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Plant height is a key agronomic trait that is closely to the plant morphology and lodging resistance in wheat. However, at present, the few dwarf genes widely used in wheat breeding have narrowed wheat genetic diversity. In this study, we selected a semi-dwarf wheat mutant dwarf33 that exhibits decreased plant height with little serious negative impact on other agronomic traits. Genetic analysis and mutant gene mapping indicated that dwarf33 contains a new recessive semi-dwarf gene Rht-SN33d, which was mapped into ~1.3 Mb interval on the 3DL chromosome. The gibberellin metabolism-related gene TraesCS3D02G542800, which encodes gibberellin 2-beta-dioxygenase, is considered a potential candidate gene of Rht-SN33d. Rht-SN33d reduced plant height by approximately 22.4% in mutant dwarf33. Further study revealed that shorter stem cell length may be the main factor causing plant height decrease. In addition, the coleoptile length of dwarf33 was just 9.3% shorter than that of wild-type Shaannong33. These results will help to expand our understanding of new mechanisms of wheat height regulation, and obtain new germplasm for wheat improvement. [ABSTRACT FROM AUTHOR]

Several health benefits are obtained from resistant starch, also known as healthy starch. Enhancing resistant starch with genetic modification has huge commercial importance. The variation of resistant starch content is narrow in wheat, in relation to which limited improvement has been attained. Hence, there is a need to produce a wheat population that has a wide range of variations in resistant starch content. In the present study, stable mutants were screened that showed significant variation in the resistant starch content. A megazyme kit was used for measuring the resistant starch content, digestible starch, and total starch. The analysis of variance showed a significant difference in the mutant population for resistant starch. Furthermore, four diverse mutant lines for resistant starch content were used to study the quantitative expression patterns of 21 starch metabolic pathway genes; and to evaluate the candidate genes for resistant starch biosynthesis. The expression pattern of 21 starch metabolic pathway genes in two diverse mutant lines showed a higher expression of key genes regulating resistant starch biosynthesis (GBSSI and their isoforms) in the high resistant starch mutant lines, in comparison to the parent variety (J411). The expression of SBEs genes was higher in the low resistant starch mutants. The other three candidate genes showed overexpression (BMY, Pho1, Pho2) and four had reduced (SSIII, SBEI, SBEIII, ISA3) expression in high resistant starch mutants. The overexpression of AMY and ISA1 in the high resistant starch mutant line JE0146 may be due to missense mutations in these genes. Similarly, there was a stop_gained mutation for PHO2; it also showed overexpression. In addition, the gene expression analysis of 21 starch metabolizing genes in four different mutants (low and high resistant starch mutants) shows that in addition to the important genes, several other genes (phosphorylase, isoamylases) may be involved and contribute to the biosynthesis of resistant starch. There is a need to do further study about these new genes, which are responsible for the fluctuation of resistant starch in the mutants. [ABSTRACT FROM AUTHOR]

The wheat AP2 family gene Q controls domestication traits, including spike morphology and threshability, which are critical for the widespread cultivation and yield improvement of wheat. Although many studies have investigated the molecular mechanisms of the Q gene, its direct target genes, especially those controlling spike morphology, are not clear, and its regulatory pathways are not well established. In this study, we conducted gene mapping of a wheat speltoid spike mutant and found that a new allele of the Q gene with protein truncation played a role in spike morphology variation in the mutant. Dynamic expression levels of the Q gene throughout the spike development process suggested that the transcript abundances of the mutant were decreased at the W6 and W7 scales compared to those of the WT. We identified several mutation sites on the Q gene and showed that mutations in different domains resulted in distinct phenotypes. In addition, we found that the Q gene produced three transcripts via alternative splicing and that they exhibited differential expression patterns in nodes, internodes, flag leaves, and spikes. Finally, we identified several target genes directly downstream of Q, including TaGRF1-2D and TaMGD-6B , and proposed a possible regulatory network. This study uncovered the target genes of Q, and the results can help to clarify the mechanism of wheat spike morphology and thereby improve wheat grain yield. [ABSTRACT FROM AUTHOR]

Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting wheat yield. In this study, we constructed a high-density genetic linkage map using the Wheat55K SNP Array to map quantitative trait loci (QTLs) for these traits in 207 recombinant inbred lines (RILs). A total of 37 QTLs were identified, including 9 QTLs for HD, 7 QTLs for PH, 12 QTLs for TGW, and 9 QTLs for SL, which explained 3.0–48.8% of the phenotypic variation. Kompetitive Allele Specific PCR (KASP) markers were developed based on sequencing data and used for validation of the stably detected QTLs on chromosomes 3A, 4B and 6A using 400 RILs. A QTL cluster on chromosome 4B for PH and TGW was delimited to a 0.8 Mb physical interval explaining 12.2–22.8% of the phenotypic variation. Gene annotations and analyses of SNP effects suggested that a gene encoding protein Photosynthesis Affected Mutant 68, which is essential for photosystem II assembly, is a candidate gene affecting PH and TGW. In addition, the QTL for HD on chromosome 3A was narrowed down to a 2.5 Mb interval, and a gene encoding an R3H domain-containing protein was speculated to be the causal gene influencing HD. The linked KASP markers developed in this study will be useful for marker-assisted selection in wheat breeding, and the candidate genes provide new insight into genetic study for those traits in wheat. [ABSTRACT FROM AUTHOR]

The stems of cereal crops provide both mechanical support for lodging resistance and a nutrient supply for reproductive organs. Elongation, which is considered a critical phase for yield determination in winter wheat (Triticum aestivum L.), begins from the first node detectable to anthesis. Previously, we characterized a heavy ion beam triggered wheat mutant qd , which exhibited an altered stem elongation pattern without affecting mature plant height. In this study, we further analyzed mutant stem developmental characteristics by using transcriptome data. More than 40.87 Mb of clean reads including at least 36.61 Mb of unique mapped reads were obtained for each biological sample in this project. We utilized our transcriptome data to identify 124,971 genes. Among these genes, 4,340 differentially expressed genes (DEG) were identified between the qd and wild-type (WT) plants. Compared to their WT counterparts, qd plants expressed 2,462 DEGs with downregulated expression levels and 1878 DEGs with upregulated expression levels. Using DEXSeq, we identified 2,391 counting bins corresponding to 1,148 genes, and 289 of them were also found in the DEG analysis, demonstrating differences between qd and WT. The 5,199 differentially expressed genes between qd and WT were employed for GO and KEGG analyses. Biological processes, including protein-DNA complex subunit organization, protein-DNA complex assembly, nucleosome organization, nucleosome assembly, and chromatin assembly, were significantly enriched by GO analysis. However, only benzoxazinoid biosynthesis pathway-associated genes were enriched by KEGG analysis. Genes encoding the benzoxazinoid biosynthesis enzymes Bx1, Bx3, Bx4, Bx5, and Bx8_9 were confirmed to be differentially expressed between qd and WT. Our results suggest that benzoxazinoids could play critical roles in regulating the stem elongation phenotype of qd. [ABSTRACT FROM AUTHOR]

Background: Heading time is one of the most important agronomic traits in wheat, as it largely affects both adaptation to different agro-ecological conditions and yield potential. Identification of genes underlying the regulation of wheat heading and the development of diagnostic markers could facilitate our understanding of genetic control of this process. Results: In this study, we developed 400 recombinant inbred lines (RILs) by crossing a γ-ray-induced early heading mutant (eh1) with the late heading cultivar, Lunxuan987. Bulked Segregant Analysis (BSA) of both RNA and DNA pools consisting of various RILs detected a quantitative trait loci (QTL) for heading date located on chromosomes 5B, and further genetic linkage analysis limited the QTL to a 3.31 cM region. We then identified a large deletion in the first intron of the vernalization gene VRN-B1 in eh1, and showed it was associated with the heading phenotype in the RIL population. However, it is not the mutation loci that resulted in early heading phonotype in the mutant compared to that of wildtype. RNA-seq analysis suggested that Vrn-B3 and several newly discovered genes, including beta-amylase 1 (BMY1) and anther-specific protein (RTS), were highly expressed in both the mutant and early heading pool with the dominant Vrn-B1 genotype compared to that of Lunxuan987 and late heading pool. Enrichment analysis of differentially expressed genes (DEGs) identified several key pathways previously reported to be associated with flowering, including fatty acid elongation, starch and sucrose metabolism, and flavonoid biosynthesis. Conclusion: The development of new markers for Vrn-B1 in this study supplies an alternative solution for marker-assisted breeding to optimize heading time in wheat and the DEGs analysis provides basic information for VRN-B1 regulation study. [ABSTRACT FROM AUTHOR]

Homeodomain proteins encoded by BEL1 - and KNAT1 -type genes are ubiquitously distributed across plant species and play important roles in growth and development, whereby a comprehensive investigation of their molecular interactions and potential functions in wheat is of great significance. In this study, we systematically investigated the phylogenetic relationships, gene structures, conserved domains, and cis -acting elements of 34 TaBEL and 34 TaKNAT genes in the wheat genome. Our analysis revealed these genes evolved under different selective pressures and showed variable transcript levels in different wheat tissues. Subcellular localization analysis further indicated the proteins encoded by these genes were either exclusively located in the nucleus or both in the nucleus and the cytoplasm. Additionally, a comprehensive protein-protein interaction network was constructed with representative genes in which each TaBEL or TaKNAT proteins interact with at least two partners. The evaluation of wheat mutants identified key genes, including TaBEL-5B , TaBEL-4A.4 , and TaKNAT6 , which are involved in grain-related traits. Finally, haplotype analysis suggests TaKNAT-6B is associated with grain-related traits and is preferentially selected among a large set of wheat accessions. Our study provides important information on BEL1 - and KNAT1 -type gene families in wheat, and lays the foundation for functional research in the future. • Selective pressures shaped composition and structure of TaBELs and TaKNATs. • Extensive protein interactions between wheat BEL1 - and KNAT1 -type members. • Mutant analysis associates key homeobox genes with wheat kernel-related traits. • Haplotypes of TaKNAT-6B are preferentially selected in wheat accessions. [ABSTRACT FROM AUTHOR]