Genome-Wide Linkage Mapping Reveals QTLs for Seed Vigor-Related Traits Under Artificial Aging in Common Wheat (Triticum aestivum)

Long-term storage of seeds leads to lose seed vigor with slow and non-uniform germination. Time, rate, homogeneity, and synchrony are important aspects during the dynamic germination process to assess seed viability after storage. The aim of this study is to identify quantitative trait loci (QTLs) using a high-density genetic linkage map of common wheat (Triticum aestivum) for seed vigor-related traits under artificial aging. Two hundred and forty-six recombinant inbred lines derived from the cross between Zhou 8425B and Chinese Spring were evaluated for seed storability. Ninety-six QTLs were detected on all wheat chromosomes except 2B, 4D, 6D, and 7D, explaining 2.9–19.4% of the phenotypic variance. These QTLs were clustered into 17 QTL-rich regions on chromosomes 1AL, 2DS, 3AS (3), 3BS, 3BL (2), 3DL, 4AS, 4AL (3), 5AS, 5DS, 6BL, and 7AL, exhibiting pleiotropic effects. Moreover, 10 stable QTLs were identified on chromosomes 2D, 3D, 4A, and 6B (QaMGT.cas-2DS.2, QaMGR.cas-2DS.2, QaFCGR.cas-2DS.2, QaGI.cas-3DL, QaGR.cas-3DL, QaFCGR.cas-3DL, QaMGT.cas-4AS, QaMGR.cas-4AS, QaZ.cas-4AS, and QaGR.cas-6BL.2). Our results indicate that one of the stable QTL-rich regions on chromosome 2D flanked by IWB21991 and IWB11197 in the position from 46 to 51 cM, presenting as a pleiotropic locus strongly impacting seed vigor-related traits under artificial aging. These new QTLs and tightly linked SNP markers may provide new valuable information and could serve as targets for fine mapping or markers assisted breeding

Attention-Based Multi-NMF Deep Neural Network with Multimodality Data for Breast Cancer Prognosis Model

Today, it has become a hot issue in cancer research to make precise prognostic prediction for breast cancer patients, which can not only effectively avoid overtreatment and medical resources waste, but also provide scientific basis to help medical staff and patients family members to make right medical decisions. As well known, cancer is a partly inherited disease with various important biological markers, especially the gene expression profile data and clinical data. Therefore, the accuracy of prediction model can be improved by integrating gene expression profile data and clinical data. In this paper, we proposed an end-to-end model, Attention-based Multi-NMF DNN (AMND), which combines clinical data and gene expression data extracted by Multiple Nonnegative Matrix Factorization algorithms (Multi-NMF) for the prognostic prediction of breast cancer. The innovation of this method is highlighted through using clinical data and combining multiple feature selection methods with the help of Attention mechanism. The results of comprehensive performance evaluation show that the proposed model reports better predictive performances than either models only using data of single modality, e.g., gene or clinical, or models based on any single NMF improved methods which only use one of the NMF algorithms to extract features. The performance of our model is competitive or even better than other previously reported models. Meanwhile, AMND can be extended to the survival prediction of other cancer diseases, providing a new strategy for breast cancer prognostic prediction

Inversion Model of GPR Imaging Characteristics of Point Objects and Fracture Detection of Heritage Building

There are often many hidden structural defects in heritage buildings. As a convenient and effective nondestructive detecting method, ground-penetrating radar (GPR) has a technical advantage in detecting and protecting heritage buildings depending on the advanced image interpretation. The analytic relationship between buried depth and radius of point object and long and short axis of hyperbolic equation was established according to derivations of formulas. The image characteristics of hyperbolic curves with different depth and radius were studied by finite-difference time-domain method (FDTD). And then, inversion models of buried depth and radius of point object were established. The buried depth and radius can be accurately deduced by long and short axis of hyperbolic image. This result was applied in the detection of pedestal defects of the heritage building, and the depth and distribution range of hidden fracture can be accurately interpreted. It provides an effective and fast method to detect hidden defects in civil engineering

A transposon‐introduced G‐quadruplex motif is selectively retained and constrained to downregulate CYP321A1

Insects utilize xenobiotic compounds to up- and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G-quadruplexes (G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes. Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored. Here, we show that CYP321A1, a xenobiotic-metabolizing P450 from Helicoverpa zea, a polyphagous insect of economic importance, has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region. The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K+. The G4 ligand N-methylmesoporphyrin IX (NMM) strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2. The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.12 month embargo; first published: 28 February 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Genesis of Significance of Carbonated Thermal Water Springs in Xining Basin, China

There are 30 carbonate hot springs in Yaoshuitan geothermal field, Xining Basin, China, with a temperature of 18~41.5 °C; and there are 10 carbonate hot springs in Qijiachuan geothermal field, with a temperature of 10~19.5 °C. Both geothermal fields are carbonate hot springs containing large amounts of CO2 gas. In order to reveal the origin of the carbonated hot springs in Yaoshuitan and Qijiachuan of Xining Basin, this paper offers a comprehensive study of the regional deep geology, tectonic setting, total analysis of carbonated hot springs, δ2H, δ18O, δ13C isotopes, main gas composition, and geochemical characteristics of travertine dating, travertine δ13C, and rare earth elements. The geological process of carbonated hot spring formation and the evolution of H+ content from deep to shallow is revealed, and the genetic mechanism of the carbonated hot spring in Xining Basin is systematically summarized. The results show that: (1) The characteristics of δ2H and δ18O isotopes indicate that the recharge source of carbonated thermal water springs in Xining Basin is mainly atmospheric precipitation. The age of carbonated thermal water springs at 14C is more than 20 ka, indicating that some of them may come from deep fluid (gas) sources. The R/Ra in carbonated thermal water springs is mostly less than 1, indicating that the helium in geothermal water is mainly crustal source helium, and there is no deep mantle source material. (2) The Piper three-plot indicates that the direction of groundwater evolution from the recharge area at the edge of Xining Basin to Yaoshuitan and Qijiachuan carbonated thermal water spring area near the edge of the basin is opposite to the normal path of groundwater evolution in the basin, which is due to the large amount of CO2 gas mixed in the deep fault along the northern margin of Laji Mountain. The ratio of (Ca2+ + Mg2+) and (HCO3− + SO42−) in the Potan and Qijiachuan carbonated thermal water springs is close to 1, and the ratio of (Na+ + K+)/HCO3− is less than 1. It indicates that the chemical composition of the Yaoshuitan carbonated thermal water spring and the Qijiachuan carbonated thermal water spring in Xining Basin is dominated by the dissolution of calcite, dolomite, and gypsum in deep carbonate reservoirs, supplemented by the dissolution of silicate minerals. The relationship between the volume fraction of CO2 and the δ13C value of carbon isotope of CO2 indicates that the source of CO2 is inorganic, which is mainly formed by metamorphism and decomposition of deep carbonate and marble. The δEu < 1 and δCe > 1 of the rare earth elements in the calcium center of the carbonated thermal water springs indicate that the groundwater supplying the travertine material has been in the acidic environment receiving CO2 from the deep crust for a long time. (3) A series of tectonic activities, such as late collision and post-collision between the Indian and Eurasian plates, has led to the uplift, asthenosphere upwelling, and thermal invasion of the northern Tibetan Plateau and other deep dynamic processes. The deep faults in the northern margin of the Laji Mountain and other deep faults with obvious neotectonic activity have provided channels for the up-invasion of deep thermal materials, and local geothermal anomalies were formed near the deep faults. The hidden carbonate rocks and silicate rocks with large thickness undergo thermal metamorphism under high temperature and high pressure in the deep geothermal anomaly area and form a large amount of CO2, which is dissolved in water and enhances the acidity of water. At the same time, the dissolution reaction of acidic water to carbonate rocks consumes H+, which keeps the carbonated thermal water spring weakly acidic. (4) The composition of travertine in carbonated thermal water springs is dominated by calcite, indicating that travertine may be formed in a deep geological environment with a temperature of 150~200 °C, indicating that there are abnormal heat sources in shallow carbonate strata with a burial depth of 3000~4000 m. The abnormal heat source may be caused by the deep fault in the northern margin of Laji Mountain, as well as other deep and large faults channeled in the deep crust and mantle heat source, indicating that the deep fault in the northern margin of Laji Mountain has an obvious heat-controlling effect, and there is a good prospect of geothermal resources exploration near the fault

Plant volatile compound methyl benzoate is highly effective against Spodoptera frugiperda and safe to non-target organisms as an eco-friendly botanical-insecticide

Recent studies have indicated that the plant volatile methyl benzoate (MB) exhibits significant insecticidal bioactivity against several common insects. However, the potential environmental hazards of MB and its safety to non-target organisms is poorly understood. In the present study, these characteristics were investigated through laboratory experiments and field investigations. The results revealed that MB was highly toxic to the agricultural pest, fall armyworm Spodoptera frugiperda. Compared with the commercial pesticide lambda-cyhalothrin, the toxicities of MB against S. frugiperda larvae and adults were comparable and 3.41 times higher, respectively. Behavioral bioassays showed that the percentage repellency of MB to S. frugiperda larvae was 56.72 %, and MB induced 69.40 % oviposition deterrence rate in S. frugiperda female adults. Furthermore, in terms of median lethal concentration (LC50) and median lethal doses (LD50), MB exhibited non-toxic effects on non-target animals with 3-d LC50 of > 1 % to natural predators (Coccinella septempunctata and Harmonia axyridis), 3-d LD50 of 467.86 µg/bee to the bumblebee Bombus terrestris, 14-d LC50 of 971.09 mg/kg to the earthworm Eisenia fetida, and 4-d LC50 of 47.30 mg/L to the zebrafish Brachydanio rerio. The accumulation of MB in the soil and earthworms was found to be extremely limited. Our comparative study clearly demonstrated that MB is effective as a selective botanical pesticide against S. frugiperda and it is safe to use in the tested environment, with no toxic effects on non-target animals and natural predators.National Key Research and Development Program of ChinaOpen access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

QTL Mapping of Adult-Plant Resistance to Leaf Rust in the Wheat Cross Zhou 8425B/Chinese Spring Using High-Density SNP Markers

Wheat leaf rust is an important disease worldwide. Growing resistant cultivars is an effective means to control the disease. In the present study, 244 recombinant inbred lines from Zhou 8425B/Chinese Spring cross were phenotyped for leaf rust severities during the 2011–2012, 2012–2013, 2013–2014, and 2014–2015 cropping seasons at Baoding, Hebei province, and 2012–2013 and 2013–2014 cropping seasons in Zhoukou, Henan province. The population was genotyped using the high-density Illumina iSelect 90K SNP assay and SSR markers. Inclusive composite interval mapping identified eight QTL, designated as QLr.hebau-2AL, QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, QLr.hebau-4AL, QLr.hebau-4B, QLr.hebau-5BL, and QLr.hebau-7DS, respectively. QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, and QLr.hebau-5BL were derived from Zhou 8425B, whereas the other four were from Chinese Spring. Three stable QTL on chromosomes 2BS, 4B and 7DS explained 7.5–10.6%, 5.5–24.4%, and 11.2–20.9% of the phenotypic variance, respectively. QLr.hebau-2BS in Zhou 8425B might be the same as LrZH22 in Zhoumai 22; QLr.hebau-4B might be the residual resistance of Lr12, and QLr.hebau-7DS is Lr34. QLr.hebau-2AL, QLr.hebau-3BS, QLr.hebau-4AL, and QLr.hebau-5BL are likely to be novel QTL for leaf rust. These QTL and their closely linked SNP and SSR markers can be used for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding

Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.)

Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene