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Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1 eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1 eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

The erect leaf plays a crucial role in determining plant architecture, with its growth and development regulated by genetic factors. However, there has been a lack of comprehensive studies on the regulatory mechanisms governing wheat lamina joint development, thus failing to meet current breeding demands. In this study, a wheat erect leaf mutant, mths29 , induced via fast neutron mutagenesis, was utilized for QTL fine mapping and investigation of lamina joint development. Genetic analysis of segregating populations derived from mths29 and Jimai22 revealed that the erect leaf trait was controlled by a dominant single gene. Using BSR sequencing and map-based cloning techniques, the QTL responsible for the erect leaf trait was mapped to a 1.03 Mb physical region on chromosome 5A. Transcriptome analysis highlighted differential expression of genes associated with cell division and proliferation, as well as several crucial transcription factors and kinases implicated in lamina joint development, particularly in the boundary cells of the preligule zone in mths29 . These findings establish a solid foundation for understanding lamina joint development and hold promise for potential improvements in wheat plant architecture.

Tiller number greatly contributes to grain yield in wheat. Using ethylmethanesulfonate mutagenesis, we previously discovered the oligo-tillering mutant ot1 . The tiller number was significantly lower in ot1 than in the corresponding wild type from the early tillering stage until the heading stage. Compared to the wild type, the thousand-grain weight and grain length were increased by 15.41% and 31.44%, respectively, whereas the plant height and spike length were decreased by 26.13% and 37.25%, respectively. Transcriptomic analysis was conducted at the regreening and jointing stages to identify differential expressed genes (DEGs). Functional enrichment analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases showed differential expression of genes associated with ADP binding, transmembrane transport, and transcriptional regulation during tiller development. Differences in tiller number in ot1 led to the upregulation of genes in the strigolactone (SL) and abscisic acid (ABA) pathways. Specifically, the SL biosynthesis genes DWARF ( D27 ), D17 , D10 , and MORE AXILLARY GROWTH 1 ( MAX1 ) were upregulated by 3.37- to 8.23-fold; the SL signal transduction genes D14 and D53 were upregulated by 1.81- and 1.32-fold, respectively; the ABA biosynthesis genes 9 - CIS - EPOXICAROTENOID DIOXIGENASE 3 ( NCED3 ) and NCED5 were upregulated by 1.66- and 3.4-fold, respectively; and SNF1-REGULATED PROTEIN KINASE2 ( SnRK2 ) and PROTEIN PHOSPHATASE 2C ( PP2C ) genes were upregulated by 1.30- to 4.79-fold. This suggested that the tiller number reduction in ot1 was due to alterations in plant hormone pathways. Genes known to promote tillering growth were upregulated, whereas those known to inhibit tillering growth were downregulated. For example, PIN-FORMED 9 ( PIN9 ), which promotes tiller development, was upregulated by 8.23-fold in ot1 ; Ideal Plant Architecture 1 ( IPA1 ), which inhibits tiller development, was downregulated by 1.74-fold. There were no significant differences in the expression levels of TILLER NUMBER 1 ( TN1 ) or TEOSINTE BRANCHED 1 ( TB1 ), indicating that the tiller reduction in ot1 was not controlled by known genes. Our findings provide valuable data for subsequent research into the genetic bases and regulatory mechanisms of wheat tillering., Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01450-3., Competing Interests: Conflict of interestThe authors declare no competing interests., (© The Author(s) 2024.)

As climate change continues to negatively impact our farmlands, abiotic factors like salinity and drought stress increasingly threaten global food security. The development of elite germplasms with resistance to multiple abiotic stresses is essential for breeding climate-resilient wheat cultivars. In this study, we determined that the previously reported salt-tolerant st1 mutant, obtained via spaceflight mutagenesis, may also resist to drought stress at the seedling stage. Moreover, our field trial revealed that yield-related traits including plant height, 1000-grain weight, and spike number per plant were significantly increased in st1 compared to the wild type. An F 2 population of 334 individuals derived from a cross between the wild type and st1 displayed a bimodal distribution indicating that st1 plant height is controlled by a single major gene. Our Bulked Segregant Analysis and exome capture sequencing indicate that this gene is located on chromosome 4D. Further genetic linkage and gene sequence analysis suggests that a reverse mutation of Rht2 is putatively responsible for plant height variation in st1. Our genotypic and phenotypic analysis of the F 2 population and F 3 lines indicate that this reverse mutation significantly increases plant height and thousand grain weight but slightly decreases spike number per plant. Together, these results supply helpful information for the utilization of Rht2 in wheat breeding and provide an important material for breeding environmentally resilient, high-yield wheat varieties., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

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., Competing Interests: Declaration of Competing Interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be constructed as influencing the position presented in the manuscript entitled., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Hexaploid wheat (Triticum aestivum), a major staple crop, has a remarkably large genome of ~14.4 Gb (containing 106 913 high-confidence [HC] and 159 840 low-confidence [LC] genes in the Chinese Spring v2.1 reference genome), which poses a major challenge for functional genomics studies. To overcome this hurdle, we performed whole-exome sequencing to generate a nearly saturated wheat mutant database containing 18 025 209 mutations induced by ethyl methanesulfonate (EMS), carbon (C)-ion beams, or γ-ray mutagenesis. This database contains an average of 47.1 mutations per kb in each gene-coding sequence: the potential functional mutations were predicted to cover 96.7% of HC genes and 70.5% of LC genes. Comparative analysis of mutations induced by EMS, γ-rays, or C-ion beam irradiation revealed that γ-ray and C-ion beam mutagenesis induced a more diverse array of variations than EMS, including large-fragment deletions, small insertions/deletions, and various non-synonymous single nucleotide polymorphisms. As a test case, we combined mutation analysis with phenotypic screening and rapidly mapped the candidate gene responsible for the phenotype of a yellow-green leaf mutant to a 2.8-Mb chromosomal region. Furthermore, a proof-of-concept reverse genetics study revealed that mutations in gibberellic acid biosynthesis and signalling genes could be associated with negative impacts on plant height. Finally, we built a publically available database of these mutations with the corresponding germplasm (seed stock) repository to facilitate advanced functional genomics studies in wheat for the broad plant research community., (© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Background: Induction of mutation through chemical mutagenesis is a novel approach for preparing diverse germplasm. Introduction of functional alleles in the starch biosynthetic genes help in the improvement of the quality and yield of cereals., Results: In the present study, a set of 350 stable mutant lines were used to evaluate dynamic variation of the total starch contents. A megazyme kits were used for measuring the total starch content, resistant starch, amylose, and amylopectin content. Analysis of variance showed significant variation (p < 0.05) in starch content within the population. Furthermore, two high starch mutants (JE0173 and JE0218) and two low starch mutants (JE0089 and JE0418) were selected for studying different traits. A multiple comparison test showed that significant variation in all physiological and morphological traits, with respect to the parent variety (J411) in 2019-2020 and 2020-2021. The quantitative expression of starch metabolic genes revealed that eleven genes of JE0173 and twelve genes of JE0218 had consistent expression in high starch mutant lines. Similarly, in low starch mutant lines, eleven genes of JE0089 and thirteen genes of JE0418 had consistent expression in all stages of seed development. An additional two candidate genes showed over-expression (PHO1, PUL) in the high starch mutant lines, indicating that other starch metabolic genes may also contribute to the starch biosynthesis. The overexpression of SSII, SSIII and SBEI in JE0173 may be due to presence of missense mutations in these genes and SSI also showed overexpression which may be due to 3-primer&#95;UTR variant. These mutations can affect the other starch related genes and help to increase the starch content in this mutant line (JE0173)., Conclusions: This study screened a large scale of mutant population and identified mutants, could provide useful genetic resources for the study of starch biosynthesis and genetic improvement of wheat in the future. Further study will help to understand new genes which are responsible for the fluctuation of total starch., (© 2023. The Author(s).)

Background: Plant height (PH) and spike compactness (SC) are important agronomic traits that affect yield improvement in wheat crops. The identification of the loci or genes responsible for these traits is thus of great importance for marker-assisted selection in wheat breeding., Results: In this study, we used a recombinant inbred line (RIL) population with 139 lines derived from a cross between the mutant Rht8-2 and the local wheat variety NongDa5181 (ND5181) to construct a high-density genetic linkage map by applying the Wheat 40 K Panel. We identified seven stable QTLs for PH (three) and SC (four) in two environments using the RIL population, and found that Rht8-B1 is the causal gene of qPH2B.1 by further genetic mapping, gene cloning and gene editing analyses. Our results also showed that two natural variants from GC to TT in the coding region of Rht8-B1 resulted in an amino acid change from G (ND5181) to V (Rht8-2) at the 175 th position, reducing PH by 3.6%~6.2% in the RIL population. Moreover, gene editing analysis suggested that the height of T 2 generation in Rht8-B1 edited plants was reduced by 5.6%, and that the impact of Rht8-B1 on PH was significantly lower than Rht8-D1. Additionally, analysis of the distribution of Rht8-B1 in various wheat resources suggested that the Rht8-B1b allele has not been widely utilized in modern wheat breeding., Conclusions: The combination of Rht8-B1b with other favorable Rht genes might be an alternative approach for developing lodging-resistant crops. Our study provides important information for marker-assisted selection in wheat breeding., (© 2023. The Author(s).)

Key Message: A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C 2 H 2 -type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C 2 H 2 -type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F 2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Plant height is one of the most important agronomic traits that affects yield in wheat, owing to that the utilization of dwarf or semi-dwarf genes is closely associated with lodging resistance. In this study, we identified a semi-dwarf mutant, jg0030 , induced by γ-ray mutagenesis of the wheat variety 'Jing411' (wild type). Compared with the 'Jing411', plant height of the jg0030 mutant was reduced by 7%-18% in two years' field experiments, and the plants showed no changes in yield-related traits. Treatment with gibberellic acid (GA) suggested that jg0030 is a GA-sensitive mutant. Analysis of the frequency distribution of plant height in 297 F 3 families derived from crossing jg0030 with the 'Jing411' indicated that the semi-dwarf phenotype is controlled by a major gene. Using the wheat 660K SNP array-based Bulked Segregant Analysis (BSA) and the exome capture sequencing-BSA assay, the dwarf gene was mapped on the long arm of chromosome 2B. We developed a set of KASP markers and mapped the dwarf gene to a region between marker PH1 and PH7. This region encompassed a genetic distance of 55.21 cM, corresponding to a physical distance of 98.3 Mb. The results of our study provide a new genetic resource and linked markers for wheat improvement in molecular breeding programs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wang, Xiong, Guo, Zhao, Xie, Gu, Zhao, Ding and Liu.)

Heading date (HD) is an important trait for wide adaptability and yield stability in wheat. The Vernalization 1 ( VRN1 ) gene is a key regulatory factor controlling HD in wheat. The identification of allelic variations in VRN1 is crucial for wheat improvement as climate change becomes more of a threat to agriculture. In this study, we identified an EMS-induced late-heading wheat mutant je0155 and crossed it with wide-type (WT) Jing411 to construct an F 2 population of 344 individuals. Through Bulk Segregant Analysis (BSA) of early and late-heading plants, we identified a Quantitative Trait Locus (QTL) for HD on chromosome 5A. Further genetic linkage analysis limited the QTL to a physical region of 0.8 Mb. Cloning and sequencing revealed three copies of VRN-A1 in the WT and mutant lines; one copy contained a missense mutation of C changed to T in exon 4 and another copy contained a mutation in intron 5. Genotype and phenotype analysis of the segregation population validated that the mutations in VRN-A1 contributed to the late HD phenotype in the mutant. Expression analysis of C- or T-type alleles in exon 4 of the WT and mutant lines indicated that this mutation led to lower expression of VRN-A1 , which resulted in the late-heading of je0155 . This study provides valuable information for the genetic regulation of HD and many important resources for HD refinement in wheat breeding programs.

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.

Seed orchards represent the link between forest breeding and conifer production forests, and their mating patterns determine the genetic quality of seed orchard crops to a large extent. We genotyped the parental clones and their open pollination offspring in the third-generation seed orchard of Chinese fir using microsatellite markers and observed the synchronization of florescence in the seed orchard to understand the genetic diversity and mating structure of the seed orchard population. Genetic coancestry among parental clones was detected in the third generation seed orchard of Chinese fir, and the genetic diversity of the open-pollinated offspring was slightly higher than that of the parental clones. The external pollen contamination rate ranged from 10.1% to 33.7%, 80% of the offspring were produced by 44% of the parental clones in the orchard, and no evidence of selfing was found. We found that 68.1% of the effective pollination occurred within 50 m, and 19.9% of the effective pollination occurred in the nearest neighbors. We also found that successful mating requires about 30% of florescence overlap between males and females, and there was a significant positive correlation between male reproductive energy and male parental contribution. Our results provide a valuable reference for the management and design of advanced generation seed orchards., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wu, Zhao, Wang, Duan and Zhang.)

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&#95;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.

Novel genetic variations can be obtained by inducing mutations in the plant which help to achieve novel traits. The useful mutant can be obtained through radiation mutation in a short period which can be used as a new material to produce new varieties with high yield and good quality wheat. In this paper, the proteomic analysis of wheat treated with different doses of 12 C and 7 Li ion beam radiation at the seedling stage was carried out through a Tandem Mass Tag (TMT) tagging quantitative proteomic analysis platform based on high-resolution liquid chromatography-mass spectrometry, and the traditional 60 Co-γ-ray radiation treatment for reference. A total of 4,764 up-regulated and 5,542 down-regulated differentially expressed proteins were identified. These proteins were mainly enriched in the KEGG pathway associated with amino acid metabolism, fatty acid metabolism, carbon metabolism, photosynthesis, signal transduction, protein synthesis, and DNA replication. Functional analysis of the differentially expressed proteins showed that the oxidative defense system in the plant defense system was fully involved in the defense response after 12 C ion beam and 7 Li ion beam radiation treatments. Photosynthesis and photorespiration were inhibited after 12 C ion beam and 60 Co-γ-ray irradiation treatments, while there was no effect on the plant with 7 Li ion beam treatment. In addition, the synthesis of biomolecules such as proteins, as well as multiple signal transduction pathways also respond to radiations. Some selected differentially expressed proteins were verified by Parallel Reaction Monitoring (PRM) and qPCR, and the experimental results were consistent with the quantitative results of TMT. The present study shows that the physiological effect of 12 C ion beam radiation treatment is different as compared to the 7 Li ion beam, but its similar to the 60 Co-γ ray depicting a significant effect on the plant by using the same dose. The results of this study will provide a theoretical basis for the application of 12 C and 7 Li ion beam radiation in the mutation breeding of wheat and other major crops and promote the development of heavy ion beam radiation mutation breeding technology., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Li, Gu, Irshad, Zhao, Guo, Xiong, Xie, Zhao, Ding, Zhou, Kong, Fang and Liu.)

Photothermal detectors have attracted tremendous research interest in uncooled infrared imaging technology but with a relatively slow response. Here, Si/SnSe-nanorod (Si/SnSe-NR) heterojunctions are fabricated as a photothermal detector to realize high-performance infrared response beyond the bandgap limitation. Vertically standing SnSe-NR arrays are deposited on Si by a sputtering method. Through manipulating the photoinduced thermoelectric (PTE) behavior along the c -axis, the Si/SnSe-NRs heterojunction exhibits a unique four-stage photoresponse with a high photoresponsivity of 106.3 V W -1 and high optical detectivity of 1.9 × 10 10 cm Hz 1/2 W -1 under 1342 nm illumination. Importantly, an ultrafast infrared photothermal response is achieved with the rise/fall time of 11.3/258.7 μs. Moreover, the coupling effect between the PTE behavior and external thermal excitation enables an improved response by 288.4%. The work not only offers a new strategy to develop high-speed photothermal detectors but also performs a deep understanding of the PTE behavior in a heterojunction system.

Induced mutagenesis is a powerful approach for the creation of novel germplasm and the improvement of agronomic traits. The evaluation of mutagenic effects and functional variations in crops is needed for breeding mutant strains. To investigate the mutagenic effects of gamma-ray irradiation in wheat, this study characterized genomic variations of wheat early heading mutant ( eh1 ) as compared to wild-type (WT) Zhongyuan 9 (ZY9). Whole-genome resequencing of eh1 and ZY9 produced 737.7 Gb sequencing data and identified a total of 23,537,117 homozygous single nucleotide polymorphism (SNP) and 1,608,468 Indel. Analysis of SNP distribution across the chromosome suggests that mutation hotspots existed in certain chromosomal regions. Among the three subgenomes, the variation frequency in subgenome D was significantly lower than in subgenomes A and B. A total of 27.8 Gb data were obtained by exome-capturing sequencing, while 217,948 SNP and 13,554 Indel were identified. Variation annotation in the gene-coding sequences demonstrated that 5.0% of the SNP and 5.3% of the Indel were functionally important. Characterization of exomic variations in 12 additional gamma-ray-induced mutant lines further provided additional insights into the mutagenic effects of this approach. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis suggested that genes with functional variations were enriched in several metabolic pathways, including plant-pathogen interactions and ADP binding. Kompetitive allele-specific PCR (KASP) genotyping with selected SNP within functional genes indicated that 85.7% of the SNPs were polymorphic between the eh1 and wild type. This study provides a basic understanding of the mechanism behind gamma-ray irradiation in hexaploid wheat., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Li, Xiong, Zhang, Guo, Zhou, Xie, Zhao, Gu, Zhao, Ding, Fang and Liu.)

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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Xiong, Guo, Li, Xie, Xie, Zhao, Gu, Zhao, Ding and Liu.)

Stem elongation is a critical phase for yield determination and, as a major trait, is targeted for manipulation for improvement in bread wheat ( Triticum aestivum L.). In a previous study, we characterized a mutant showing rapid stem elongation but with no effect on plant height at maturity. The present study aimed to finely map the underlying mutated gene, qd1 , in this mutant. By analyzing an F 2 segregating population consisting of 606 individuals, we found that the qd1 gene behaved in a dominant manner. Moreover, by using the bulked segregant RNA sequencing (BSR-seq)-based linkage analysis method, we initially mapped the qd1 gene to a 13.55 Mb region on chromosome 4B (from 15.41 to 28.96 Mb). This result was further confirmed in F 2 and BC 3 F 2 segregating populations. Furthermore, by using transcriptome sequencing data, we developed 14 Kompetitive Allele-Specific PCR (KASP) markers and then mapped the qd1 gene to a smaller and more precise 5.08 Mb interval from 26.80 to 31.88 Mb. To develop additional markers to finely map the qd1 gene, a total of 4,481 single-nucleotide polymorphisms (SNPs) within the 5.08 Mb interval were screened, and 25 KASP markers were developed based on 10x-depth genome resequencing data from both wild-type (WT) and mutant plants. The qd1 gene was finally mapped to a 1.33 Mb interval from 28.86 to 30.19 Mb on chromosome 4B. Four candidate genes were identified in this region. Among them, the expression pattern of only TraesCS4B02G042300 in the stems was concurrent with the stem development of the mutant and WT. The qd1 gene could be used in conjunction with molecular markers to manipulate stem development in the future., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xie, Zeng, Wang, Xu, Guo, Xiong, Fang, Zhao, Gu, Zhao, Ding and Liu.)

Objectives: High-frequent opioid use tends to increase an individual's risk of opioid use disorder, overdose and death. Thus, it is important to predict an individuals' opioid use frequency to improve opioid prescription utilization outcomes., Methods: Individuals receiving at least one opioid prescription from 2016 to 2018 in the national representative data, Medical Expenditure Panel Survey, were included. This study applied five machine learning (ML) techniques, including support vector machine, random forest, neural network, gradient boosting and XGBoost (extreme gradient boosting), to predict opioid use frequency. This study compared the performance of these ML models with penalized logistic regression. The study outcome was whether an individual lied in the upper 10% of the opioid prescription distribution. Predictors were selected based on Gelberg-Andersen's Behavioral Model of Health Services Utilization. The prediction performance was assessed using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC) in the test data. Patient characteristics as predictors for high-frequency use of opioids were ranked by the relative importance in prediction in the test data., Key Findings: Random forest and gradient boosting achieved the top values of both AUROC and AUPRC, outperforming logistic regression and three other ML methods. In the best performing model, the random forest, the following characteristics had high predictive power in the frequency of opioid use: age, number of chronic conditions, public insurance and self-perceived health status., Conclusions: The results of this study demonstrate that ML techniques can be a promising and powerful technique in predicting the frequency of opioid use and health outcomes., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Pharmaceutical Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Substantial research has documented inequalities between US minorities and whites in meeting the eligibility criteria for the Medicare Part D medication therapy management (MTM) program. Even though the Centers for Medicare & Medicaid Services attempted to relax the eligibility criteria, a critical barrier to effective MTM reform is a lack of stronger evidence about the effects of MTM on minorities' health outcomes., Objective: To examine the effects of comprehensive medication review (CMR), an MTM core component, on racial and ethnic disparities in adherence to diabetes, hypertension, and hyperlipidemia medications among Medicare beneficiaries aged ≥65 years., Methods: This study used full-year 2017 Medicare Parts A, B, and D claims data, including MTM data, linked to the Area Health Resources Files. Racial and ethnic disparities in nonadherence to diabetes, hypertension, and hyperlipidemia medications were compared between CMR recipients and nonrecipients matched by their propensity scores. To determine the changes in racial and ethnic disparities after receiving CMR, a difference-in-differences framework was applied, by including in logistic regression analyses interaction terms between dummy variables for CMR receipt and each racial or ethnic minority group., Results: Compared with CMR nonrecipients, CMR recipients had significantly lower racial and ethnic disparities across the 3 outcome measures, with the exception of the difference between whites and blacks in nonadherence to diabetes medications. For example, compared with CMR nonrecipients, among CMR recipients the differences in the odds of nonadherence to hypertension medications were reduced, respectively, by 8% (95% confidence interval [CI], 0.88-0.96) between whites and blacks; by 18% (95% CI, 0.78-0.86) between whites and Hispanics; by 16% (95% CI, 0.77-0.91) between whites and Asians; and by 9% (95% CI, 0.85-0.98) between whites and other racial and ethnic groups., Conclusion: Receiving a CMR reduced the racial and ethnic disparities in adherence to diabetes, hypertension, and hyperlipidemia medications among Medicare beneficiaries aged ≥65 years. These findings provide critical empirical evidence that may inform the future design of the Medicare Part D MTM program, which is valuable for improving pharmacotherapy outcomes and could further realize its potential when additional people from racial and ethnic minorities are enrolled., (Copyright © 2021 by Engage Healthcare Communications, LLC.)

Objective: Older patients with Alzheimer's disease (AD) are challenged with adhering to complex medication regimens. We examined effects of Comprehensive Medication Review (CMR), a required Medicare Part D Medication Therapy Management (MTM) program component, on medication adherence among AD patients., Methods: This retrospective study analyzed 100% of 2016-2017 Medicare claims covering the entire United States, linked to Area Health Resources Files. Medicare beneficiaries aged ≥65 years were included. Propensity score matching identified comparable intervention and comparison groups with the intervention defined as receiving a CMR in 2017. A difference-in-differences analysis included in multivariate logistic regressions an interaction term between CMR receipt and year 2017. The outcome measured was nonadherence to diabetes, hypertension and hyperlipidemia medications, with nonadherence defined as proportion of days covered <80% for study medications., Results: Unadjusted comparisons indicated the proportion of nonadherence for intervention group members decreased from 2016 to 2017 but increased for the comparison group. In adjusted analyses, reduction in medication nonadherence among the intervention group remained higher: odds ratios for the interaction term were 0.62 (95% confidence interval [CI] = 0.54-0.71), 0.54 (95% CI = 0.50-0.58) and 0.50 (95% CI = 0.47-0.53) respectively for diabetes, hypertension and hyperlipidemia medications. This suggests that the likelihood of nonadherence in the intervention group was respectively reduced by 38%, 46% and 50% more than the comparison group., Conclusions: CMR was found to reduce nonadherence to diabetes, hypertension and hyperlipidemia medications among older Medicare beneficiaries with AD. This provides evidence that the MTM program is effective for a population with unique medication compliance challenges.

To explore the metabolic basis of carotenoid accumulation in different developmental periods of apricot fruits, targeted metabonomic and transcriptomic analyses were conducted in four developmental periods (S1-S4) in two cultivars ( Prunus armeniaca cv. "Kuchebaixing" with white flesh and P. armeniaca cv. "Shushangganxing" with orange flesh) with different carotenoid contents. 14 types of carotenes and 27 types of carotene lipids were identified in apricot flesh in different developmental periods. In S3 and S4, the carotenoid contents of the two cultivars were significantly different, and β-carotene and ( E / Z )-phytoene were the key metabolites that caused the difference in the total carotenoid content between the examined cultivars. Twenty-five structural genes (including genes in the methylerythritol 4-phosphate and carotenoid biosynthesis pathways) related to carotenoid biosynthesis were identified among the differentially expressed genes in different developmental periods of the two cultivars, and a carotenoid metabolic pathway map of apricot fruits was drawn according to the KEGG pathway map. The combined analysis of carotenoid metabolism data and transcriptome data showed that PSY , NCED1 , and CCD4 were the key genes leading to the great differences in the total carotenoid content. The results provide a new approach to study the synthesis and accumulation of carotenoids in apricot fruits.

Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A , which formed the allelic marker allele-T . Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C ; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Irshad, Guo, Ur Rehman, Wang, Gu, Xiong, Xie, Zhao, Zhao, Wang and Liu.)

Ethylene metabolism is very important for climacteric fruit, and apricots are typical climacteric fruit. The activity of pectinase is closely related to fruit firmness, which further affects fruit quality. To better understand ethylene metabolism, pectinase activity and their molecular regulation mechanisms during the development and ripening of apricot fruit, ethylene metabolism, pectinase activity and the "Luntaibaixing" apricot fruit transcriptome were analyzed at different developmental stages. Ethylene metabolic precursors, enzyme activities and ethylene release increased during fruit development and ripening, with significant differences between the ripening stage and other stages (P < 0.05). Fruit firmness decreased significantly from the S1 to S5 stages, and polygalacturonase, pectin methylesterase, and pectin lyase activities were significantly higher in the S5 stage than in other stages. RNA sequencing (RNA-seq) analysis of fruit resulted in the identification of 22,337 unigenes and 6629 differentially expressed genes (DEGs) during development and ripening, of which 20,989 unigenes are annotated in public protein databases. In functional enrichment analysis, DEGs among the three stages were found to be involved in plant hormone signal transduction. Four key genes affecting ethylene metabolism, six key ethylene signal transduction genes and seven genes related to pectinase in apricot fruit were identified by KEGG pathway analysis. By RNA-sequencing, we not only clarified the molecular mechanism of ethylene metabolism during the ripening of "Luntaibaixing" apricot fruit but also provided a theoretical basis for understanding pectin metabolism in apricot fruit.

Blast is caused by the host-specific lineages of the fungus Magnaporthe oryzae and is the most important destructive disease in major crop plants, including rice and wheat. The first wheat blast outbreak that occurred in Bangladesh in 2016 and the recent epidemic in Zambia were caused by the M. oryzae Triticum ( MoT ) pathotype, a fungal lineage belonging to M. oryzae . Although a few reported wheat cultivars show modest resistance to MoT , the patterns of genetic variation and diversity of this pathotype make it crucial to identify additional lines of resistant wheat germplasm. Nearly 40 rice blast resistant and susceptible genes have so far been cloned. Here, we used BLAST analysis to locate two rice blast susceptible genes in the wheat reference genome, bsr-d1 and bsr-k1 , and identified six identical homologous genes located on subgenomes A, B, and D. We uncovered a total of 171 single nucleotide polymorphisms (SNPs) in an ethyl methanesulfonate (EMS)-induced population, with mutation densities ranging from 1/1107.1 to 1/230.7 kb through Targeting Induced Local Lesions IN Genomes (TILLING) by sequencing. These included 81 SNPs located in exonic and promoter regions, and 13 coding alleles that are predicted to have severe effects on protein function, including two pre-mature mutants that might affect wheat blast resistance. The loss-of-function alleles identified in this study provide insights into new wheat blast resistant lines, which represent a valuable breeding resource., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Guo, Du, Xie, Xiong, Zhao, Gu, Zhao, Song, Islam and Liu.)

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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xiong, Li, Guo, Xie, Zhao, Gu, Zhao, Ding and Liu.)

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&#95;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 ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xu, Xie, Guo, Zeng, Xiong, Zhao, Gu, Zhao, Ding and Liu.)

The carotenoids in the peel and flesh of 41 apricot cultivars were qualitatively and quantitatively analysed by UHPLC-APCI-MS/MS, and the L*, a*, b* and quality indexes of the fruits were determined. The results showed that the L*, a*, b* and quality indexes of the fruits were quite different, and 13 carotenoids were detected in the peel and flesh of apricots, among which ε-carotene, α-cryptoxanthin and apocarotenal were newly detected carotenoids in apricots. The total carotenoid content of the 41 apricot cultivars varied from 20.983 to 320.278 μg/g FW, and the total carotenoid content varied from 17.353 to 222.098 μg/g FW in the peel and from 2.536 to 98.179 μg/g FW in the flesh. The main components of apricot fruits were β-carotene and (E/Z)-phytoene, followed by β-cryptoxanthin and lutein. This study shows that carotenoids in apricot fruits have rich metabolic diversity., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

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.

Induced mutation is an important approach for creating novel plant germplasms. The introduction of dwarf or semi-dwarf genes into wheat has led to great advancements in yield improvement. In this study, four elite dwarf wheat mutants, named dm1-dm4, induced from γ-ray irradiation or ethyl methanesulfonate (EMS) mutagenesis, were used to identify transcriptome variations and dwarfing mechanisms. The results showed that the hotspot regions of mutations distributed on the chromosomes were consistent among the four mutant lines and these regions were mainly located around the 50, 360 and 400 Mb positions of chromosome 1A and the distal regions of chromosomes 2A and 2BL. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that 'protein processing in endoplasmic reticulum' was the most common significantly enriched pathway based on the differentially expressed genes (DEGs) between wildtype (WT) and the mutants. Notably, 18 out of 20 genes involved in this process encode heat shock proteins (HSPs). The results implied that HSPs might participate in wheat dwarfism response and function in the dwarfism process through protein folding and/or degradation. Moreover, seven genes in dm4 involved in modulating auxin levels were down-regulated and dm4 was more sensitive to auxin treatment compared with WT, indicating the important roles of auxin in regulation of dwarf phenotype in dm4. This study not only identified transcriptome sequence variation induced by physical and chemical mutagenesis but also revealed potential dwarfing mechanisms in the wheat mutant lines., (© The Author(s) 2019. Published by Oxford University Press on behalf of The Japanese Radiation Research Society and Japanese Society for Radiation Oncology.)

Background: Wheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. Plant architecture and yield-related features are important agronomic traits for wheat breeders and mining favorable alleles of these traits will improve wheat characteristics., Results: Here we used 190 wheat phenotypic mutants as material and by analyzing their SNP variation and phenotypic data, mutation alleles for plant architecture and yield-related traits were identified, and the genetic effects of these alleles were evaluated. In total, 32 mutation alleles, including three pleiotropic alleles, significantly associated with agronomic traits were identified from the 190 wheat mutant lines. The SNPs were distributed on 12 chromosomes and were associated with plant height (PH), tiller number, flag leaf angle (FLA), thousand grain weight (TGW), and other yield-related traits. Further phenotypic analysis of multiple lines carrying the same mutant allele was performed to determine the effect of the allele on the traits of interest. PH-associated SNPs on chromosomes 2BL, 3BS, 3DL, and 5DL might show additive effects, reducing PH by 10.0 cm to 31.3 cm compared with wild type, which means that these alleles may be favorable for wheat improvement. Only unfavorable mutation alleles that reduced TGW and tiller number were identified. A region on chromosome 5DL with mutation alleles for PH and TGW contained several long ncRNAs, and their sequences shared more than 90% identity with cytokinin oxidase/dehydrogenase genes. Some of the mutation alleles we mined were colocalized with previously reported QTLs or genes while others were novel; these novel alleles could also result in phenotypic variation., Conclusion: Our results demonstrate that favorable mutation alleles are present in mutant resources, and the region between 409.5 to 419.8 Mb on chromosome 5DL affects wheat plant height and thousand grain weight.

Starch is synthesized from a series of reactions catalyzed by enzymes. ADP-glucose pyrophosphorylase (AGPase) initiates the synthesis pathway and synthesizes ADP-glucose, the substrate of starch synthase (SS), of which SSIV is an isoform. Mutations of the AGPase subunit and SSIV-coding genes affect starch content and cause variation in the number of granules. Here, we pyramided the functional mutation alleles of the AGPase subunit gene TaAGP.L-B1 and the SSIV-coding gene TaSSIVb-D to elucidate their synergistic effects on other key starch biosynthesis genes and their impact on starch content. Both the TaAGP.L-B1 and TaSSIVb-D genes were expressed in wheat grain development, and the expression level of TaAGP.L-B1 was higher than that of TaSSIVb-D. The TaAGP.L-B1 gene was downregulated in the agp.L-B1 single and agp.L-B1/ssIV-D double mutants at 12 to 18 days after flowering (DAF). TaSSIVb-D expression was significantly reduced at 6 DAF in both ssIV-D single and double mutants. In the agp.L-B1/ssIV-D double mutant, TaGBSSII was upregulated, while TaAGPSS, TaSSI, and TaSBEII were downregulated. Under the interaction of these genes, the total starch and amylopectin contents were significantly decreased in agp.L-B1 and agp.L-B1/ssIV-D mutants. The results suggested that the mutations of TaAGP.L-B1 and TaSSIVb-D genes resulted in variation in the expression patterns of the other four starch synthetic genes and led to a reduction in starch and amylopectin contents. These mutants could be used further as germplasm for resistant starch analysis., Competing Interests: The authors have declared that no competing interests exist.

Wheat is a staple food commodity grown worldwide, and wheat starch is a valuable source of energy and carbon that constitutes 80% of the grain weight. Manipulation of genes involved in starch synthesis significantly affects wheat grain weight and yield. TaSSIV plays an important role in starch synthesis and its main function is granule formation. To mine and stack more favorable alleles, single nucleotide polymorphisms (SNPs) of TaSSIV-A , B , and D were investigated across 362 wheat accessions by Ecotype-Targeting Induced Local Lesions IN Genome (EcoTILLING). As a result, a total of 38 SNPs in the amplified regions of three TaSSIV genes were identified, of which 10, 15, and 13 were in TaSSIV-A , B , and D , respectively. These 38 SNPs were evaluated by using KASP and six SNPs showed an allele frequency >5% whereas the rest were <5%, i.e., considered to be minor alleles. In the Chinese mini core collection, three haplotypes were detected for TaSSIV-A and three for TaSSIV-B. The results of an association study in the Chinese mini core collection with thousand grain weight (TGW) and spike length (SPL) showed that Hap-2-1A was significantly associated with TGW and Hap-3-1B with SPL. Allelic frequency and geographic distribution indicated that the favored haplotype ( Hap-2-1A ) has been positively selected in Chinese wheat breeding. These results suggested that the Kompetitive Allele Specific PCR (KASP) markers can be applied in starch improvement to ultimately improve wheat yield by marker assisted selection in wheat breeding., Competing Interests: On behalf of all authors, the corresponding author states that there is no conflict of interest.

Crop productivity is highly dependent on the application of N fertilizers, but ever-increasing N application is causing serious environmental impacts. To facilitate the development of new wheat cultivars that can thrive in low N growth conditions, key loci and genes associated with wheat responses to low N must be identified. In this GWAS and t-test study of 190 M6 mutant wheat lines (Jing 411-derived) based on genotype data from the wheat 660k SNP array, we identified a total of 221 significant SNPs associated four seedling phenotypic traits that have been implicated in resistance to low N: relative root length, relative shoot length, relative root weight, and relative shoot weight. Notably, we detected large numbers of significantly associated SNP in what appear to be genomic 'hotspots' for resistance to low N on chromosomes 2A and 6B, strongly suggesting that these regions are functionally related to the resistance phenotypes that we observed in some of the mutant lines. Moreover, the candidate genes, including genes encoding high-affinity nitrate transporter 2.1, gibberellin responsive protein, were identified for resistance to low N. This study raises plausible mechanistic hypotheses that can be evaluated in future applied or basic efforts by breeders or plant biologists seeking to develop new high-NUE wheat cultivars., Competing Interests: The authors have declared that no competing interests exist.

Mutated genetic resources play an important role in gene/allele characterization. Currently, there are few hexaploid winter wheat mutated resources available. Here, we developed a hexaploid winter wheat resource by inducing mutations via EMS treatment by the single seed descent method. A broad mutation spectrum with high mutation frequency (∼19%) on phenotypic variations was identified. These mutations included spike, leaf and seed morphology, plant architecture, and heading date variations. To evaluate the efficiency of the resource for reverse genetic analysis, allelic variations in the TaAGP.L-B1 gene, encoding the AGPase large subunit, were screened by the TILLING approach. Four missense mutations were identified and one allele in line E3-1-3, resulted in an amino acid change predicated to have severe effects on gene function. The other three mutations were predicted to have no effect. Results of gene expression patterns and grain starch content demonstrated that the novel allele in E3-1-3 altered the function of TaAGP.L-B1 . Our results indicated that this mutated genetic wheat resource contained broad spectrum phenotypic and genotypic variations, that may be useful for wheat improvement, gene discovery, and functional genomics.

Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named salinity tolerance 1 (st1), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in st1. Furthermore, GO and KEGG enrichment analysis of differentially expressed genes (DEGs) between salinity-treated st1 and wild type suggested that the homeostasis of oxidation-reduction process is important for salt tolerance in st1. Through KEGG pathway analysis, "Butanoate metabolism" was identified as a new pathway for salinity responses. Additionally, key genes for salinity tolerance, such as genes encoding arginine decarboxylase, polyamine oxidase, hormones-related, were not only salt-induced in st1 but also showed higher expression in salt-treated st1 compared with salt-treated WT, indicating that these genes may play important roles in salinity tolerance in st1. This study presents valuable genetic resources for studies on transcriptome variation caused by induced mutation and the identification of salt tolerance genes in crops.

Chloroplast development is an integral part of plant survival and growth, and occurs in parallel with chlorophyll biosynthesis. However, little is known about the mechanisms underlying chloroplast development in hexaploid wheat. Here, we obtained a spaceflight-induced wheat albino mutant mta. Chloroplast ultra-structural observation showed that chloroplasts of mta exhibit abnormal morphology and distribution compared to wild type. Photosynthetic pigments content was also significantly decreased in mta. Transcriptome and chloroplast proteome profiling of mta and wild type were done to identify differentially expressed genes (DEGs) and proteins (DEPs), respectively. In total 4,588 DEGs including 1,980 up- and 2,608 down-regulated, and 48 chloroplast DEPs including 15 up- and 33 down-regulated were identified in mta. Classification of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. Besides, transcription factors such as PIF3, GLK and MYB which might participate in those pathways were also identified. The correlation analysis between DEGs and DEPs revealed that the transcript-to-protein in abundance was functioned into photosynthesis and chloroplast relevant groups. Real time qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in mta. Together, our results suggest that the molecular mechanism for albino leaf color formation in mta is a thoroughly regulated and complicated process. The combined analysis of transcriptome and proteome afford comprehensive information for further research on chloroplast development mechanism in wheat. And spaceflight provides a potential means for mutagenesis in crop breeding.

Background: Transient starch provides carbon and energy for plant growth, and its synthesis is regulated by the joint action of a series of enzymes. Starch synthesis IV (SSIV) is one of the important starch synthase isoforms, but its impact on wheat starch synthesis has not yet been reported due to the lack of mutant lines., Results: Using the TILLING approach, we identified 54 mutations in the wheat gene TaSSIVb-D, with a mutation density of 1/165 Kb. Among these, three missense mutations and one nonsense mutation were predicted to have severe impacts on protein function. In the mutants, TaSSIVb-D was significantly down-regulated without compensatory increases in the homoeologous genes TaSSIVb-A and TaSSIVb-B. Altered expression of TaSSIVb-D affected granule number per chloroplast; compared with wild type, the number of chloroplasts containing 0-2 granules was significantly increased, while the number containing 3-4 granules was decreased. Photosynthesis was affected accordingly; the maximum quantum yield and yield of PSII were significantly reduced in the nonsense mutant at the heading stage., Conclusions: These results indicate that TaSSIVb-D plays an important role in the formation of transient starch granules in wheat, which in turn impact the efficiency of photosynthesis. The mutagenized population created in this study allows the efficient identification of novel alleles of target genes and could be used as a resource for wheat functional genomics.

Understanding the radiosensitivity of plants, an important factor in crop mutation breeding programs, requires a thorough investigation of the factors that contribute to this trait. In this study, we used the highly radiosensitive wheat (Triticum aestivum L.) variety HY1 and J411, a γ-irradiation-insensitive control, which were screened from a natural population, to examine the factors affecting radiosensitivity, including free radical content and total antioxidant capacity, as well as the expression of TaKu70 and TaKu80 (DNA repair-related genes) as measured by real-time PCR. We also investigated the alternative splicing of this gene in the wild-type wheat ecotype by sequence analysis. Free radical contents and total antioxidant capacity significantly increased upon exposure of HY1 wheat to γ-irradiation in a dose-dependent manner. By contrast, in J411, the free radical contents exhibited a similar trend, but the total antioxidant capacity exhibited a downward trend upon increasing γ-irradiation. Additionally, we detected dose-dependent increases in TaKu70 and TaKu80 expression levels in γ-irradiated HY1, while in J411, TaKu70 expression levels increased, followed by a decline. We also detected alternative splicing of TaKu70 mRNA, namely, intron retention, in HY1 but not in J411. Our findings indicate that γ-irradiation induces oxidative stress and DNA damage in hexaploid wheat, resulting in growth retardation of seedlings, and they suggest that TaKu70 may play a causal role in radiosensitivity in HY1. Further studies are required to exploit these factors to improve radiosensitivity in other wheat varieties., Competing Interests: The authors have declared that no competing interests exist.

Background: The molecular pathogenesis of infection by hepatitis B virus with human is extremely complex and heterogeneous. To date the molecular information is not clearly defined despite intensive research efforts. Thus, studies aimed at transcription and regulation during virus infection or combined researches of those already known to be beneficial are needed., Aims: With the purpose of identifying the transcriptional regulators related to infection of hepatitis B virus in gene level, the gene expression profiles from some normal individuals and hepatitis B patients were analyzed in our study., Methods: In this work, the differential expressed genes were selected primarily. The several genes among those were validated in an independent set by qRT-PCR. Then the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes. Next, the analysis of the regulatory impact factors was performed through mapping the links and regulatory data. In order to give a further insight to these regulators, the co-expression gene modules were identified using a threshold-based hierarchical clustering method. Incidentally, the construction of the regulatory network was generated using the computer software., Results: A total of 137,284 differentially co-expressed links and 780 differential co-expressed genes were identified. These co-expressed genes were significantly enriched inflammatory response. The results of regulatory impact factors revealed several crucial regulators related to hepatocellular carcinoma and other high-rank regulators. Meanwhile, more than one hundred co-expression gene modules were identified using clustering method., Conclusions: In our study, some important transcriptional regulators were identified using a computational method, which may enhance the understanding of disease mechanisms and lead to an improved treatment of hepatitis B. However, further experimental studies are required to confirm these findings., (Copyright © 2015 Elsevier Masson SAS. All rights reserved.)

Background: Several de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these de novo assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms., Results: When we de novo assembled transcriptomes of sweet potato (hexaploid), Trametes gallica (a diploid fungus), Oryza meyeriana (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined De novo Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes., Conclusion: Based on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.

Background: Wheat with high anther culture ability would be beneficial for breeding. We aimed to screen a wheat germplasm to with high anther culture ability as well as good agronomic characteristics., Results: The F1 young spikes of winter wheat cross combination Yanfu188/Jimai37 were irradiated with gamma rays at a dose of 1.5 Gy to develop a new germplasm H307 with high anther culture ability. The proportion of green plantlets per 100 anthers (GP/100A) of H307 was 14.50% which was higher than other H2 lines (P < 0.05). Analysis over three successive years (2006-2008) revealed that the green plantlet regeneration ability of H307 remained high in all 3 years. Reciprocal crosses between H307 and Nongda3308 showed no significant differences in their values for calli per 100 anthers (CA/100A), green plantlets per 100 calli (GP/100C) and GP/100A (P > 0.05). Five main wheat varieties used in production, namely Yumai68, Yanzhan4110, Bainongaikang58, Zhoumai18 and Xinmai18, were selected to cross with the new H307. CA/100A, GP/100C and GP/100A were used to assess the anther culture ability of F1 hybrids, demonstrating that the anther culture ability of H307 was heritable., Conclusion: H307 possessed high anther culture ability that was heritable, which would be potential germplasm for improving wheat anther breeding ability., (© 2014 Society of Chemical Industry.)