UV-aged polystyrene nanoplastics aggravate intestinal barrier damage by overproduction of ROS.

UV irradiation significantly alters nanoplastics (NPs) physicochemical properties, thus affecting their biological toxicity. This study is the first to assess the influence of virgin and UV-aged polystyrene NPs (v-PS NPs, a-PS NPs) on the intestinal barrier of ICR mice. We found that a-PS NPs can cause more severe intestinal barrier damage compared with v-PS NPs. The reason may be attributed to that a-PS NPs produced more ROS in intestinal tissue. Moreover, the strong oxidizing property of hydroxyl radicals (·OH) generated from the a-PS NPs can damage cell membranes through lipid peroxidation, thereby leading to a low clearance rate of ·OH due to the impaired intestinal tissue function, in turn, causing more ROS to accumulate and inducing severe oxidative damage. This research underscores the crucial role of ·OH in mediating oxidative damage from UV-aged nanoparticles, emphasizing the need to consider environmental factors in assessing NPs toxicity.

POU6F1 promotes ferroptosis by increasing lncRNA-CASC2 transcription to regulate SOCS2/SLC7A11 signaling in gastric cancer.

OBJECTIVE: This study investigated the effect and mechanism of POU6F1 and lncRNA-CASC2 on ferroptosis of gastric cancer (GC) cells. METHODS: GC cells treated with erastin and RSL3 were detected for ferroptosis, reactive oxygen species (ROS) level, and cell viability. The expression levels of POU6F1, lncRNA-CASC2, SOCS2, and ferroptosis-related molecules (GPX4 and SLC7A11) were also measured. The regulations among POU6F1, lncRNA-CASC2, FMR1, SOCS2, and SLC7A11 were determined. Subcutaneous tumor models were established, in which the expressions of Ki-67, SOCS2, and GPX4 were detected by immunohistochemistry. RESULTS: GC patients with decreased expressions of POU6F1 and lncRNA-CASC2 had lower survival rate. Overexpression of POU6F1 or lncRNA-CASC2 decreased cell proliferation and GSH levels in GC cells, in addition to increasing total iron, Fe2+, MDA, and ROS levels. POU6F1 directly binds to the lncRNA-CASC2 promoter to promote its transcription. LncRNA-CASC2 can target FMR1 and increase SOCS2 mRNA stability to promote SLC7A11 ubiquitination degradation and activate ferroptosis signaling. Knockdown of SOCS2 inhibited the ferroptosis sensitivity of GC cells and reversed the effects of POU6F1 and lncRNA-CASC2 overexpression on ferroptosis in GC cells. CONCLUSION: Transcription factor POU6F1 binds directly to the lncRNA-CASC2 promoter to promote its expression, while upregulated lncRNA-CASC2 increases SOCS2 stability and expression by targeting FMR1, thereby inhibiting SLC7A11 signaling to promote ferroptosis in GC cells and inhibit GC progression.

iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.

The advent of full-length transcriptome sequencing technologies has accelerated the discovery of novel splicing isoforms. However, existing alternative splicing (AS) tools are either tailored for short-read RNA-Seq data or designed for human and animal studies. The disparities in AS patterns between plants and animals still pose a challenge to the reliable identification and functional exploration of novel isoforms in plants. Here, we developed integrated full-length alternative splicing analysis (iFLAS), a plant-optimized AS toolkit that introduced a semi-supervised machine learning method known as positive-unlabeled (PU) learning to accurately identify novel isoforms. iFLAS also enables the investigation of AS functions from various perspectives, such as differential AS, poly(A) tail length, and allele-specific AS (ASAS) analyses. By applying iFLAS to three full-length transcriptome sequencing datasets, we systematically identified and functionally characterized maize (Zea mays) AS patterns. We found intron retention not only introduces premature termination codons, resulting in lower expression levels of isoforms, but may also regulate the length of 3'UTR and poly(A) tail, thereby affecting the functional differentiation of isoforms. Moreover, we observed distinct ASAS patterns in two genes within heterosis offspring, highlighting their potential value in breeding. These results underscore the broad applicability of iFLAS in plant full-length transcriptome-based AS research.

New Sight of Renal Toxicity Caused by UV-Aged Polystyrene Nanoplastics: Induced Ferroptosis via Adsorption of Transferrin.

Secondary nanoplastics (NPs) caused by degradation and aging due to environmental factors are the main source of human exposure, and alterations in the physicochemical and biological properties of NPs induced by environmental factors cannot be overlooked. In this study, pristine polystyrene (PS) NPs to obtain ultraviolet (UV)-aged PS NPs (aPS NPs) as secondary NPs is artificially aged. In a mouse oral exposure model, the nephrotoxicity of PS NPs and aPS NPs is compared, and the results showed that aPS NPs exposure induced more serious destruction of kidney tissue structure and function, along with characteristic changes in ferroptosis. Subsequent in vitro experiments revealed that aPS NPs-induced cell death in human renal tubular epithelial cells involved ferroptosis, which is supported by the use of ferrostatin-1, a ferroptosis inhibitor. Notably, it is discovered that aPS NPs can enhance the binding of serum transferrin (TF) to its receptor on the cell membrane by forming an aPS-TF complex, leading to an increase in intracellular Fe2+ and then exacerbation of oxidative stress and lipid peroxidation, which render cells more sensitive to ferroptosis. These findings indicated that UV irradiation can alter the physicochemical and biological properties of NPs, enhancing their kidney biological toxicity risk by inducing ferroptosis.

Phycoremediation and valorization of hypersaline pickled mustard wastewater via Chaetoceros muelleri and indigenous bacteria.

Hypersaline pickled mustard wastewater (PMW), a typical food wastewater with high nutrient content, was successfully bioremediated via the co-treatment of Chaetoceros muelleri and indigenous bacteria in this study. Chemical oxygen demand, ammonia nitrogen, total nitrogen and total phosphorus in 10 % PMW could be effectively reduced by 82 %, 90 %, 94 % and 96 %, respectively, after 12 days treatment. Oxygen species activities, malondialdehyde content, microalgal biomass, photosynthesis and extracellular polymeric substances were characterized during the treatment to determine the responses of the consortium when exposed to different concentration of PMW. Microbial community analysis demonstrated a significant increase in the relative abundance of Halomonas and Marinobacter in the 10 % PMW after 12 days treatment, which was beneficial for nutrients recycling by the diatoms. Meanwhile, C. muelleri was effective in reducing the relative abundance of potentially pathogenic bacteria Malaciobacter. In conclusion, the work here offers a promising and environmentally friendly approach for hypersaline wastewater treatment.

Correlation between serum vitamin D level and uterine volume in girls with idiopathic central precocious puberty.

OBJECTIVES: Investigate serum vitamin D (vit D) levels' relation to uterine volume in idiopathic central precocious puberty (ICPP) girls and compare findings with normal peers. METHODS: Analyzed 278 ICPP cases from January 2017 to September 2022 alongside 239 normally developing girls. Collected clinical data and lab markers and performed subgroup analysis based on vit D levels. Correlation and regression analyses were conducted. RESULTS: The ICPP group exhibited elevated uterine volume and lower serum vit D compared to controls (p<0.05). A weak negative correlation was noted between vit D and uterine volume in ICPP (r=-0.193, p=0.004), and no such correlation in controls (r=-0.073, p=0.319). The ICPP vit D deficiency subgroup displayed higher uterine volume than the insufficiency and sufficiency subgroups (p<0.05). Uterine volume in the insufficiency subgroup exceeded the sufficiency subgroup (p<0.05). After adjusting for confounders, lower vit D is linked to increased ICPP uterine volume (non-standardized regression coefficient ß=-25.55, 95 % CI= -46.23, -4.87, p=0.016). A Limited correlation between vit D and uterine volume was seen in girls with normal pubertal timing. CONCLUSIONS: We demonstrated a correlation between vit D and uterine volume in ICPP girls, absent in normal peers. ICPP girls often exhibit lower vit D levels and increased uterine volume. Further research is vital for understanding vit D's role in ICPP pathogenesis and guiding prevention and treatment strategies.

18 F-FDG PET/CT Versus 18 F-FAPI PET/CT in a Case of Recurrent Malignant Phyllodes Breast Tumor.

ABSTRACT: A 52-year-old woman with medical history of surgery for left malignant phyllodes breast tumor found a mass on the left chest 3 months ago. A suspicion of recurrent malignant phyllodes breast tumor was made. The patient was enrolled in the clinical trial of 18 F-FAPI PET/CT in recurrent sarcoma (no. NCT05485792). 18 F-FAPI PET/CT and 18 F-FDG PET/CT were performed, and the images demonstrated intense uptake in a huge mass in the left anterior chest wall. Then the patient underwent extended resection of left chest wall tumor. The tumor proved to be recurrent malignant phyllodes breast tumor pathologically.

Head-to-head comparison of 18F-FAPI and 18F-FDG PET/CT in staging and therapeutic management of hepatocellular carcinoma.

BACKGROUND: Fluorine 18 (18F) fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) has limitations in staging hepatocellular carcinoma (HCC). The recently introduced 18F-labeled fibroblast-activation protein inhibitor (FAPI) has shown promising prospects in detection of HCC lesions. This study aimed to investigate the initial staging and restaging performance of 18F-FAPI PET/CT compared to 18F-FDG PET/CT in HCC. METHODS: This prospective study enrolled histologically confirmed HCC patients from March 2021 to September 2022. All patients were examined with 18F-FDG PET/CT and 18F-FAPI PET/CT within 1 week. The maximum standard uptake value (SUVmax), tumor-to-background ratio (TBR), and diagnostic accuracy were compared between the two modalities. RESULTS: A total of 67 patients (57 men; median age, 57 [range, 32-83] years old) were included. 18F-FAPI PET showed higher SUVmax and TBR values than 18F-FDG PET in the intrahepatic lesions (SUVmax: 6.7 vs. 4.3, P < 0.0001; TBR: 3.9 vs. 1.7, P < 0.0001). In diagnostic performance, 18F-FAPI PET/CT had higher detection rate than 18F-FDG PET/CT in intrahepatic lesions [92.2% (238/258) vs 41.1% (106/258), P < 0.0001] and lymph node metastases [97.9% (126/129) vs 89.1% (115/129), P = 0.01], comparable in distant metastases [63.6% (42/66) vs 69.7% (46/66), P > 0.05]. 18F-FAPI PET/CT detected primary tumors in 16 patients with negative 18F-FDG, upgraded T-stages in 12 patients and identified 4 true positive findings for local recurrence than 18F-FDG PET, leading to planning therapy changes in 47.8% (32/67) of patients. CONCLUSIONS: 18F-FAPI PET/CT identified more primary lesions, lymph node metastases than 18F-FDG PET/CT in HCC, which is helpful to improve the clinical management of HCC patients. TRIAL REGISTRATION: Clinical Trials, NCT05485792 . Registered 1 August 2022, Retrospectively registered.

Increased 18F-FAPI Uptake in Radiation-Induced Liver Injury.

ABSTRACT: A 51-year-old woman with breast cancer underwent a complete surgical resection and chemoradiotherapy approximately 3 months ago. Follow-up abdominal ultrasound detected a new lesion with decreased echogenicity in the hepatic segment IV/VIII. 18F-FDG PET/CT showed the hepatic lesion without abnormal uptake. The patient was subsequently enrolled in a clinical trial of 18F-FAPI PET/CT to assess the hepatic lesion. An intense 18F-FAPI activity was identified in the hepatic lesion. Finally, pathological analysis combined with imaging follow-up confirmed the diagnosis of radiation-induced liver injury.

G2P Provides an Integrative Environment for Multi-model genomic selection analysis to improve genotype-to-phenotype prediction.

Genotype-to-phenotype (G2P) prediction has become a mainstream paradigm to facilitate genomic selection (GS)-assisted breeding in the seed industry. Many methods have been introduced for building GS models, but their prediction precision may vary depending on species and specific traits. Therefore, evaluation of multiple models and selection of the appropriate one is crucial to effective GS analysis. Here, we present the G2P container developed for the Singularity platform, which not only contains a library of 16 state-of-the-art GS models and 13 evaluation metrics. G2P works as an integrative environment offering comprehensive, unbiased evaluation analyses of the 16 GS models, which may be run in parallel on high-performance computing clusters. Based on the evaluation outcome, G2P performs auto-ensemble algorithms that not only can automatically select the most precise models but also can integrate prediction results from multiple models. This functionality should further improve the precision of G2P prediction. Another noteworthy function is the refinement design of the training set, in which G2P optimizes the training set based on the genetic diversity analysis of a studied population. Although the training samples in the optimized set are fewer than in the original set, the prediction precision is almost equivalent to that obtained when using the whole set. This functionality is quite useful in practice, as it reduces the cost of phenotyping when constructing training population. The G2P container and source codes are freely accessible at https://g2p-env.github.io/.

Integrative analysis of γδT cells and dietary factors reveals predictive values for autism spectrum disorder in children.

BACKGROUND: Autism spectrum disorder (ASD) includes a range of multifactorial neurodevelopmental disabilities characterized by a variable set of neuropsychiatric symptoms. Immunological abnormalities have been considered to play important roles in the pathogenesis of ASD, but it is still unknown which abnormalities are more prominent. METHODS: A total of 105 children with ASD and 105 age and gender-matched typically developing (TD) children were recruited. An eating and mealtime behavior questionnaire, dietary habits, and the Bristol Stool Scale were investigated. The immune cell profiles in peripheral blood were analyzed by flow cytometry, and cytokines (IFN-γ, IL-8, IL-10, IL-17A, and TNF-α) in plasma were examined by Luminex assay. The obtained results were further validated using an external validation cohort including 82 children with ASD and 51 TD children. RESULTS: Compared to TD children, children with ASD had significant eating and mealtime behavioral changes and gastrointestinal symptoms characterized by increased food fussiness and emotional eating, decreased fruit and vegetable consumption, and increased stool astriction. The proportion of γδT cells was significantly higher in children with ASD than TD children (ß: 0.156; 95% CI: 0.888 âˆ¼ 2.135, p < 0.001) even after adjusting for gender, eating and mealtime behaviors, and dietary habits. In addition, the increased γδT cells were evident in all age groups (age < 48 months: ß: 0.288; 95% CI: 0.420 âˆ¼ 4.899, p = 0.020; age ≥ 48 months: ß: 0.458; 95% CI: 0.694 âˆ¼ 9.352, p = 0.024), as well as in boys (ß: 0.174; 95% CI: 0.834 âˆ¼ 2.625, p < 0.001) but not in girls. These findings were also confirmed by an external validation cohort. Furthermore, IL-17, but not IFN-γ, secretion by the circulating γδT cells was increased in ASD children. Machine learning revealed that the area under the curve in nomogram plots for increased γδT cells combined with eating behavior/dietary factors was 0.905, which held true in both boys and girls and in all the age groups of ASD children. The decision curves showed that children can receive significantly higher diagnostic benefit within the threshold probability range from 0 to 1.0 in the nomogram model. CONCLUSIONS: Children with ASD present with divergent eating and mealtime behaviors and dietary habits as well as gastrointestinal symptoms. In peripheral blood, γδT cells but not αßT cells are associated with ASD. The increased γδT cells combined with eating and mealtime behavior/dietary factors have a high value for assisting in the diagnosis of ASD.

IP4GS: Bringing genomic selection analysis to breeders.

Genomic selection (GS), a strategy to use genotypes to predict phenotypes via statistical or machine learning models, has become a routine practice in plant breeding programs. GS can speed up the genetic gain by reducing phenotyping costs and/or shortening the breeding cycles. GS analysis is complicated involving data clean up and formatting, training and test population analysis, model selection and evaluation, and parameter optimization. In addition, GS analysis also requires some programming skills and knowledge of statistical modeling. Thus, we need a more practical GS tools for breeders. To alleviate this difficulty, we developed the web-based platform IP4GS (https://ngdc.cncb.ac.cn/ip4gs/), which offers a user-friendly interface to perform GS analysis simply through point-and-click actions. IP4GS currently includes seven commonly used models, eleven evaluation metrics, and visualization modules, offering great convenience for plant breeders with limited bioinformatics knowledge to apply GS analysis.

[18F]FAPI PET/CT in the evaluation of focal liver lesions with [18F]FDG non-avidity.

PURPOSE: This prospective study was aimed to investigate the potential utility of [18F]fibroblast activation protein inhibitor (FAPI) PET/CT for evaluating focal liver lesions (FLLs) with [18F]FDG non-avidity. METHODS: From January 2021 to March 2022, this prospective study included 80 FLLs that were not avid on [18F]FDG PET/CT from 37 patients, then underwent [18F]FAPI PET/CT. All patients with FLL(s) with biopsy-proof or follow-up confirmation were categorized into four subgroups (20 hepatocellular carcinomas [HCCs]/5 non-HCC malignancies/4 inflammatory FLLs/8 benign noninflammatory FLLs). The diagnostic value of [18F]FAPI for detecting liver malignancy was determined by visual evaluation. Differences in the maximum standardized uptake value (SUVmax) and lesion-to-background ratio (LBR) obtained from [18F]FAPI PET/CT among the four subgroups were analyzed by semiquantitative analysis. RESULTS: Among the thirty-seven enrolled participants (34 males; median age 57 years, range 48-67 years), on visual evaluation, the sensitivity, specificity, and accuracy of [18F]FAPI PET for detecting liver malignancy in the patient-based analysis were 96.0% (24/25), 58.3% (7/12), and 83.8% (31/37), respectively. On semiquantitative analysis, the SUVmax and LBR of [18F]FAPI PET in liver malignancy (33 HCC lesions; 19 non-HCC malignant lesions) were significantly higher than those in 11 benign noninflammatory FLLs [HCC: SUVmax: 6.4 vs. 4.5, P = 0.017; LBR: 5.1 vs. 1.5, P = 0.003; non-HCC: SUVmax: 5.5 vs. 4.5, P = 0.008; LBR: 4.4 vs. 1.5, P = 0.042]. Notably, there was no significant difference in the SUVmax of [18F]FAPI PET between 33 HCC lesions and 17 inflammatory FLLs (6.4 vs. 8.2, P = 0.37), but the LBR of [18F]FAPI PET in HCC were significantly lower than that in inflammatory FLLs (5.1 vs. 9.1, P = 0.003). CONCLUSIONS: [18F]FAPI PET/CT shows high sensitivity in detecting HCC and non-HCC malignancy with [18F]FDG non-avidity. [18F]FAPI might be a promising radiopharmaceutical for the differential diagnosis of benign noninflammatory FLLs and liver malignancy with [18F]FDG non-avidity.

Oriented Crystallization of Hydroxyapatite in Self-Assembled Peptide Fibrils as a Bonelike Material.

Controlling oriented crystallization is key to producing bonelike composite materials with a well-organized structure. However, producing this type of composite material using synthetic biopolymers as scaffolds is challenging. Inspired by the molecular structure of collagen-I, a collagenlike peptide─(Pro-Hyp-Gly)10 (POG10)─was designed to produce self-assembled fibrils that resemble the structure of collagen-I fibrils. In addition, the oriented mineralization of HAP crystals is formed in the fibrils that reproduces a bonelike material similar to collagen-I fibril mineralization. Unlike collagen-I fibrils, POG10 fibrils do not contain gap spaces. The molecular simulation results indicate that in addition to space confinement, the molecular field generated by POG10 can also confine the orientation of HAP, enriching our understanding of physical confinement and shedding light on the design of synthetic biopolymer scaffolds for bonelike material fabrication.

68 Ga-FAPI Versus 18 F-FDG PET/CT in Recurrent Undifferentiated Pleomorphic Sarcoma of Colon Mesentery.

ABSTRACT: A 56-year-old woman presented with primary undifferentiated pleomorphic sarcoma of colon mesentery underwent complete surgical resection approximately 7 months ago. Abdominal contrast-enhanced CT showed a new mass in the descending colon, suggesting a high probability of tumor recurrence. Under a clinical trial, the patient underwent 68 Ga-FAPI and 18 F-FDG PET/CT to detect whether there are additional recurrent lesions. Compared with 18 F-FDG PET/CT, the recurrent undifferentiated pleomorphic sarcoma of colon mesentery, peritoneum, pelvic lymph node, and lung metastases showed higher uptake in 68 Ga-FAPI PET/CT. This case showed that 68 Ga-FAPI might be a promising radiopharmaceutical in the evaluation of undifferentiated pleomorphic sarcoma.

Combined Treatment of Salinity Stress and Fruit Thinning Effect on Tomato.

This was an experimental investigation of the combined treatments of salinity (SAL) stress and fruit thinning (FT) on the growth, yield, fruit quality, and water use efficiency (WUE) of tomatoes with non-soil cultivation. The experiment was carried out in a plastic tunnel, Japan. Tomato (Solanum lycopersicum) cv. Momotaro seedlings were transplanted in a randomized complete block (RCB) manner with six plants/treatment, and an overall 36 plants in 18 pots (2 plants/pot). The experiment involved varying SAL treatment (no-SAL, moderate SAL, and serious SAL, with electroconductivity of 0.8, 3.0, and 4.5 dS m-1, separately) and FT treatment (NT: no thinning and 3FT: three-fruit treatment). The tomato growth, yield, and WUE were significantly suppressed with increasing SAL. In comparison, FT treatment had less effect on tomato growth and water consumption. Either SAL stress or FT treatment significantly improved fruit quality. The combined treatment proved better than single treatment of either SAL stress or FT, avoided the subsize fruit following SAL stress treatment, reduced fruit cracking found with FT treatment, and greatly improved fruit quality. The SAL thresholds of WUEs in relation to biomass, yield, and marketable yield were approximately 3.0 dS m-1 under these soilless conditions. Path analysis showed that biomass and water consumption were important indexes affecting yield. Logistic equation fitting showed that SAL stress tended to inhibit and delay plant growth; however, FT tended to advance and shorten the period of plant growth.

Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks.

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in breeding. In this study, we sequenced the genomes of 250 soybean landraces and cultivars from China, America, and Europe, and investigated their population structure, genetic diversity and architecture, and the selective sweep regions of these accessions. Five novel agronomically important genes were identified, and the effects of functional mutations in respective genes were examined. The candidate genes GSTT1, GL3, and GSTL3 associated with the isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits were found. The phenotype-gene network analysis revealed that hub nodes play a crucial role in complex phenotypic associations. This study describes novel agronomic trait-associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

Decabromodiphenyl ether induces male reproductive toxicity by activating mitochondrial apoptotic pathway through glycolipid metabolism dysbiosis.

Decabromodiphenyl ether (BDE-209), an extensively used flame retardant, exists widely in the environment. Although male reproductive toxicity induced by BDE-209 has been reported, its mechanisms remain unclear. To explore the role of glycolipid metabolism in male reproductive toxicity and the potential mechanisms, forty male SD rats were divided into four groups and given gavage with BDE-209 at 0, 5, 50, and 500 mg/kg/d for 28 days. In vitro, the spermatogenic cell lines GC-2spd cells were divided into four groups: the control group, 32 µg/mL BDE-209 group, 32 µg/mL BDE-209 + 0.4 µM Fatostatin (the inhibitor of SREBP-1) group, and 0.4 µM Fatostatin group. Our results showed that BDE-209 decreased sperm quality and quantity, which was correlated with glycolipid metabolism dysbiosis of testis. The levels of glucose, triglyceride, and total cholesterol were negatively correlated with sperm concentration, and triglyceride and total cholesterol levels were negatively correlated with sperm motility, while positively correlated with the sperm malformation rate. Moreover, BDE-209 exposure activated the glycolipid metabolism pathways (PPARγ/RXRα/SCAP/SREBP-1) and mitochondrial apoptotic pathway, thereby inducing the apoptosis of spermatogenic cells. In vitro, BDE-209 caused triglyceride and total cholesterol disorder and apoptosis of GC-2spd cells, the lipid metabolism pathways inhibitor fatostain downregulated the elevation of triglyceride and total cholesterol concentrations, and suppressed apoptosis and the activation of the mitochondrial apoptotic pathway in GC-2spd cells caused by BDE-209. Our results indicated that BDE-209 induced male reproductive toxicity by causing glycolipid metabolism dysbiosis of testis resulting in activating of the mitochondrial apoptotic pathway in spermatogenic cells. The study provides new insight into the mechanisms of male reproductive toxicity caused by BDE-209.

LightGBM: accelerated genomically designed crop breeding through ensemble learning.

LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performance in terms of prediction precision, model stability, and computing efficiency through a series of benchmark tests. We also assess the factors that are essential to ensure the best performance of genomic selection prediction by taking complex scenarios in crop hybrid breeding into account. LightGBM has been implemented as a toolbox, CropGBM, encompassing multiple novel functions and analytical modules to facilitate genomically designed breeding in crops.

The genetic mechanism of heterosis utilization in maize improvement.

BACKGROUND: In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits. RESULTS: We show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages. Floral transition is probably one critical stage for heterosis formation, in which epistatic QTLs are activated by paternal contributions of alleles that counteract the recessive, deleterious maternal alleles. These deleterious alleles, while rare, epistatically repress other favorable QTLs. We demonstrate this with one example, showing that Brachytic2 represses the Ubiquitin3 locus in the maternal lines; in hybrids, the paternal allele alleviates this repression, which in turn recovers the height of the plant and enhances the weight of the ear. Finally, we propose a molecular design breeding by manipulating key genes underlying the transition from vegetative-to-reproductive growth. CONCLUSION: The new population design is used to dissect the genetic basis of heterosis which accelerates maize molecular design breeding by diminishing deleterious epistatic interactions.