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Use of genomic prediction to screen sorghum B‐lines in hybrid testcrosses

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Abstract

Use of trifluoromethanesulfonamide (TFMSA), a male gametocide, increases the opportunities to identify promising B-lines because large quantities of F1 seed can be generated prior to the laborious task of B-line sterilization. Combining TFMSA technology with genomic selection could efficiently evaluate sorghum B-lines in hybrid combination to maximize the rates of genetic gain of the crop. This study used two recombinant inbred B-line populations, consisting of 217 lines, which were testcrossed to two R-lines to produce 434 hybrids. Each population of testcross hybrids were evaluated across five environments. Population-based genomic prediction models were assessed across environments using three different cross-validation (CV) schemes, each with 70% training and 30% validation sets. The validation schemes were as follows: CV1—hybrids chosen randomly for validation; CV2—B-lines were randomly chosen, and each chosen B-line had one of the two corresponding testcross hybrids randomly chosen for the validation; and CV3—B-lines were randomly chosen, and each chosen B-line had both corresponding testcross hybrids chosen for the validation. CV1 and CV2 presented the highest prediction accuracies; nonetheless, the prediction accuracies of the CV schemes were not statistically different in many environments. We determined that combining the B-line populations could improve prediction accuracies, and the genomic prediction models were able to effectively rank the poorest 70% of hybrids even when genomic prediction accuracies themselves were low. Results indicate that combining genomic prediction models and TFMSA technology can effectively aid breeders in predicting B-line hybrid performance in early generations prior to the laborious task of generating A/B-line pairs.

Core Ideas

Genomic prediction can be used to screen sorghum B-lines for hybrid grain yield and days to mid-anthesis. Using genomic prediction and the chemical gametocide TFMSA can increase the rate of genetic gain in sorghum B-lines. Using testers to screen sorghum B-line populations is an effective method for screening with genomic prediction. Genomic prediction can effectively predict hybrid performance within and across populations of sorghum B-lines. The ability to accurately rank hybrid performance remained relatively consistent regardless of prediction accuracy.

Breast cancer diagnosis and management guided by data augmentation, utilizing an integrated framework of SHAP and random augmentation

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Breast cancer diagnosis and management guided by data augmentation, utilizing an integrated framework of SHAP and random augmentation

The use of SHAP for feature engineering alongside random augmentation for data balancing for the diagnosis of breast cancer (BC) proposed some management strategies for BC before and after diagnosis Developed models that could help in the diagnosis of BC by prediction using various machine learning algorithms.


Abstract

Recent research indicates that early detection of breast cancer (BC) is critical in achieving favorable treatment outcomes and reducing the mortality rate associated with it. With the difficulty in obtaining a balanced dataset that is primarily sourced for the diagnosis of the disease, many researchers have relied on data augmentation techniques, thereby having varying datasets with varying quality and results. The dataset we focused on in this study is crafted from SHapley Additive exPlanations (SHAP)-augmentation and random augmentation (RA) approaches to dealing with imbalanced data. This was carried out on the Wisconsin BC dataset and the effectiveness of this approach to the diagnosis of BC was checked using six machine-learning algorithms. RA synthetically generated some parts of the dataset while SHAP helped in assessing the quality of the attributes, which were selected and used for the training of the models. The result from our analysis shows that the performance of the models used generally increased to more than 3% for most of the models using the dataset obtained by the integration of SHAP and RA. Additionally, after diagnosis, it is important to focus on providing quality care to ensure the best possible outcomes for patients. The need for proper management of the disease state is crucial so as to reduce the recurrence of the disease and other associated complications. Thus the interpretability provided by SHAP enlightens the management strategies in this study focusing on the quality of care given to the patient and how timely the care is.

Occurrence of copper‐resistant Pseudomonas syringae pv. actinidiae strains in kiwifruit orchards of Central Italy

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Abstract

Bacterial isolates belonging to Pseudomonas syringae pv. actinidiae, the causal agent of kiwifruit bacterial canker, have been isolated, during 2021 and 2022, from Actinidia chinensis orchards of Central Italy planted with cultivars Hayward and Zespri G3®. A total of 23 isolates were obtained from twigs and leaves that showed the typical symptoms of bacterial canker, including leaf spotting and twig canker. All of them showed resistance to 1.2 mM copper sulphate added to mannitol–glutamate–yeast extract (MGY) medium. No other Pseudomonas syringae pv. actinidiae strains were isolated from the orchards. The P. s. pv. actinidiae strains that showed resistance to copper have the copA and copD genes that regulate the efflux of copper through the inner membrane and the copper sensor copS gene. They do not possess the cusABC complex that confers resistance to high concentration of copper. Representative copper-resistant strains were proven pathogenic to kiwifruit plants upon artificial inoculation. This is the first record of copper-resistant P. s. pv. actinidiae strains in Italy and, as far as we know, in Europe.

Analysis of genetic diversity and population structure of Puccinia striiformis f. sp. tritici infers inoculum relationships from Yunnan to the middle and lower reaches of the Yangtze River

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Analysis of genetic diversity and population structure of Puccinia striiformis f. sp. tritici infers inoculum relationships from Yunnan to the middle and lower reaches of the Yangtze River

Puccinia striiformis f. sp. tritici uredinia from the middle/lower Yangtze River area in 2019 were analysed with SSR markers; the autumn inoculum probably came from south-western over-summering areas by long-distance migration.


Abstract

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an important cereal fungal disease worldwide, including in the major wheat-producing areas in China. In 2019, there was a widespread epidemic of the disease in the middle and lower reaches of the Yangtze River (MLRYR) area, including Zhejiang, Jiangsu, Anhui and Guangxi. However, in north-western China, the postulated inoculum source of MLRYR, disease occurred mildly. Therefore, the origin of the Pst inoculum source for the MLRYR epidemic is still an open question. To address it, we collected 210 Pst uredinium samples from the Yangtze River basin and analysed their genetic structure with 13 pairs of simple-sequence repeat (SSR) markers that we coupled with an upper airflow trajectory analysis. Our results suggest that the autumn inoculum sources of wheat stripe rust in MLRYR in 2019 probably came from south-western over-summering areas of Pst through long-distance migration. We also found that Jingzhou and adjacent areas in Hubei Province function as an important bridge or stopover for inoculum sources.

Watermelon mosaic virus in the Czech Republic, its recent and historical origins

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Watermelon mosaic virus in the Czech Republic, its recent and historical origins

Watermelon mosaic virus probably moved from non-cucurbit hosts (Ailanthus altissima, Alcea rosea, Panax ginseng, etc.) to watermelon around 1000 years ago. (Pictures from Wikimedia)


Abstract

Watermelon mosaic virus (WMV) is a potyvirus and a member of the bean common mosaic virus (BCMV) lineage. It is one of the most economically important viral pathogens of cucurbits worldwide and was first reported in the Czech Republic in 2011 from serological surveys (2005–2011). In this study, we confirmed this identification by determining the complete coding regions of five Czech WMV isolates using high-throughput sequencing and Sanger sequencing (MW188031; OP585149–OP585152), together with the coat protein (CP) genes of 26 additional isolates. Phylogenies were made from these and more than 128 genomes or 128 CP genes from GenBank. They showed that the Czech isolates were most closely related to other European isolates, but, surprisingly, 96.2% of the genomes were recombinant. The nonrecombinant sequences mostly came from basal isolates, all originating from China, and some from unusual hosts (Ailanthus altissima, Alcea rosea and Panax ginseng). The complete WMV genomes form three phylogenetic clades, two of them small and basal, and the third includes all other isolates. Comparative dating suggests that the basal Chinese isolates are descendants of a potyvirus population infecting various dicotyledonous plant species in China at least 2000 years ago. WMV became a crop pathogen around 1000 years ago, a few years after watermelon was taken to northern China and first grown as a crop during the Five Dynasties (907–960 ce).

Banana bunchy top disease in Africa—Predicting continent‐wide disease risks by combining survey data and expert knowledge

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Banana bunchy top disease in Africa—Predicting continent-wide disease risks by combining survey data and expert knowledge

Visualizing and mitigating the growing risks of BBTD spread across Africa, leveraging a decade's worth of survey data and expert insights for strategic decision-making.


Abstract

Across Africa, banana bunchy top disease (BBTD) severely impacts banana production and livelihoods of millions of smallholder farmers. Mapping vulnerability of landscapes to monitor BBTD establishment and spread is crucial for proactive measures of disease exclusion. To highlight current and future risks of BBTD in Africa, the relationship between 1160 field observations from 14 BBTD surveys and environmental covariate maps was determined using logistic regression. From these relationships, we inferred the environmental suitability of the African landscape for the possible wider spread of BBTD. Using this information and expert knowledge, we generated a map highlighting the main banana production areas at risk of BBTD entry and establishment. We combined these maps to create a priority map that highlights the areas that need most attention in combating BBTD through surveillance and measures to prevent its spread. Our analysis shows that BBTD is widespread across tropical Africa, with dispersal over several hotspots. Central and Western Africa are most favourable for the development of BBTD. Central, West and South-East Africa are most at risk of BBTD entry and initial establishment. Areas in West and Central Africa, in the Great Lakes Region in Eastern Africa and in South-East Africa, particularly in Malawi and Mozambique, score high on the prioritization index for surveillance and mitigation efforts. Recent reports of BBTD presence in north-western Uganda and western Tanzania support these risk predictions. For these and other not-yet-infected areas, measures for close surveillance and proactive management of the disease are needed.

HCPro affects heterologous virus infection through salicylic acid and auxin pathways

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HCPro affects heterologous virus infection through salicylic acid and auxin pathways

Transgenic Nicotiana tabacum plants expressing HCPro of chilli veinal mottle virus respond to the infection by tobacco mosaic virus or cucumber mosaic virus via salicylic acid and auxin pathways.


Abstract

Mixed infection by plant viruses is common in nature, but how a key viral protein of one virus affects the infection by heterologous viruses is not yet fully understood. The helper component proteinase (HCPro) is a widely studied RNA silencing suppressor encoded by viruses of the family Potyviridae. Here, we investigated the defence response of Nicotiana tabacum plants overexpressing HCPro of chilli veinal mottle virus (HCPro-OX) to tobacco mosaic virus and cucumber mosaic virus infection. We monitored the physiological and molecular changes of HCPro-OX plants in response to virus infection. The results showed that HCPro-OX plants under virus infection exhibited higher susceptibility at the early stage but stronger tolerance at the later stage compared to wild-type plants. The tolerance to heterologous virus infection of HCPro-OX plants corresponded to a lower level of reactive oxygen species accumulation and higher activities of several antioxidant enzymes. Reverse transcription-quantitative PCR assays showed that the expression of genes related to salicylic acid (SA) pathways was significantly upregulated, but the expression of genes related to the auxin pathways was downregulated at the late stage of virus infection in HCPro-OX plants compared to wild-type plants. By contrast, the situation in the early stage of virus infection was reversed. In addition, pretreatment with SA, the auxin naphthylacetic acid (NAA) and their respective inhibitors 1-aminobenzotriazole (ABT) and naphthalam (NPA) further confirmed the antagonistic effects of SA and NAA in the response of HCPro-OX plants to heterologous virus infection. Thus, our results demonstrate that HCPro affects heterologous virus infection through SA and auxin pathways.

Plant growth stage and Phoma medicaginis inoculum concentration together determine severity of Phoma black stem and leaf spot and consequent phytoestrogen production in annual Medicago spp.

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Plant growth stage and Phoma medicaginis inoculum concentration together determine severity of Phoma black stem and leaf spot and consequent phytoestrogen production in annual Medicago spp.

Studies highlighted how Phoma disease incidence and severity and resultant phytoestrogen production in annual Medicago depend on plant developmental stage, inoculum concentration and cultivar.


Abstract

Phoma black stem and leaf spot disease (Phoma medicaginis) not only destroys annual Medicago spp. forage and seed yield but also reduces herbage quality by consequent phytoestrogen production that reduces ovulation of grazing animals. Two controlled environment studies evaluated the effects of plant developmental stage in annual Medicago rugosa ‘Paraponto’ and M. scutellata ‘Sava’ and different inoculum concentrations of P. medicaginis in M. littoralis ‘Harbinger’ and M. polymorpha ‘Serena’ on disease development and coumestrol production. Disease incidence and severity and coumestrol production were dependent on plant developmental stage, cultivar and inoculum level (all p ≤ 0.001). Disease was least in 4-week-old plants; highest coumestrol was in inoculated 10-week-old Sava (1353 mg/kg) and least coumestrol in uninoculated 4-week-old Paraponto (87 mg/kg); and there was a positive correlation of disease incidence/severity factors with coumestrol across cultivars and plant growth stages (p < 0.001). Disease levels and coumestrol production were determined by inoculum concentration and cultivar (both p ≤ 0.001). Highest coumestrol was in Serena inoculated with 107 conidia/mL (265 mg/kg); lowest coumestrol was in uninoculated Harbinger (6 mg/kg); and there was a significant positive correlation of disease incidence/severity factors with coumestrol across cultivars and inoculum concentrations (p < 0.001). These studies emphasize both the opportunity for farmers to better use annual Medicago spp. stands for grazing reproducing animals early in the growing season when both disease and coumestrol levels are lowest, and the need for heightened farmer vigilance at later growth stages with greater disease and consequent phytoestrogen risk for grazing animals.

Synergistic effects of Bacillus velezensis SDTB038 and phenamacril on Fusarium crown and root rot of tomato

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Synergistic effects of Bacillus velezensis SDTB038 and phenamacril on Fusarium crown and root rot of tomato

Bacillus velezensis SDTB038 had strong antifungal activity. The combination of phenamacril and SDTB038 had the most effective in controlling Fusarium crown and root rot of tomato, while also improving tomato yields in greenhouse.


Abstract

Fusarium crown and root rot (FCRR) is a damaging ailment that can affect tomato production. It is caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). The use of biological agents, in conjunction with fungicides, has become a practical strategy for combating fungal diseases in crops. Lipopeptide extracts from a potential biocontrol strain of Bacillus velezensis (SDTB038) exhibited an inhibitory effect on the mycelial growth of FORL; the EC50 value was 59.95 mg/L, and at a concentration of 256 mg/L the inhibition rate reached 97.4%. The SDTB038 strain produces metabolites such as protease and siderophores. Additionally, it is capable of forming a biofilm and swimming. Phenamacril, an antifungal agent, also displayed an inhibitory effect on FORL, demonstrating an EC50 value of 1.074 mg/L. The control effects of the combination of Bacillus velezensis SDTB038 and phenamacril against FORL on tomato plants were also studied in the greenhouse. The combination of phenamacril and 108 CFU/mL SDTB038 fermentation broth exhibited a strong synergistic control effect on FORL, of up to 84.0%. The combination also led to a 35.6% increase in tomato yield compared to the control. These results demonstrate that SDTB038 possesses antifungal activity. Moreover, when combined with phenamacril, it exhibits a strong synergistic effect against FORL. This solution proves to be an effective means of controlling FCRR in tomato plants.

Grapevine yellows in Jordan: Associated phytoplasmas, putative insect vectors and reservoir plants

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Grapevine yellows in Jordan: Associated phytoplasmas, putative insect vectors and reservoir plants

In Jordan, genetic diversity, distribution and ecology of phytoplasmas associated with grapevine yellows are more complex than previously known.


Abstract

Field surveys were conducted in wine and table grape vineyards from June to October 2020 in 13 locations belonging to five governorates in North and South Jordan. Typical grapevine yellows symptoms, including leaf reddening/yellowing and rolling were observed on 10% to 55% of vines. Nested PCR-based amplification of the 16S rRNA gene detected phytoplasmas in 22% and 15.7% of the analysed symptomatic wine and table grape cultivar plants, respectively. Amplicon nucleotide sequence analyses identified the detected phytoplasmas as “Candidatus Phytoplasma solani” (taxonomic subgroup 16SrXII-A), “Ca. P. omanense” (16SrXXIX-A and -B), “Ca. P. aurantifolia” (16SrII-C) and “Ca. P. asteris” (16SrI-R) in 72.4%, 17.2%, 6.9% and 3.4% of infected plants, respectively. Such phytoplasmas were found differentially distributed in wine and table grape cultivar vineyards surveyed. Further investigation identified “Ca. P. solani” in the putative insect vectors Orosius cellulosus (first report in Jordan), Euscelidius mundus, Laodelphax striatellus, and Circulifer sp., and in bindweed; “Ca. P. aurantifolia” in the insect O. cellulosus and in bindweed; “Ca. P. omanense” in the insect Psammotettix striatus; and “Ca. P. asteris” in the insects Arboridia adanae, Cicadulina bipunctata, Circulifer sp., L. striatellus, Hyalesthes obsoletus, and P. striatus. Based on this preliminary data, ecological cycles of such phytoplasmas are discussed. Results suggest that the diversity and ecology of grapevine yellows phytoplasmas in Jordan are more complex than previously known, leading to a potential risk of disease outbreaks.