this study. Of these, 22 alleles from synthetic wheat SHW-L1 and seven alleles from the progeny line of the synthetic wheat Chuanmai 42 showed an increase in micronutrient concentrations. Five QTLs on chromosomes 2A, 3D, 4D, and 5B found in both the populations showed significant phenotypic variation for 2–3 micronutrient concentrations. Our results might help understand the genetic control of micronutrient concentration and allow the utilization of genetic resources of synthetic hexaploid wheat for improving micronutrient efficiency of cultivated wheat by using molecular marker-assisted selection.

Aegiliops tauschii is classified into two subspecies: Ae. tauschii ssp. tauschii and Ae. tauschii ssp. strangulata. Novel genetic variations exist in Ae. tauschii ssp. tauschii that can be utilized in wheat improvement. We synthesized a hexaploid wheat genotype (SHW-L1) by crossing an Ae. tauschii ssp. tauschii accession (AS60) with a tetraploid wheat genotype (AS2255). A population consisting of 171 F8 recombinant inbred lines was developed from SHW-L1 and Chuanmai 32 to identify QTLs associated with agronomic traits. A new genetic map with high density was constructed and used to detect the QTLs for heading date, kernel width, spike length, spikelet number, and thousand kernel weight. A total of 30 putative QTLs were identified for five investigated traits. Thirteen QTLs were located on D genomes of SHW-L1, six of them showed positive effect on agronomic traits. Chromosome region flanked by wPt-6133–wPt-8134 on 2D carried five environment-independent QTLs. Each QTL accounted for more than 10% phenotypic variance. These QTLs were highly consistent across environments and should be used in wheat breeding.

γ-Gliadins are an important component of wheat seed storage proteins. Four novel γ-gliadin genes (Gli-ng1 to Gli-ng4) were cloned from wheat (Triticum aestivum) and Aegilops species. The novel γ-gliadins were much smaller in molecular size when compared to the typical γ-gliadins, which was caused by deletion of the non-repetitive domain, glutamine-rich region, 3' part of the repetitive domain, and 5' part of the C-terminal, possibly due to illegitimate recombination between the repetitive domain and the C-terminal. As a result, Gli-ng1 and Gli-ng4 only contained two and three cysteine residues, respectively. Gli-ng1, as the representative of novel γ-gliadin genes, has been sub-cloned into an Escherichia coli expression system. SDS-PAGE indicated that the both cysteine residues of Gli-ng1 could participate in the formation of intermolecular disulphide bonds in vitro. Successful cloning of Gli-ng1 from seed cDNA of T. aestivum cv. Chinese Spring suggested that these novel γ-gliadin genes were normally transcribed during the development of seeds. Phylogenic analysis indicated that the four novel γ-gliadin genes had a closer relationship with those from the B (S) genome of wheat.

Waterlogging is a widespread limiting factor for wheat production throughout the world. To identify quantitative trait loci (QTLs) associated with waterlogging tolerance at early stages of growth, survival rate (SR), germination rate index (GRI), leaf chlorophyll content index (CCI), root length index (RLI), plant height index (PHI), root dry weight index (RDWI), shoot dry weight index (SDWI), and total dry weight index (DWI) were assessed using the International Triticeae Mapping Initiative (ITMI) population W7984/Opata85. Significant and positive correlations were detected for all traits in this population except RLI. A total of 32 QTLs were associated with waterlogging tolerance on all chromosomes except 3A, 3D, 4B, 5A, 5D, 6A, and 6D. Some of the QTLs explained large proportions of the phenotypic variance. One of these is the QTL for GRI on 7A, which explained 23.92% of the phenotypic variation. Of them, 22 alleles from the synthetic hexaploid wheat W7984 contributed positively. These results suggested that synthetic hexaploid wheat W7984 is an important genetic resource for waterlogging tolerance in wheat. These alleles conferring waterlogging tolerance at early stages of growth in wheat could be utilized in wheat breeding for improving waterlogging tolerance.

Genetic diversity of 62 Sichuan wheat landraces accessions of China was investigated by agronomic traits and SSR markers. The landrace population showed the characters of higher tiller capability and more kernels/spike, especially tiller no./plant of six accessions was over 40 and kernels/spike of three accessions was more than 70. A total of 547 alleles in 124 polymorphic loci were detected with an average of 4.76 alleles per locus by 114 SSR markers. Parameters analysis indicated that the genetic diversity ranked as genome A > genome B > genome D, and the homoeologous groups ranked as 5>4>3>1>2>7>6 based on genetic richness (Ri). Furthermore, chromosomes 2A, 1B and 3D had more diversity than that of chromosomes 4A, 7A and 6B. The variation of SSR loci on chromosomes 1B, 2A, 2D, 3B, and 4B implied that, in the past, different selective pressures might have acted on different chromosome regions of these landraces. Our results suggested that Sichuan common wheat landraces is a useful genetic resource for genetic research and wheat improvement.