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Background Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant, which not only causes permanent and irreversible health problems for humans, but also causes a significant reduction in crop yields. Results This study examined the chemical forms of Cd in the roots of two wheat varieties (M1019 and Xinong20) by continuous extraction and analyzed differences in distribution characteristics of Cd in the root cell wall, cytoplasm, and organelles by elemental content determination and subcellular separation. Furthermore, we conducted proteomics analysis of the roots of the two varieties under Cd pollution using mass spectrometry quantitative proteomics techniques. A total of 11,651 proteins were identified, of which 10,532 proteins contained quantitative information. In addition, the differentially expressed proteins in the two varieties were related to DNA replication and repair, protein metabolism, and the glutathione metabolism pathway. Conclusion The results of this study improve our understanding of the mechanism of plant responses to Cd stress.

One RIL population derived from the cross between Dalibao and BYL8 was used to examine the phenotypes of kernel-related traits in four different environments. Six important kernel traits, kernel length (KL), kernel width (KW), kernel perimeter (KP), kernel area (KA), kernel length/width ratio (KLW), and thousand-kernel weight (TKW) were evaluated in Yangling, Shaanxi Province, China (2016 and 2017), Nanyang, Henan Province, China (2017) and Suqian, Jiangsu Province, China (2017). A genetic linkage map was constructed using 205 SSR markers, and a total of 21 significant QTLs for KL, KW, KP, KA, KLW and TKW were located on 10 of the 21 wheat chromosomes, including 1A, 1B, 2A, 2B, 2D, 3D, 4D, 5A, 5B, and 7D, with a single QTL in different environments explaining 3.495–30.130% of the phenotypic variation. There were four loci for KLW, five for KA, five for KL, three for KP, two for KW, and two for TKW among the detected QTLs. We used BSA + 660 K gene chip technology to reveal the positions of major novel QTLs for KLW. A total of 670 out of 5285 polymorphic SNPs were detected on chromosome 2A. The SNPs in 2A are most likely related to the major QTL, and there may be minor QTLs on 5B, 7A, 3A and 4B. SSR markers were developed to verify the chromosome region associated with KLW. A linkage map was constructed with 7 SSR markers, and a major effect QTL was identified within a 21.55 cM interval, corresponding to a physical interval of 10.8 Mb in the Chinese Spring RefSeq v1.0 sequence. This study can provide useful information for subsequent construction of fine mapping and marker-assisted selection breeding.

The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.

Soil cadmium (Cd) contamination can reduce wheat yield and quality, thus threatening food security and human health. Herein, morphological physiology, Cd accumulation and distribution, proteomic and metabolomic analyses were performed (using wheat cultivars 'Luomai23' (LM, Cd-sensitive) and 'Zhongyu10' (ZY, Cd-tolerant) at the seedling stage with sand culture) to reveal Cd tolerance mechanism. Cd inhibited wheat growth, caused oxidative stress, hindered carbon and nitrogen metabolism, and altered the quantity and composition of root exudates. The root Cd concentration was lower in ZY than in LM by about 35% under 15 μM Cd treatments. ZY reduced Cd uptake through root exudation of amino acids and alkaloids. ZY also reduced Cd accumulation through specific up-regulation (twice) of major facilitator superfamily (MFS) proteins. Furthermore, ZY enhanced Cd cell wall fixation and vacuolar compartmentalization by increasing pectin contents, hemicellulose1 contents, and adenosine triphosphate binding cassette subfamily C member 1 (ABCC1) transporter expression, thus reducing the Cd organelle fraction of ZY by about 12% and 44% in root and shoot, respectively, compared with LM. Additionally, ZY had enhanced resilience to Cd due to increased antioxidant capacity, plasma membrane stability, nitrogen metabolism, and endoplasmic reticulum homeostasis, indicating that the increased Cd tolerance could be because of multi-level coordination. These findings provide a reference for exploring the molecular mechanism of Cd tolerance and accumulation, providing a basis for safe utilization of Cd-contaminated soil by breeding Cd-tolerant and low Cd-accumulating wheat varieties.

Heterosis can improve the stress resistance, quality, and yield of crops, and the male sterility of wheat can be utilized to accelerate the breeding process of hybrid. To determine whether mitochondrial genes are involved in the fertility of K-type cytoplasmic male-sterile (CMS) line and the YS-type thermosensitive male-sterile (TMS) line in wheat, we sequenced and assembled the mitochondrial genomes of K519A, 519B, and YS3038 by next-generation sequencing (NGS). The non-synonymous mutations were analyzed, and the first-generation sequencing was conducted to verify the non-synonymous mutation sites. Furthermore, the expression patterns of genes with non-synonymous mutations were analyzed. Finally, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to test the functions of the candidate genes. The results revealed that the mitochondrial genomes of K519A, 519B, and YS3038 were 420,543, 433,560, and 452,567 bp in length, respectively. Besides, 33, 31, and 37 protein-coding genes were identified in K519A, 519B, and YS3038, respectively. There were 14 protein-coding genes and 83 open reading frame (ORF) sequences that differed between K519A and 519B and 10 protein-coding genes and 122 ORF sequences that differed between K519A and YS3038. At the binucleate stage, seven genes (nad6, ORF256, ORF216, ORF138, atp6, nad3, and cox1) were downregulated in K519A compared with 519B, and 10 genes (nad6, atp6, cox3, atp8, nad3, cox1, rps3, ORF216, ORF138, and ORF224) were downregulated in YS3038 compared with K519A. Besides, six genes (nad6, ORF138, cox3, cox1, rps3, and ORF224) were downregulated under fertile conditions relative to sterile conditions in YS3038. Gene silencing analysis showed that the silencing of cox1 significantly reduced the seed setting rate of YS3038, indicating that the cox1 gene may be involved in the fertility transformation of YS3038. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-021-01252-x.

Class III peroxidases are classical secretory plant peroxidases belonging to a large multi-gene family. Class III peroxidases are involved in various physical processes and the response to biotic and abiotic stress to protect plants from environmental adversities. In this study, 151 BdPrx genes were identified using HMM and Blastp program. According to their physical location, the 151 BdPrx genes were mapped on five chromosomes. The results of Gene Structure Display Serve and MEME revealed that BdPrxs in the same subgroup shared similar gene structure, and their protein sequences were highly conserved. Based on the analysis of evolutionary relationships and Ka/Ks, 151 BdPrx genes were divided into 15 subgroups, they have undergone purifying selection. In addition, the result of GO annotation showed that 100% of the BdPrxs participated in antioxidant. The protein-protein interaction network was constructed using the orthology-based method, found that 66 BdPrxs were involved in the regulatory network and 183 network branches were identified. Furthermore, analysis of the transcriptome data indicated that the BdPrx genes responded to low concentration of exogenous phytohormones and exhibited different levels of expression in the different tissues. Subsequently, 19 genes were selected for quantitative real-time PCR and found to be mainly expressed in the roots, might preferentially respond to hydrogen peroxide and gibberellin. Our results provide a foundation for further evolutionary and functional study of Prx genes in B. distachyon.

Thermosensitive sterile lines are natural materials for exploring the effects of anther development on male fertility. To study the possible molecular mechanisms regulating protein activity during the induction of male sterility, proteomic and phosphoproteomic analyses with tandem mass tags (TMTs) were used to study the binucleate anther of the thermosensitive sterile wheat line YS3038. A total of 9072 proteins, including 5019 phosphoproteins, were identified. Enrichment analyses of differentially abundant proteins (DAPs) and phosphoproteins (DAPPs) in metabolic pathways showed that both were mainly related to energy metabolism. Soluble sugar and ATP content were significantly decreased, free fatty acid content was significantly increased, and ROS was abnormally accumulated in male sterile YS3038-A. In addition, 233 kinase–substrate pairs involved in potential phosphorylation control networks were predicted to regulate fertility. Candidate proteins were identified, and a quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to validate the TMT results. TaPDCD5 is likely to be involved in fertility conversion of YS3038 by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS). Our data provide new insights into the mechanism of TCMS, which has value for identifying potential candidate proteins associated with the formation or abortion of pollen and promotion of wheat heterosis utilization.

Crops are challenged by the increasing high temperature. Heat shock protein 90 (HSP90), a molecular chaperone, plays a critical role in the heat response in plants. However, the evolutionary conservation and divergence of HSP90s homeologs in polyploidy crops are largely unknown. Using the newly released hexaploid wheat reference sequence, we identified 18 TaHSP90s that are evenly distributed as homeologous genes among three wheat subgenomes, and were highly conserved in terms of sequence identity and gene structure among homeologs. Intensive time-course transcriptomes showed uniform expression and transcriptional response profiles among the three TaHSP90 homeologs. Based on the comprehensive isoforms generated by combining full-length single-molecule sequencing and Illumina short read sequencing, 126 isoforms, including 90 newly identified isoforms of TaHSP90s, were identified, and each TaHSP90 generated one to three major isoforms. Intriguingly, the numbers and the splicing modes of the major isoforms generated by three TaHSP90 homeologs were obviously different. Furthermore, the quantified expression profiles of the major isoforms generated by three TaHSP90 homeologs are also distinctly varied, exhibiting differential alternative splicing (AS) responses of homeologs. Our results showed that the AS diversified the heat response of the conserved TaHSP90s and provided a new perspective for understanding about functional conservation and divergence of homologous genes.

Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

Previous studies have indicated that noncoding RNAs are important factors in gene functions. To explore the mechanism of male sterility of YS3038, the sterile genes were mapped, and based on previous work, the expression of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and their target genes was studied. Weighted gene coexpression network analysis (WGCNA) and competitive endogenous RNA (ceRNA) analysis were further performed for differentially expressed noncoding RNAs and target genes. At last, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to prove their function. The sterile genes were mapped on chromosomes 1B and 6B based on chip mix pool analysis, and one major effect QTL (27.3190% variation) was found based on SSR primers. The WGCNA analysis revealed that the dark turquoise and steel blue modules were highly correlated with anther development and fertility conversion, respectively. The ceRNA analysis showed that a total of 184 RNAs interacted with each other, including 115 mRNAs, 55 microRNAs (miRNAs), eight circRNAs, and six lncRNAs. Finally, the seed setting rate of the plant was significantly decreased after fatty acyl-CoA reductase 5 silencing. This study provides breeders with a new option for the development of thermosensitive cytoplasmic male-sterile (TCMS) wheat lines, which will favor the sustainable development of two-line hybrid wheat.

The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.), and the cytoplasmic male sterility (CMS) line has more practical significance in the utilization of heterosis. To reveal the sterile mechanism of wheat K-CMS line K519A from the perspective of the chloroplast genome, the chloroplast genomes of the K519A and its same nuclear genotype maintainer line 519B were sequenced using second-generation high-throughput technology and assembled. Then the chloroplast genomic contents, SSR sequences, long repeat fragments, and qPCR were analyzed. The results showed that the total length of K519A and 519B were 136,996 bp and 136,235 bp, respectively. Both chloroplast genomes encode 126 genes, including 89 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. There were 186 and 188 SSRs in K519A and 519B, respectively. And a developed SSR maker, which from atpF, can be used to distinguish the cytoplasmic type of Aegilops kotschyi and Triticum aestivum, respectively. There were 50 and 52 long repeat fragments, which come from the gene sequences, in K519A and 519B, respectively. A total of 107 mutations between K519A and 519B, which from 45 genes, were identified, of which, 16 genes (matK, rps16, rpoB, rpoC2, atpI, ndhK, atpB, rbcL, psbB, psbH, rpl14, ndhH, ndhF, rpl32, ccsA, ndhA) contained non-synonymous mutations. Further, the qPCR analysis was performed, and the gene expression levels of selected six genes for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development, thus, these non-synonymous mutant genes might affect the fertility of K519A.

Root radial transport is important for cadmium (Cd) absorption and root-shoot translocation. However, the relationship between root structural characteristics and radial transport of Cd in wheat is still unclear. Six wheat cultivars with different Cd tolerance and accumulation characteristics were used to investigate the roles of root phenotype, microstructure, and apoplastic and symplastic pathways in Cd uptake and root-shoot transport in pot culture. Longer root length, smaller root diameter, and more numerous root tips were more conducive to Cd absorption, while thicker roots were able to retain more Cd, thus reducing root-shoot transport and improving Cd tolerance of shoots. Cd stress can induce the deposition of apoplastic barriers in wheat roots, and the deposition of the apoplastic barrier increases under greater stress. The formation of apoplastic barriers can reduce Cd absorption and transfer to the shoot, and the presence of passage cells can weaken this effect. The cell wall thickening induced by Cd stress enhanced Cd adsorption capacity in wheat roots, but there was no significant correlation between Cd content and polysaccharide content in the cell wall. The up-regulated expression of TaHMA3 and TaVP1, which encode proteins related to Cd compartmentalization, was associated with increased Cd tolerance in wheat and decreased Cd translocation to aboveground parts. The morphology and anatomy of roots appear to play critical roles in Cd tolerance, uptake, and translocation in wheat. The present study provides useful information for the selection of wheat cultivars with low Cd accumulation.

Background Crops are challenged by the increasing high temperature. Heat shock protein 90 (HSP90), a molecular chaperone, plays a critical role in the heat response in plants. However, the comprehensive response profiles of HSP90s are largely unknown.Results Using the newly released wheat reference sequence, we identified 18 HSP90s that were highly conserved and presented as triplets. Transcriptome analysis showed that the expression and transcriptional regulation of HSP90s displayed conserved trends among the three HSP90 homologs within a triplet. Based on our previous data generated by combining full-length single-molecule sequencing and Illumina short read sequencing, 126 isoforms of HSP90 were identified and each HSP90 comprised one to three major isoforms. Intriguingly, unlike the conserved transcriptional regulation of HSP90s , different alternative splicing events were characterized among major isoforms generated by HSP90s in triplets under heat stress. Furthermore, many heat-responsive alternative events were also characterized, especially in the early heat response when transcriptional regulation had not been initiated, and the alternative splicing regulation between HSP90s in the triplets was distinctly different.Conclusions This study shows that alternative splicing diversified the heat response of the conserved HSP90 gene family and highlighted the evolutionary divergence of polyploidy wheat.

In the wheat TCMS line YS3038, the anther development is inhibited from late uninucleate stage to the binucleate stage. The disruption of energy metabolism pathways by aberrant transcriptional regulation causes the male sterility under low temperatures. The utilization of thermosensitive male sterile (TMS) lines provides a basis for two-line breeding. Previous work, including morphological and cytological observations, has shown that the development process of the TMS line YS3038 is inhibited from the late uninucleate stage to the binucleate stage. Transcriptomics studies could now help to elucidate the overall expression of related genes in a specific reproductive process, revealing the metabolic network and its regulatory mechanism of the reproductive process from the transcription level. Considering the fertility characteristics of YS3038, three important stages for transcriptome analysis were determined to be the early uninucleate, late uninucleate and binucleate stages. The number of differentially expressed genes (DEGs) was found to be highest in the binucleate stage, and most were related to energy metabolism. Quantitative PCR analysis of selected genes related to energy metabolism revealed that their expression patterns were consistent with the sequencing results. Analysis of the fertility mechanism of YS3038 showed that although the tapetum of anthers was degraded in advance of the tetrad stage, the development of microspores did not result in obvious abnormalities until the binucleate stage, because the genes involved in energy metabolism pathways, including starch and sucrose metabolism (SSM), glycolysis, the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and respiration electron transport chain are differentially expressed under sterile and fertile conditions. Therefore, the pollen in YS3038 was sterile.

Late embryogenesis-abundant (LEA) proteins are the products of an important gene family in plants that play vital roles in regulating growth and development as well as a variety of stress responses. In our study, 67 members of LEA (BdLEA) were identified in the genome of Brachypodium distachyon L. Analyses of gene structure, evolutionary relationships and protein motifs showed that the BdLEAs belonged to six subfamilies. Analyses of chromosomal locations and duplication events revealed that the 67 BdLEAs were distributed over all five chromosomes and 26 BdLEAs were identified as products of duplication events. Gene Ontology (GO) annotation results suggested that nearly 60% of BdLEAs could be involved in stress response. Furthermore, transcriptomic analysis showed that the BdLEAs were differentially expressed in nine organs and responded to low stringency of exogenous phytohormones. Subsequently, 18 BdLEAs from six subfamilies were randomly selected for quantitative real-time PCR (qRT-PCR) analysis, which showed that they were mainly expressed in the spikelets and they may preferentially respond to salt, drought and abscisic acid (ABA) stress. This study is the first to report the characteristics of the BdLEA family, providing valuable information for understanding the evolution of LEAs in the model plant B. distachyon and supporting future functional research on these proteins.

Sharp eyespot, caused mainly by the necrotrophic fungus Rhizoctonia cerealis, limits wheat production worldwide. Here, TaCPK7-D, encoding a subgroup III member of the calcium-dependent protein kinase (CPK) family, was identified from the sharp eyespot-resistant wheat line CI12633 through comparative transcriptomic analysis. Subsequently, the defence role of TaCPK7-D against R. cerealis infection was studied by the generation and characterization of TaCPK7-D-silenced and TaCPK7-D-overexpressing wheat plants. Rhizoctonia cerealis inoculation induced a higher transcriptional level of TaCPK7-D in the resistant wheat line CI12633 than in the susceptible cultivar Wenmai 6. The expression of TaCPK7-D was significantly induced after exogenous application of 1-aminocyclopropane-1-carboxylic acid (an ethylene biosynthesis precursor). The green fluorescent protein signal distribution assays indicated that TaCPK7-D localizes to the plasma membrane in both onion epidermal cells and wheat protoplasts. Following R. cerealis inoculation, TaCPK7-D-silenced wheat CI12633 plants displayed more severe sharp eyespot symptoms than control CI12633 plants. Four defence-associated genes (β-1,3-glucanase, chitinase 1, defensin and TaPIE1) and an ethylene biosynthesis key gene, ACO2, were significantly suppressed in the TaCPK7-D-silenced wheat plants compared with control plants. Conversely, TaCPK7-D-overexpressing wheat lines showed increased resistance to sharp eyespot compared with untransformed recipient wheat Yangmai 16. Furthermore, the transcriptional levels of these four defence-related genes and ACO2 gene were significantly elevated in TaCPK7-D-overexpressing plants compared with untransformed recipient wheat plants. These results suggest that TaCPK7-D positively regulates the wheat resistance response to R. cerealis infection through the modulation of the expression of these defence-associated genes, and that TaCPK7-D is a candidate to improve sharp eyespot resistance in wheat.

Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetraploid G. hirsutum and diploid G. raimondii, little is known about the sequence variation of the members between G. hirsutum and G. barbadense and their involvement in the natural quantitative variation in fiber quality and yield. In this study, a comprehensive genome-wide comparative analysis was performed among the four Gossypium species using whole genome sequences, i.e., tetraploid G. hirsutum (AD1) and G. barbadense (AD2) as well as their likely ancestral diploid extants G. raimondii (D5) and G. arboreum (A2), leading to the identification of 406, 393, 216, and 213 R2R3-MYB genes, respectively. To elucidate whether the R2R3-MYB genes are genetically associated with fiber quality traits, 86 R2R3-MYB genes were co-localized with quantitative trait loci (QTL) hotspots for fiber quality and yield, including 42 genes localized within the fiber length QTL hotspots, in interspecific G. hirsutum × G. barbadense populations. There were 20 interspecific nonsynonymous single-nucleotide polymorphism (SNP) sites between the two tetraploid cultivated species, of which 16 developed from 11 R2R3-MYB genes were significantly correlated with fiber quality and yield in a backcross inbred population (BIL) of G. hirsutum × G. barbadense in at least one of the four field tests. Taken together, these results indicate that the sequence variation in these 11 R2R3-MYB genes is associated with the natural variation (i.e., QTL) in fiber quality and yield. Moreover, the functional SNPs of five R2R3-MYB allele pairs from the AD1 and AD2 genomes were significantly correlated with the gene expression related to fiber quality in fiber development. The results will be useful in further elucidating the role of the R2R3-MYB genes during fiber development.

Association mapping is a method to identify associations between target traits and genetic markers based on linkage disequilibrium (LD) of a quantitative trait locus. Synthetic hexaploid wheat (SHW) is derived from a cross between Triticum durum Desf. and Aegilops tauschii Coss. that enhances genetic diversity and broadens breeding resources. In this study, phenotypic diversity in 110 wheat accessions (86 SHW germplasm specimens and 24 conventional wheat varieties) was evaluated quantitatively for yield characteristics of grains per spike, thousand kernel weight, and spike length. Phenotypic data were collected over two years at two locations, and 1785 alleles were detected (mean 6.59), ranging from 3 to 11 alleles per locus. The average genetic diversity index was 0.749, with a range from 0.239 to 0.923. The polymorphic information content (PIC) ranged from 0.145 to 0.968, with a mean value of 0.695. The genetic diversity index and PIC indicated that genome B > D > A. Accessions were grouped into three subgroups based on STRUCTURE and unweighted pair-group with arithmetic mean clustering. The mean LD decay across the genome was 11.78 cM. Association mapping between traits and simple sequence repeat markers was performed using the generalized linear model approach. Forty-six SSR loci were significantly associated with the measured agronomic traits in two geographic locations. Together, these results broaden our knowledge of how to harness elite genes and genetic diversity in SHW in genomic and marker-assisted selection.

Fusarium head blight (FHB) is a devastating disease that threatens wheat (Triticum aestivum) production in many areas worldwide. FHB infection results in Fusarium-damaged kernels (FDK) and deoxynivalenol (DON) that dramatically reduce grain yield and quality. More effective and accurate disease evaluation methods are imperative for successful identification of FHB-resistant sources and selection of resistant cultivars. To determine the relationships among different types of resistance, 363 (74 soft and 289 hard) U.S. winter wheat accessions were repeatedly evaluated for FDK and DON concentration in greenhouse and field experiments. Single-kernel near-infrared (SKNIR)-estimated FDK and DON were compared with visually estimated FDK and gas chromatography-mass spectroscopy-estimated DON. Significant correlations were detected between percentage of symptomatic spikelets and visual FDK in the greenhouse and field, although correlations were slightly lower in the field. High correlation coefficients also were observed between visually scored FDK and SKNIR-estimated FDK (0.72, P < 0.001) and SKNIR-estimated DON (0.68, P < 0.001); therefore, both visual scoring and SKNIR methods are useful for estimating FDK and DON in breeding programs.

Male sterility, especially cytoplasmic male sterility (CMS) where no functional pollen is produced, plays an important role in wheat breeding. Some specific proteins are related to male sterility in wheat, especially those present in pollen. To elucidate these sterility-related proteins, we applied two-dimensional gel electrophoresis (2-DE) to the proteomic analysis of pollen from a CMS line (732A) and its maintainer (732B) in wheat (Triticum aestivum L.), where trichloroacetic acid/acetone precipitation was used to extract pollen proteins from the wheat anthers. Analysis using PDQuest detected >350 reproducible protein spots on each 2-DE gel, where pI 4–7. In total, 41 spots were found to be differentially expressed, where 7/41 were identified by MALDI TOF/TOF–mass spectrometry analysis and protein database searching. The proteins comprised NADPH-producing dehydrogenase in the oxidative pentose phosphate pathway, cinnamyl alcohol dehydrogenase, cytosolic 3-phosphoglycerate kinase, caffeic acid O-methyltransferase, ascorbate peroxidase, glutamine synthetase isoform GS1a, and one unknown protein. In the uninucleate stage, all of the identified protein spots were downregulated in 732A, except the unknown protein, whereas there were no obvious differences in 732B. In the binucleate stage, the expression level of glutamine synthetase isoform GS1a did not differ between 732A and 732B, but caffeic acid O-methyltransferase was downregulated in 732A and the other five proteins were upregulated in 732A. These results suggest that male sterility in 732A is related to energy metabolism perturbation, active oxygen accumulation, programmed cell death, the pentose phosphate pathway, and glycolysis.

Background Among the largest and most diverse transcription factor families in plants, basic leucine zipper (bZIP) family participate in regulating various processes, including floral induction and development, stress and hormone signaling, photomorphogenesis, seed maturation and germination, and pathogen defense. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, there is no comprehensive analysis of bZIPs in wheat, especially those involved in anther development. Previous studies have demonstrated wheat, T. urartu, Ae. tauschii, barley and Brachypodium are evolutionarily close in Gramineae family, however, the real evolutionary relationship still remains mysterious. Results In this study, 187 bZIP family genes were comprehensively identified from current wheat genome. 98, 96 and 107 members of bZIP family were also identified from the genomes of T.urartu, Ae.tauschii and barley, respectively. Orthology analyses suggested 69.4 % of TubZIPs were orthologous to 68.8 % of AetbZIPs and wheat had many more in-paralogs in the bZIP family than its relatives. It was deduced wheat had a closer phylogenetic relationship with barley and Brachypodium than T.urartu and Ae.tauschii. bZIP proteins in wheat, T.urartu and Ae.tauschii were divided into 14 subgroups based on phylogenetic analyses. Using Affymetrix microarray data, 48 differentially expressed TabZIP genes were identified to be related to anther development from comparison between the male sterility line and the restorer line. Genes with close evolutionary relationship tended to share similar gene structures. 15 of 23 selected TabZIP genes contained LTR elements in their promoter regions. Expression of 21 among these 23 TabZIP genes were obviously responsive to low temperature. These 23 TabZIP genes all exhibited distinct tissue-specific expression pattern. Among them, 11 TabZIP genes were predominantly expressed in anther and most of them showed over-dominance expression mode in the cross combination TY806 × BS366. Conclusions The genome-wide identification provided an overall insight of bZIP gene family in wheat and its relatives. The evolutionary relationship of wheat and its relatives was proposed based on orthology analyses. Microarray and expression analyses suggested the potential involvement of bZIP genes in anther development and facilitated selection of anther development related gene for further functional characterization. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2196-7) contains supplementary material, which is available to authorized users.

The disease take-all, caused by the fungus Gaeumannomyces graminis, is one of the most destructive root diseases of wheat worldwide. Breeding resistant cultivars is an effective way to protect wheat from take-all. However, little progress has been made in improving the disease resistance level in commercial wheat cultivars. MYB transcription factors play important roles in plant responses to environmental stresses. In this study, an R2R3-MYB gene in Thinopyrum intermedium, TiMYB2R-1, was cloned and characterized. The gene sequence includes two exons and an intron. The expression of TiMYB2R-1 was significantly induced following G. graminis infection. An in vitro DNA binding assay proved that TiMYB2R-1 protein could bind to the MYB-binding site cis-element ACI. Subcellular localization assays revealed that TiMYB2R-1 was localized in the nucleus. TiMYB2R-1 transgenic wheat plants were generated, characterized molecularly, and evaluated for take-all resistance. PCR and Southern blot analyses confirmed that TiMYB2R-1 was integrated into the genomes of three independent transgenic wheat lines by distinct patterns and the transgene was heritable. Reverse transcription-PCR and western blot analyses revealed that TiMYB2R-1 was highly expressed in the transgenic wheat lines. Based on disease response assessments for three successive generations, the significantly enhanced resistance to take-all was observed in the three TiMYB2R-1-overexpressing transgenic wheat lines. Furthermore, the transcript levels of at least six wheat defence-related genes were significantly elevated in the TiMYB2R-1 transgenic wheat lines. These results suggest that engineering and overexpression of TiMYB2R-1 may be used for improving take-all resistance of wheat and other cereal crops.