Characterization of Synthetic Wheat Line Largo for Resistance to Stem Rust

Resistance breeding is an effective approach against wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The synthetic hexaploid wheat line Largo (pedigree: durum wheat ‘Langdon’ × Aegilops tauschii PI 268210) was found to have resistance to a broad spectrum of Pgt races including the Ug99 race group. To identify the stem rust resistance (Sr) genes, we genotyped a population of 188 recombinant inbred lines developed from a cross between the susceptible wheat line ND495 and Largo using the wheat Infinium 90 K SNP iSelect array and evaluated the population for seedling resistance to the Pgt races TTKSK, TRTTF, and TTTTF in the greenhouse conditions. Based on genetic linkage analysis using the marker and rust data, we identified six quantitative trait loci (QTL) with effectiveness against different races. Three QTL on chromosome arms 6AL, 2BL, and 2BS corresponded to Sr genes Sr13c, Sr9e, and a likely new gene from Langdon, respectively. Two other QTL from PI 268210 on 2DS and 1DS were associated with a potentially new allele of Sr46 and a likely new Sr gene, respectively. Additionally, Sr7a was identified as the underlying gene for the 4AL QTL from ND495. Knowledge of the Sr genes in Largo will help to design breeding experiments aimed to develop new stem rust-resistant wheat varieties. Largo and its derived lines are particularly useful for introducing two Ug99-effective genes Sr13c and Sr46 into modern bread wheat varieties. The 90 K SNP-based high-density map will be useful for identifying the other important genes in Largo.

Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures

Alternative splicing is an important mechanism for the regulation of gene expression in eukaryotes during development, cell differentiation or stress response. Alterations in the splicing profiles of genes under high temperatures that cause heat stress (HS) can impact the maintenance of cellular homeostasis and thermotolerance. Consequently, information on factors involved in HS-sensitive alternative splicing is required to formulate the principles of HS response. Serine/arginine-rich (SR) proteins have a central role in alternative splicing. We aimed for the identification and characterization of SR-coding genes in tomato (Solanum lycopersicum), a plant extensively used in HS studies. We identified 17 canonical SR and two SR-like genes. Several SR-coding genes show differential expression and altered splicing profiles in different organs as well as in response to HS. The transcriptional induction of five SR and one SR-like genes is partially dependent on the master regulator of HS response, HS transcription factor HsfA1a. Cis-elements in the promoters of these SR genes were predicted, which can be putatively recognized by HS-induced transcription factors. Further, transiently expressed SRs show reduced or steady-state protein levels in response to HS. Thus, the levels of SRs under HS are regulated by changes in transcription, alternative splicing and protein stability. We propose that the accumulation or reduction of SRs under HS can impact temperature-sensitive alternative splicing.

Distribution, Epidemics dynamics and physiological races of wheat stem rust (Puccinia graminis f.sp. tritici Eriks and E. Henn) on irrigated wheat in the Awash River basin of Ethiopia

ABSTRACTWheat is one of the high value important major crops of the globe. However, wheat stem rust is considered one of the determinant threats to wheat production in Ethiopia and the globe. So this study was conducted with the objective to assess disease intensity, seasonal distribution dynamics, and genetic variability and to determine virulence spectrum of stem rust in the irrigated wheat areas of Ethiopia. A total of 137 wheat farms were evaluated from 2014/15 - 2019/20 in six districts of Awash River basin. Farm plots were assessed every 5 - 10 km interval with ‘X’ fashion, and data on disease incidence, severity, and healthy plants were scored with diseased wheat plant samples collection for stem rust race analysis. The seasonal trend of wheat stem rust disease was also compared to see the future importance of the diseases. The result revealed that the prevalence, incidence, and severity of stem rust were significantly varied among the different districts and seasons in the two regions. The survey results also indicated that about 71.7% of the wheat fields were affected by stem rust during the 2018/19 growing season. The overall incidence and mean severity of the disease during the same season were 49.02% and 29.27%, respectively. During 2019/20 about 63.7% of the wheat fields were affected by stem rust, which, however, the incidence (30.97%) and severity (17.22%) were lower than the previous season. Although the seasonal disease distribution was decreased, its spatial distribution was expanding into Lower Awash. The physiological and the genetic race analysis identified four dominant races (TTTTF, TKTTF TKKTF, and TTKTF) during 2018/19 and additional race (TKPTF) during 2019/20. Thus races are highly virulent and affect most of the Sr genes except Sr – 31 and Sr – 24. TTTTF and TKKTF are the widest virulence spectrum which affects 90% of the Sr genes. Thus, it can be concluded that the spatial and seasonal distribution of the disease was expanding. Moreover, most of the races were similar with rain-fed production, and thus care must be given for effective management of the diseases to both agro-ecologies. Therefore, these findings provide inputs or insight for breeders to think about the breeding programs in their crossing lines and wheat producers to reduce the damage of the disease in the irrigated ecologies.ETHICAL STATEMENTThus, surveys were conducted with the lateral aim of rust epidemics early warning and monitoring support program in the Awash River basin. Samples for this study were collected from farmers’ fields of the irrigated production areas in the Awash River basin. The disease was an air-borne disease that is difficult to contain. Still, we give maximum care during surveying through spore-free through self-sanitation after Pgt infested field observation to minimize induced disease dissemination to the communities in the production areas that no specific permissions were required for these locations. Field sites are on public access, and P. graminis f. sp. tritici is already an air-born pathogen that doesn’t need special protection kinds. This work was our study experience in the endeavor in irrigated wheat technology dissemination.

Short Survival-Related Genes Harbor EMT Processes and Dendritic Cell Infiltration in Glioblastoma

Background: Glioblastoma is an aggressive primary tumour with the lowest survival time among brain tumours. Tumour-infiltrating immune cells (TIICs) are involved in tumour progression and determine the prognosis, while the association of immune cell infiltration with glioblastoma is rarely unknown. This study aimed to screen survival-related (SR) genes and major biological processes through bioinformatic analysis and to identify the relationship between SR genes and TIICs.Methods:SR genes were screened by comparing the long-term (>36 months) and short-term (<12 months) survivors in the database GSE53733. Gene set enrichment analysis (GSEA) was applied to compare the differences in biological processes between long-term survivors and short-term survivors. The SR genes were identified using the limma package of R. Gene Ontology (GO) analysis was conducted through Metascape. The protein-protein interaction (PPI) network of the SR genes was established through the Search Tool for the Retrieval of Interacting Genes (STRING) website and further analysed by the Molecular Complex Detection (MCODE) algorithm. UALCAN and GlioVis were employed to analyse the expression levels and prognostic value of hub genes. The correlation of hub genes with immune cell filtration was estimated by the Tumor Immune Estimation Resource (TIMER). The gene-drug interaction network was constructed using the Comparative Toxicogenomics Database (CTD).Results: The functions of the detected genes were mainly enriched in epithelial mesenchymal transition (EMT) and oxidative phosphorylation. Of the detected genes, a total of 220 SR genes were identified, including 78 upregulated genes and 142 downregulated genes in long-term survivors. The upregulated genes were mainly related to neuron projection morphogenesis, extracellular matrix, and cation channel activity. The downregulated genes were mainly related to extracellular matrix organization and angiogenesis. The PPI network for SR genes was constructed with 65 edges and 195 nodes, and two significant modules were selected. The results indicated that COL1A2, COL6A2, COL8A1, and COL8A2 were hub SR genes. In addition, they were correlated with immune cell infiltration, especially dendritic cell infiltration.Conclusions: These results revealed that collagens accounted for the progression and prognosis of glioblastoma. In addition, DC infiltration is a risk factor for glioblastoma patients. The expression of collagen protein COL6A2 was significantly correlated with the DC infiltration level and poor prognosis. Further, potential drugs that affect the function of COL6A2 could improve the outcomes of glioblastoma.

Characterization of Wheat Monogenic Lines with Known Sr Genes and Wheat Lines with Resistance to the Ug99 Race Group for Resistance to Prevalent Races of Puccinia graminis f. sp. tritici in China

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is one of the most serious fungal diseases in wheat production, seriously threatening the global supply of wheat and endangering food security. The present study was conducted to evaluate wheat monogenic lines with known Sr genes to the most prevalent P. graminis f. sp. tritici races in China. In addition, wheat lines introduced from the International Maize and Wheat improvement Center (CIMMYT) with resistance to the Ug99 race group were also evaluated with the prevalent Chinese P. graminis f. sp. tritici races. The monogenic lines containing Sr9e, Sr21, Sr26, Sr31, Sr33, Sr35, Sr37, Sr38, Sr47, and SrTt3 were effective against races 21C3CTTTM, 34C0MRGSM, and 34C3MTGQM at both seedling and adult-plant stages. In contrast, monogenic lines containing Sr6, Sr7b, Sr8a, Sr9a, Sr9b, Sr9d, Sr9f, Sr9g, Sr13, Sr16, Sr18, Sr19, Sr20, Sr24, Sr28, Sr29, and Sr34 were highly susceptible to these races at both seedling and adult-plant stages. Lines with Sr5, Sr10, Sr13, Sr14, Sr15, Sr17, Sr21, Sr22, Sr23, Sr25, Sr27, Sr29, Sr30, Sr32, Sr36, and Sr39 were resistant to one or more of the tested races. Among the 123 CIMMYT lines, 38 (30.9%) showed varying levels of susceptibility to Chinese P. graminis f. sp. tritici races. The results should be useful for breeding wheat cultivars with resistance to stem rust.

Stem rust in Western Siberia – race composition and effective resistance genes

Stem rust in recent years has acquired an epiphytotic character, causing significant economic damage for wheat production in some parts of Western Siberia. On the basis of a race composition study of the stem rust populations collected in 2016–2017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 in Altai population were identified. The race differentiation of stem rust using a tester set of 20 North American Sr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulent only to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A low frequency of virulence (10–25 %) of the Omsk population pathotypes was found for Sr11, Sr24,Sr30, and for Altai population – Sr7b,Sr9b,Sr11,SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stem rust were made in 2016–2018 in Omsk region in the varieties and spring wheat lines from three different sources. The first set included 58 lines and spring bread wheat varieties with identified Sr genes – the so-called trap nursery (ISRTN – International Stem Rust Trap Nursery). The second set included spring wheat lines from the Arsenal collection, that were previously selected according to a complex of economically valuable traits, with genes for resistance to stem rust, including genes introgressed into the common wheat genome from wild cereal species. The third set included spring bread wheat varieties created in the Omsk State Agrarian University within the framework of a shuttle breeding program, with a synthetic wheat with the Ae. tauschiigenome in their pedigrees. It was established that the resistance genes Sr31, Sr40,Sr2 complexare effective against stem rust in the conditions of Western Siberia. The following sources with effective Srgenes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10, Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24,1RS-Am), Siouxland (Sr24,Sr31), Roughrider (Sr6, Sr36), Sisson (Sr6,Sr31,Sr36), and Fleming (Sr6,Sr24,Sr36,1RS-Am), Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC 1F2 (96 × 113) × 145 × 113 (Sr2,Sr36,Sr44), No. 14а F 3(96 × 113) × 145 (Sr36,Sr44), No. 19 BC 2F3(96 × 113) × 113 (Sr2, Sr36, Sr44), and No. 20 F 3 (96 × 113) × 145 (Sr2,Sr36,Sr40, Sr44) from the Arsenal collection; and the Omsk State Agrarian University varieties Element 22 (Sr31,Sr35), Lutescens 27-12, Lutescens 87-12 (Sr23,Sr36), Lutescens 70-13, and Lutescens 87-13 (Sr23,Sr31,Sr36). These sources are recommended for inclusion in the breeding process for developing stem rust resistant varieties in the region.

Identification, evolution and alternative splicing profile analysis of Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) in poplar, Arabidopsis, grape, and papaya

Alternative splicing (AS) regulates gene expression and produces proteome diversity. Serine/Arginine-Rich Protein Splicing Factors (SR Proteins) are important splicing factors that play significant roles in spliceosome assembly and splicing regulation, and play roles in regulating plant stress. In this report, we analyzed 30 SR genes in Populus trichocarpa, 18 genes in Arabidopsis thaliana, 14 genes in Vitis vinifera and 9 genes in Carica papaya. The SR proteins contained RRM and RS conserved domains, and based on different structural domain organization were divided into six subfamilies (SR, SC, SCL, RS, RSZ and RS2Z). Gene duplication analysis revealed 94 paralogs and 408 orthologs in the four species, and the SR genes had undergone strong purifying selection. A number of stress-related cis-elements (ABRE, LTR, MBS, TC-rich repeats cis-acting element) were identified in the promoters of the SR genes. Microarray and RNA-seq data showed that SR genes expression in different tissues of the four species responded differently to abiotic stress. Poplar, Arabidopsis and grape SR genes had many splice isoforms. Moreover, 26 of 30 poplar SR genes had intron retention (IR) events, and the relative IR rates of 27 intron sites in the poplar SR genes changed significantly under cold, heat, drought and salt stress conditions. This study provides valuable resources for the gene structure, function, and evolution of poplar SR proteins.

Genome-Wide Identification of Cassava Serine/Arginine-Rich Proteins: Insights into Alternative Splicing of Pre-mRNAs and Response to Abiotic Stress

Serine/arginine-rich (SR) proteins have an essential role in the splicing of pre-messenger RNA (pre-mRNA) in eukaryote. Pre-mRNA with introns can be alternatively spliced to generate multiple transcripts, thereby increasing adaptation to the external stress conditions in planta. However, pre-mRNA of SR proteins can also be alternatively spliced in different plant tissues and in response to diverse stress treatments, indicating that SR proteins might be involved in regulating plant development and adaptation to environmental changes. We identified and named 18 SR proteins in cassava and systematically studied their splicing and transcriptional changes under tissue-specific and abiotic stress conditions. Fifteen out of 18 SR genes showed alternative splicing in the tissues. 45 transcripts were found from 18 SR genes under normal conditions, whereas 55 transcripts were identified, and 21 transcripts were alternate spliced in some SR genes under salt stress, suggesting that SR proteins might participate in the plant adaptation to salt stress. We then found that overexpression of MeSR34 in Arabidopsis enhanced the tolerance to salt stress through maintaining reactive oxygen species homeostasis and increasing the expression of calcineurin B-like proteins (CBL)–CBL-interacting protein kinases and osmotic stress-related genes. Therefore, our findings highlight the critical role of cassava SR proteins as regulators of RNA splicing and salt tolerance in planta.

Inheritance and Bulked Segregant Analysis of Leaf Rust and Stem Rust Resistance in Durum Wheat Genotypes

Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and bulked segregant analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized in durum. The single dominant Lr genes in PI 209274, PI 244061, PI387263, and PI 313096 were mapped to chromosome arms 6BS, 2BS, 6BL, and 6BS, respectively. The Sr gene in PI 534304 mapped to 6AL and is most likely Sr13, while the Sr gene in PI 192051 could be uncharacterized in durum.