Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain

Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen

The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.

Strigolactones modulate stem length and diameter of cherry rootstocks through interaction with other hormone signaling pathways

Stem growth and development has considerable effects on plant architecture and yield performance. Strigolactones (SLs) modulate shoot branching and root architecture in plants. However, the molecular mechanisms underlying SLs regulate cherry rootstocks stem growth and development remain unclear. Our studies showed that the synthetic SL analog rac-GR24 and the biosynthetic inhibitor TIS108 affected stem length and diameter, aboveground weight, and chlorophyll content. The stem length of cherry rootstocks following TIS108 treatment reached a maximum value of 6.97 cm, which was much higher than that following rac-GR24 treatments at 30 days after treatment. Stem paraffin section showed that SLs affected cell size. A total of 1936, 743, and 1656 differentially expressed genes (DEGs) were observed in stems treated with 10 μM rac-GR24, 0.1 μM rac-GR24, and 10 μM TIS108, respectively. RNA-seq results highlighted several DEGs, including CKX, LOG, YUCCA, AUX, and EXP, which play vital roles in stem growth and development. UPLC-3Q-MS analysis revealed that SL analogs and inhibitors affected the levels of several hormones in the stems. The endogenous GA₃ content of stems increased significantly with 0.1 μM rac-GR24 or 10 μM TIS108 treatment, which is consistent with changes in the stem length following the same treatments. This study demonstrated that SLs affected stem growth of cherry rootstocks by changing other endogenous hormone levels. These results provide a solid theoretical basis for using SLs to modulate plant height and achieve sweet cherry dwarfing and high-density cultivation.

Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

Background

Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive study on the molecular characterization, phylogenetic relationship and expression profiling of common wheat (Triticum aestivum) expansin gene family using the recently released wheat genome database (IWGSC RefSeq v1.1 with a coverage rate of 94%).

Results

Genome-wide analysis identified 241 expansin genes in the wheat genome, which were grouped into three subfamilies (EXPA, EXPB and EXLA) by phylogenetic tree. Molecular structure analysis showed that wheat expansin gene family showed high evolutionary conservation although some differences were present in different subfamilies. Some key amino acid sites that contribute to functional divergence, positive selection, and coevolution were detected. Evolutionary analysis revealed that wheat expansin gene superfamily underwent strong positive selection. The transcriptome map and qRT-PCR analysis found that wheat expansin genes had tissue/organ expression specificity and preference, and generally highly expressed in the roots. The expression levels of some expansin genes were significantly induced by NaCl and polyethylene glycol stresses, which was consistent with the differential distribution of the cis-elements in the promoter region.

Conclusions

Wheat expansin gene family showed high evolutionary conservation and wide range of functional divergence. Different selection constraints may influence the evolution of the three expansin subfamilies. The different expression patterns demonstrated that expansin genes could play important roles in plant growth and abiotic stress responses. This study provides new insights into the structures, evolution and functions of wheat expansin gene family.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5455-1) contains supplementary material, which is available to authorized users.

Genome-wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold-tolerant and cold-sensitive wheat cultivars

Plant expansins are proteins involved in cell wall loosening, plant growth, and development, as well as in response to plant diseases and other stresses. In this study, we identified 128 expansin coding sequences from the wheat (Triticum aestivum) genome. These sequences belong to 45 homoeologous copies of TaEXPs, including 26 TaEXPAs, 15 TaEXPBs and four TaEXLAs. No TaEXLB was identified. Gene expression and sub-expression profiles revealed that most of the TaEXPs were expressed either only in root tissues or in multiple organs. Real-time qPCR analysis showed that many TaEXPs were differentially expressed in four different tissues of the two wheat cultivars—the cold-sensitive ‘Chinese Spring (CS)’ and the cold-tolerant ‘Dongnongdongmai 1 (D1)’ cultivars. Our results suggest that the differential expression of TaEXPs could be related to low-temperature tolerance or sensitivity of different wheat cultivars. Our study expands our knowledge on wheat expansins and sheds new light on the functions of expansins in plant development and stress response.

Overexpression of the wheat expansin gene TaEXPA2 improves oxidative stress tolerance in transgenic Arabidopsis plants

Expansins play an important role in plant stress tolerance. In a previous study, we cloned the wheat expansin gene TaEXPA2. Here, we analyze its involvement in oxidative stress tolerance. First, we observed that the expression of TaEXPA2 in wheat seedlings was upregulated during H₂O₂ stress. Then, we assembled a TaEXPA2 gene expression vector, transformed it to Arabidopsis, and obtained transgenic plants overexpressing TaEXPA2 (labeled OE). When exposed to H₂O₂, both OE and wild-type (Col) plants were damaged by oxidative stress, as indicated by decolored leaves and increased malondialdehyde (MDA) content. Damage in OE plants was less severe than in Col plants (WT), and this was accompanied by higher activity of cell wall peroxidase (POD) enzymes, including soluble POD, ionically bound POD, and covalently bound POD. The expansin activities of the OE plants were also higher than WT under oxidative stress. We further obtained the Arabidopsis mutant atexpa2 (AtEXPA2 is homologous to TaEXPA2), and found that the antioxidant ability of atexpa2 was lower than that in Col plants, accompanied by depressed activity of POD enzymes and expansins in cell walls. We transformed wheat TaEXPA2 to atexpa2 and obtained plants (labeled Rs) capable of recovering the antioxidant capacity. Oxidative stress tolerance in Rs plants was higher than that of Col plants, and the Rs plants also had higher levels of cell wall POD enzyme and expansin activity. Finally, we identified 13 POD genes in Arabidopsis thaliana and analyzed their expression patterns using quantitative real-time PCR. The expression of 4 of these genes (AtPOD31, AtPOD33, AtPOD34 and AtPOD71) was significantly upregulated during exposure to H₂O₂. We speculate that the 4 genes upregulated by H₂O₂ treatment are involved in the increased activity of POD in the cell wall. We suggest that TaEXPA2 may regulate antioxidant capacity in plants by regulating the activity of cell wall peroxidase.

Fine mapping of LrSV2, a race-specific adult plant leaf rust resistance gene on wheat chromosome 3BS

Fine mapping permits the precise positioning of genes within chromosomes, prerequisite for positional cloning that will allow its rational use and the study of the underlying molecular action mechanism. Three leaf rust resistance genes were identified in the durable leaf rust resistant Argentinean wheat variety Sinvalocho MA: the seedling resistance gene Lr3 on distal 6BL and two adult plant resistance genes, LrSV1 and LrSV2, on chromosomes 2DS and 3BS, respectively. To develop a high-resolution genetic map for LrSV2, 10 markers were genotyped on 343 F2 individuals from a cross between Sinvalocho MA and Gama6. The closest co-dominant markers on both sides of the gene (3 microsatellites and 2 STMs) were analyzed on 965 additional F2s from the same cross. Microsatellite marker cfb5010 cosegregated with LrSV2 whereas flanking markers were found at 1 cM distal and at 0.3 cM proximal to the gene. SSR markers designed from the sequences of cv Chinese Spring BAC clones spanning the LrSV2 genetic interval were tested on the recombinants, allowing the identification of microsatellite swm13 at 0.15 cM distal to LrSV2. This delimited an interval of 0.45 cM around the gene flanked by the SSR markers swm13 and gwm533 at the subtelomeric end of chromosome 3BS.

Integrating cereal genomics to support innovation in the Triticeae

The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.

Integrating cereal genomics to support innovation in the Triticeae

The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.

A molecular and proteomic investigation of proteins rapidly released from triticale pollen upon hydration

Analysis of Triticale (×Triticosecale Wittmack cv. AC Alta) mature pollen proteins quickly released upon hydration was performed using two-dimensional gel electrophoresis followed by mass spectrometry. A total of 17 distinct protein families were identified and these included expansins, profilins, and various enzymes, many of which are pollen allergens. The corresponding genes were obtained and expression studies revealed that the majority of these genes were only expressed in developing anthers and pollen. Some genes including glucanase, glutathione peroxidase, glutaredoxin, and a profilin were found to be widely expressed in different reproductive and vegetative tissues. Group 11 pollen allergens, polygalacturonase, and actin depolymerizing factor were characterized for the first time in the Triticeae. This study represents a distinctive combination of proteomic and molecular analyses of the major cereal pollen proteins released upon hydration and therefore at the forefront of pollen-stigma interactions.

A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew

Sr2 is the only known durable, race non-specific adult plant stem rust resistance gene in wheat. The Sr2 gene was shown to be tightly linked to the leaf rust resistance gene Lr27 and to powdery mildew resistance. An analysis of recombinants and mutants suggests that a single gene on chromosome arm 3BS may be responsible for resistance to these three fungal pathogens. The resistance functions of the Sr2 locus are compared and contrasted with those of the adult plant resistance gene Lr34.

Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage

The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC libraries. The conserved orthologous NUMT regions from tetraploid and hexaploid wheat Langdon and Chinese Spring shared identical gene haplotypes even though mutations (insertions, deletions, and substitutions) had occurred. The 52-kb NUMT was present in hexaploid variety Chinese Spring, but absent in variety Hope, by sequence comparison of their corresponding region. Amplifying the NUMT junctions using a set of the wheat materials including diploid, tetraploid, and hexaploid lines showed that none of the diploid wheat carried the region and only some tetraploid and hexaploid wheat were positive for the NUMT. Age estimation of the NUMT displayed the mean ages of Langdon NUMT and Chinese Spring NUMT to be 378,000 and 416,000 years ago, respectively. Reverse transcription PCR and sequencing of the nad7 gene showed 28 C → U RNA editing sites and four partial editing sites, as expected for mitochondrial DNA expression. Specific SNPs discriminated between cDNA from the nucleus and the mitochondria and suggested that the nuclear copy was not expressed. The mitochondrial DNA studied was inserted into the genome quite recently within the wheat lineage and gave rise to the non-coding nuclear nad7 gene. The NUMT segment could be lost and acquired frequently during the wheat evolution.