Genetic combining, heterosis analysis for horticultural traits in tomato (Solanum lycopersicum L.) using ToLCV-resistant lines and molecular validation of Ty genes

Tomato is a pivotal vegetable crop worldwide concerning human nutrition, economy and in service to biotechnology. Tomato leaf curl virus (ToLCV) is a begomovirus transmitted through the whitefly (Bemisia tabaci) and is responsible for severe losses in tomato production. In this context, the current investigation was carried out to determine heterotic combiners with high yield, resistance to ToLCV and mode of gene action for economically important traits. For this, 11 prescreened inbred lines were crossed in a half diallel fashion to generate 55 F1 hybrids. The 55 crosses with 11 parents and commercial checks were evaluated for different horticultural traits and resistance to ToLCV. The molecular validation with SCAR markers TG0302 and SCAR1 confirmed the presence of ToLCV-resistant genes in parents and their crosses. The hybrid IIHR-2902 × IIHR-2852 showed the presence of both Ty-2 and Ty-3 alleles in the homozygous state. The estimation of σSCA2 and σGCA2 was significant. It also indicated that the genetic control of target traits was under additive and non-additive gene effects. The values of σA/D2 along with σGCA2/σSCA2 found to be less than unity indicates the preponderance of non-additive gene action in the expression of the studied traits except for percent disease incidence. The parental line IIHR-2919 was the best combiner for fruit and yield traits. The cross combinations IIHR-2913 × IIHR-2898 exhibited significantly higher economic heterosis for yield along with the presence of Ty-2 and Ty-3 genes. The study paves the way for breeding high yielding and ToLCV-resistant hybrids in tomato.

Identification of Neoantigens in Two Murine Gastric Cancer Cell Lines Leading to the Neoantigen-Based Immunotherapy

To develop combination immunotherapies for gastric cancers, immunologically well-characterized preclinical models are crucial. Here, we leveraged two transplantable murine gastric cancer cell lines, YTN2 and YTN16, derived from the same parental line but differing in their susceptibility to immune rejection. We established their differential sensitivity to immune checkpoint inhibitors (ICI) and identified neoantigens. Although anti-CTLA-4 mAbs eradicated YTN16 tumors in 4 of 5 mice, anti-PD-1 and anti-PD-L1 mAbs failed to eradicate YTN16 tumors. Using whole-exome and RNA sequencing, we identified two and three neoantigens in YTN2 and YTN16, respectively. MHC class I ligandome analysis detected the expression of only one of these neoantigens, mutated Cdt1, but the exact length of MHC binding peptide was determined. Dendritic cell vaccine loaded with neoepitope peptides and adoptive transfer of neoantigen-specific CD8+ T cells successfully inhibited the YTN16 tumor growth. Targeting mutated Cdt1 had better efficacy for controlling the tumor. Therefore, mutated Cdt1 was the dominant neoantigen in these tumor cells. More mCdt1 peptides were bound to MHC class I and presented on YTN2 surface than YTN16. This might be one of the reasons why YTN2 was rejected while YTN16 grew in immune-competent mice.

Rice backcross population assessment for iron tolerance through phenotypic and genotypic analyses

Iron toxicity has become a serious issue affecting rice (Oryza sativa L.) production in many irrigated lowland areas. The selection of Fe2+-tolerant rice cultivars under iron toxicity conditions and the identification of molecular markers are good approaches to obtaining tangible results. This study aimed to identify simple sequence repeat (SSR) markers that were associated with iron tolerance traits in a rice backcross population. A total of 117 seedlings from the backcross (BC3F2) of ‘OM6830’/‘AS996’//‘AS996’ were phenotyped at the 4-week-seedling stage at Ton Duc Thang University, Ho Chi Minh City, Vietnam. The rice population was screened in Yoshida nutrient medium supplemented with FeCl2 at a concentration of 150 mg L−1 under greenhouse conditions. Phenotypic analysis was conducted by scoring two parameters, namely, root length and leaf bronzing. Genotypic analysis was carried out on the BC3F2 population by using four markers, i.e., RM6, RM240, RM252, and RM451, for association analysis with iron tolerance. A total of 23 BC3F2 lines were selected on the basis of their higher tolerance (score 1) for Fe2+ compared with the tolerant parental line ‘AS996’. The markers RM6 and RM240 were highly polymorphic and identified different Fe2+-tolerant lines in the BC3F2 population. Among the BC3F3 progeny derived from the selected 23 BC3F2 lines, BC3F3-7 was identified as the most Fe2+-tolerant line. BC3F3-15 was also found to be Fe2+ tolerant. Both lines showed good development capability and provided high yields under stress conditions. These tolerant BC3F3 lines could be further screened with additional SSR markers in future breeding programs aiming to increase rice production in iron-contaminated areas of the Mekong Delta, Vietnam.

Allelic Variation Analysis at the Vernalization Response and Photoperiod Genes in Russian Wheat Varieties Identified Two Novel Alleles of Vrn-B3

Heading time is an important agronomic trait affecting the adaptability and productivity of common wheat. In this study, 95 common wheat varieties from Russia and the late-maturing breeding line ‘Velut’ were tested for allelic diversity of genes having the strongest effect on heading. In this research, allelic variation at the Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 loci was tested. The Vrn-B1 and Vrn-B3 loci provided the largest contribution to genetic diversity. We found two novel allelic variants of the Vrn-B3 gene in the studied varieties. Ten varieties carried a 160 bp insertion in the promoter region, and the breeding line ‘Velut’ carried a 1617 bp insertion. These alleles were designated Vrn-B3e and Vrn-B3d, respectively. The analysis of the sequences showed the recent insertion of a retrotransposon homologous to the LTR retrotransposon (RLX_Hvul_Dacia_ RND-1) in the Vrn-B3d allele. Plants with the Vrn-B3e and the ‘Velut’ line with the Vrn-B3d allele headed later than the plants with the wild-type allele; among these plants, ‘Velut’ is the latest maturing wheat variety. Analysis of the gene expression of two groups of lines differing by the Vrn-B3 alleles (Vrn-B3d or vrn-B3) from the F2 population with ‘Velut’ as a parental line did not reveal a significant difference in the expression level between the groups. Additional research is required to study the reasons for the late maturation of the ‘Velut’ line. However, the studied wheat varieties could be used as a potential source of natural variation in genes controlling heading times.

Gene Expression Variation Explains Maize Seed Germination Heterosis

BackgroundHeterosis has been extensively utilization in plant breeding, however, the underlying molecular mechanism remain largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis.ResultsIn this study, there is a faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses was conducted between reciprocal crossing hybrids and their parental lines. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the different expression genes between hybrids and either parental line display parental dominance up or higher levels in Zhengdan958 and Zhengdan958 reciprocal-cross, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc.ConclusionOur results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryo and improve the understanding of maize seed germination heterosis.

Breeding a Soybean Cultivar Heinong 531 with Peking-Type Cyst Nematode Resistance, Enhanced Yield and High Seed-Oil Contents

Soybean cyst nematode (SCN) is a destructive threat to soybean production. It’s of economic importance to develop a new SCN-resistant soybean cultivar with high yield and other good agronomic traits. In this study, a yellow-seed-coated and yellow-hilum-pigmented cultivar Heinong 531 belonging to maturity group I was developed by a pedigree breeding method through a testcross between a female parental SCN-resistant soybean cultivar Pengdou 158 and a male parental line F1 (high-yield but SCN-susceptible Hefeng 55 x SCN-resistant Kangxian 12). Heinong 531 was evaluated for SCN resistance in both SCN-infested field and autoclaved soil inoculated with hatched second-stage juveniles of SCN HG Type 0. The results indicated that SCN development at all stages in Heinong 531 was suppressed and the female index was only 1.6-5.6%. Heinong 531 as well as Pengdou 158 and Kangxian 12 were identified to carry the Peking-type resistance with both rhg1-a GmSNAP18 and Rhg4 GmSHMT08 genes. In the two-year regional trials, the average yield of Heinong 531 reached 2805.0 Kg/ha and the one-year production trial demonstrated an average yield of 2751.5 Kg/ha with yield increase of over 12.0% when compared to the local cultivars. The average seed-fat (oil) contents of Heinong 531 reached up to 22.3%. The Peking-type SCN-resistant Heilong 531 cultivar with enhanced yield and high seed-oil contents was just released in China in June, 2021 with certified number of ‘Heishendou 20210004’. These good agronomic traits make Heinong 531 prospective in a wide extension to control SCN in the main soybean-producing areas of Northeast China.

A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons

Fully automated proteomic pipelines have the potential to achieve deep coverage of cellular proteomes with high throughput and scalability. However, it is important to evaluate performance, including both reproducibility and ability to provide meaningful levels of biological insight. Here, we present an approach combining high field asymmetric waveform ion mobility spectrometer (FAIMS) interface and data independent acquisition (DIA) proteomics approach developed as part of the induced pluripotent stem cell (iPSC) Neurodegenerative Disease Initiative (iNDI), a large-scale effort to understand how inherited diseases may manifest in neuronal cells. Our FAIMS-DIA approach identified more than 8000 proteins per mass spectrometry (MS) acquisition as well as superior total identification, reproducibility, and accuracy compared to other existing DIA methods. Next, we applied this approach to perform a longitudinal proteomic profiling of the differentiation of iPSC-derived neurons from the KOLF2.1J parental line used in iNDI. This analysis demonstrated a steady increase in expression of mature cortical neuron markers over the course of neuron differentiation. We validated the performance of our proteomics pipeline by comparing it to single cell RNA-Seq datasets obtained in parallel, confirming expression of key markers and cell type annotations. An interactive webapp of this temporal data is available for aligned-UMAP visualization and data browsing (https://share.streamlit.io/anant-droid/singlecellumap). In summary, we report an extensively optimized and validated proteomic pipeline that will be suitable for large-scale studies such as iNDI.

Characterization and inheritance of dicamba resistance in a multiple-resistant waterhemp (Amaranthus tuberculatus) population from Illinois

Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) is one of the most troublesome agronomic weeds in the midwestern US. The rapid evolution and selection of herbicide-resistance traits in A. tuberculatus is a major challenge in managing this species. An A. tuberculatus population, designated CHR, was identified in 2012 in Champaign County, IL, and previously characterized as resistant to herbicides from six site-of-action groups: 2,4-D (Group 4), acetolactate synthase inhibitors (Group 2), protoporphyrinogen oxidase inhibitors (Group 14), 4-hydroxyphenylpyruvate dioxygenase inhibitors (Group 27), photosystem II inhibitors (Group 5), and very long chain fatty acid synthesis inhibitors (Group 15). Recently, ineffective control of CHR was observed in the field after dicamba application. Therefore, this research was initiated to confirm dicamba resistance, quantify the resistance level and investigate its inheritance in CHR. Multiple field trials were conducted at the CHR location to confirm poor control with dicamba and compare dicamba treatments with other herbicides. Greenhouse trials were conducted to quantify the resistance level in CHR and confirm genetic inheritance of the resistance. In field trials, dicamba did not provide more than 65% control, while glyphosate and glufosinate provided at least 90% control. Multiple accessions were generated from controlled crosses and evaluated in greenhouse trials. Greenhouse dicamba dose-response experiments indicated a resistance level of 5 to 10-fold relative to sensitive parental line. Dose-response experiments using F1 lines indicated that dicamba resistance was an incompletely dominant trait. Segregation analysis with F2 and backcross populations indicated that dicamba resistance had moderate heritability and was potentially a multigenic trait. Although dicamba resistance was predominantly inherited as a nuclear treat, minor maternal inheritance was not completely ruled out. To our knowledge, CHR is one of the first cases of dicamba resistance in A. tuberculatus. Further studies will focus on elucidating the genes involved in dicamba resistance.

Combining ability and heterotic value of ten lines maize genotypes tolerant to tidal-swamp soil stress

Development of maize hybrid for tidal swampland was initiated by selecting and combinate some superior line genotypes that tolerate to the restrictions in target environment. This study aimed was to evaluate the capability of ten maize lines result of selection on tidal swamp acid sulphate soils to obtain GCU, GCA, and heterosis values based on parental yield averages. The experiment has consisted of ten fine line genotypes which have selected in 2019 at the tidal swamp. Each parent was crossed in half-diallel combination, resulting in 46 entries, including the inbred parents. The entries were planted in a randomized complete block design with three replications. The research was conducted on Bajeng Research Station Experiment 5°18’S and 119°30’E from September 2020 to January 2021. The result shows that GCA ability and SCA ability was significant to yield in the form of grain (15% moisture content), the number of ear per plot, ten ear weight, ten corncob weight, ear harvested weight, 1000 seeds weight, plant height, ear length and the number of seed per ear. Grain yield of W6xW9 crosses obtains the highest value of 9.36 tha−1, non-significantly different to hybrid check P35 (9.35 tha-1). The highest GCA value in the grain yield character was obtained on W9 parental line (0.64**). The highest SCA was obtained on the crossing of W7 x W8 (2.61). The highest heterosis value was revealed in W5 x W10 hybrid (4.80). However, W7 x W8 crossing heterosis value was 2.34, indicate that a high SCA effect did not usually generate high heterosis. To perform high heterosis value, W10 was good as female parental.

Elevated phosphorylation of EGFR in NSCLC due to mutations in PTPRH

The role of EGFR in lung cancer is well described with numerous activating mutations that result in phosphorylation and tyrosine kinase inhibitors that target EGFR. While the role of the EGFR kinase in non-small cell lung cancer (NSCLC) is appreciated, control of EGFR signaling pathways through dephosphorylation by phosphatases is not as clear. In recent work we identified mutations in Protein Tyrosine Phosphatase Receptor Type H (Ptprh, also known as SAP-1) as being associated with elevated phosphorylation of EGFR in a mouse model of breast cancer. We have examined a series of tumors from this mouse model, revealing conserved V483M Ptprh mutations within the FVB background, but a series of varied mutations in other backgrounds. Despite the varied Ptprh mutations in other background strains, matched primary and metastatic tumors largely shared mutational profiles. Profiling the downstream events of Ptprh mutant tumors revealed AKT activation, suggesting a key target of PTPRH was EGFR tyrosine 1197. Given the role of EGFR in lung cancer, we explored TCGA data which revealed that a subset of PTPRH mutant tumors shared gene expression profiles with EGFR mutant tumors, but that EGFR mutations and PTPRH mutations were mutually exclusive. Generation of a PTPRH knockout NSCLC cell line resulted in Y1197 phosphorylation of EGFR, and a rescue with expression of wild type PTPRH returned EGFR phosphorylation to parental line values while a rescue with a D986A catalytically dead mutant PTPRH did not, demonstrating that PTPRH targets EGFR. As expected with active EGFR, the knockout of PTPRH was associated with increased growth rate. Moreover, a dose response curve illustrated that two human NSCLC lines that had naturally occurring PTPRH mutations responded to EGFR tyrosine kinase inhibition. Injection of one of the NSCLC human lines into mice resulted in tumors, and Osimertinib treatment resulted in a reduction of tumor volume relative to vehicle controls. Consistent with prior literature from breast cancer, PTPRH mutation resulted in nuclear pEGFR as seen in immunohistochemistry, suggesting that there may also be a role for EGFR as a transcriptional co-factor. Other roles for PTPRH were explored through a receptor tyrosine kinase array, noting elevated phosphorylation of FGFR1. Knockout of PTPRH in NSCLC cell lines resulted in elevated phosphorylated FGFR1 relative to controls, indicating that PTPRH has a number of targets that may be aberrantly activated in NSCLC with mutations in PTPRH. Together these data suggest that mutations in PTPRH in NSCLC may result in clinically actionable alterations using existing therapies.