Mining for QTL controlling maize low-phosphorus response genes combined with deep resequencing of RIL parental genomes and in silico GWAS analysis.

KEY MESSAGE: Extensive and comprehensive phenotypic data from a maize RIL population under both low- and normal-Pi treatments were used to conduct QTL mapping. Additionally, we integrated parental resequencing data from the RIL population, GWAS results, and transcriptome data to identify candidate genes associated with low-Pi stress in maize. Phosphorus (Pi) is one of the essential nutrients that greatly affect the maize yield. However, the genes underlying the QTL controlling maize low-Pi response remain largely unknown. In this study, a total of 38 traits at both seedling and maturity stages were evaluated under low- and normal-Pi conditions using a RIL population constructed from X178 (tolerant) and 9782 (sensitive), and most traits varied significantly between low- and normal-Pi treatments. Twenty-nine QTLs specific to low-Pi conditions were identified after excluding those with common intervals under both low- and normal-Pi conditions. Furthermore, 45 additional QTLs were identified based on the index value ((Trait_under_LowPi-Trait_under_NormalPi)/Trait_under_NormalPi) of each trait. These 74 QTLs collectively were classified as Pi-dependent QTLs. Additionally, 39 Pi-dependent QTLs were clustered in nine HotspotQTLs. The Pi-dependent QTL interval contained 19,613 unique genes, 6,999 of which exhibited sequence differences with non-synonymous mutation sites between X178 and 9782. Combined with in silico GWAS results, 277 consistent candidate genes were identified, with 124 genes located within the HotspotQTL intervals. The transcriptome analysis revealed that 21 genes, including the Pi transporter ZmPT7 and the strigolactones pathway-related gene ZmPDR1, exhibited consistent low-Pi stress response patterns across various maize inbred lines or tissues. It is noteworthy that ZmPDR1 in maize roots can be sharply up-regulated by low-Pi stress, suggesting its potential importance as a candidate gene for responding to low-Pi stress through the strigolactones pathway.

Genome-wide association studies dissect low-phosphorus stress response genes underling field and seedling traits in maize.

Phosphorus (P) is an essential element for plant growth, and its deficiency can cause decreased crop yield. This study systematically evaluated the low-phosphate (Pi) response traits in a large population at maturity and seedling stages, and explored candidate genes and their interrelationships with specific traits. The results revealed a greater sensitivity of seedling maize to low-Pi stress compared to that at maturity stage. The phenotypic response patterns to low-Pi stress at different stages were independent. Chlorophyll content was found to be a potential indicator for screening low-Pi-tolerant materials in the field. A total of 2900 and 1446 significantly associated genes at the maturity and seedling stages were identified, respectively. Among these genes, 972 were uniquely associated with maturity traits, while 330 were specifically detected at the seedling stage under low-Pi stress. Moreover, 768 and 733 genes were specifically associated with index values (low-Pi trait/normal-Pi trait) at maturity and seedling stage, respectively. Genetic network diagrams showed that the low-Pi response gene Zm00001d022226 was specifically associated with multiple primary P-related traits under low-Pi conditions. A total of 963 out of 2966 genes specifically associated with traits under low-Pi conditions or index values were found to be induced by low-Pi stress. Notably, ZmSPX4.1 and ZmSPX2 were sharply up-regulated in response to low-Pi stress across different lines or tissues. These findings advance our understanding of maize's response to low-Pi stress at different developmental stages, shedding light on the genes and pathways implicated in this response.

Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize.

Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.

Mining synergistic genes for nutrient utilization and disease resistance in maize based on co-expression network and consensus QTLs.

Nutrient restrictions and large-scale emergence of diseases are threatening the maize production. Recent findings demonstrated that there is a certain synergistic interaction between nutrition and diseases pathways in model plants, however there are few studies on the synergistic genes of nutrients and diseases in maize. Thus, the transcriptome data of nitrogen (N) and phosphorus (P) nutrients and diseases treatments in maize, rice, wheat and Arabidopsis thaliana were collected in this study, and four and 22 weighted co-expression modules were obtained by using Weighted Gene Co-expression Network Analysis (WGCNA) in leaf and root tissues, respectively. With a total of 5252 genes, MFUZZ cluster analysis screened 26 clusters with the same expression trend under nutrition and disease treatments. In the meantime, 1427 genes and 22 specific consensus quantitative trait loci (scQTLs) loci were identified by meta-QTL analysis of nitrogen and phosphorus nutrition and disease stress in maize. Combined with the results of cluster analysis and scQTLs, a total of 195 consistent genes were screened, of which six genes were shown to synergistically respond to nutrition and disease both in roots and leaves. Moreover, the six candidate genes were found in scQTLs associated with gray leaf spot (GLS) and corn leaf blight (CLB). In addition, subcellular localization and bioinformatics analysis of the six candidate genes revealed that they were primarily expressed in endoplasmic reticulum, mitochondria, nucleus and plasma membrane, and were involved in defense and stress, MeJA and abscisic acid response pathways. The fluorescence quantitative PCR confirmed their responsiveness to nitrogen and phosphorus nutrition as well as GLS treatments. Taken together, findings of this study indicated that the nutrition and disease have a significant synergistic response in maize.

Chinese red yeast rice attenuates the development of angiotensin II-induced abdominal aortic aneurysm and atherosclerosis.

OBJECTIVE: Abdominal aortic aneurysm (AAA) is a chronic vascular disease characterized by medial degradation and inflammation. No medical approaches have been validated for treating AAA, and therapeutic options are limited to regular surveillance leading to surgical intervention. This study aimed to investigate whether administration of Chinese red yeast rice (Monascus purpureus; RYR) suppressed angiotensin II (AngII)-induced AAA and atherosclerosis. METHODS AND RESULTS: Apolipoprotein E-deficient male mice fed a normal diet were administered either RYR extract (200 mg/kg/day) or vehicle by gavage for 1 week before initiating AngII infusion (1000 ng/kg/min) via subcutaneous osmotic pumps for 28 days. Red yeast rice extract administration significantly suppressed AngII-induced expansion of suprarenal diameter and area (P<.05). Furthermore, RYR extract significantly reduced atherosclerotic lesion areas in both the intima of aortic arches and cross sections of aortic roots (P<.05). These effects were associated with reductions of serum total cholesterol, intercellular adhesion molecule 1, vascular cell adhesion molecule 1, matrix metalloproteinase (MMP) 2 and increases of serum macrophage migration inhibitory factor, but no changes in serum interleukin (IL) 1α, IL-6, monocyte chemoattractant protein 1, MMP-9 and expression of MMP-2 and MMP-9 in aortic walls. CONCLUSIONS: This study demonstrated that RYR extract administration suppressed AngII-induced AAA and atherosclerosis associated with regulating inflammation responses independent of lipid-lowering effects. Red yeast rice may have preventive potential for patients with AAA.

[Study on the interface of human hepatocyte L-02 polypropylene:simple culture method of human hepatocyte with spheroidal aggregate culture].

OBJECTIVE: To found new interface of human hepatocyte/poly propylene with good cytocompatibility for made polypropylene hollow fibers bioreactor of bioartificial liver in future. METHODS: Using the macromolecular hydroperoxide groups on the polypropylene membrane surface as initiators, acrylamides were polymerized on the polypropylene membranes, under induction by both UV irradiation and Fe2+ reduction. Growth characteristics of human hepatocyte L-02 were detected when it was cultured on polystyrene, polypropylene and modified polypropylene membrane surface. RESULTS: Water contact angle measurement of the polypropylene and the modified polypropylene membranes decreased from (72 +/- 5) degrees to (30 +/- 4) degrees , which indicated that the hydrophilicity of the membrane was improved obviously after the grafting modification. Human hepatocyte L-02 could not adhere and spread on modified polypropylene membrane surface, and grown in spheroidal aggregate with higher density and higher proliferation ratio measured by MTT method. CONCLUSIONS: Acrylamide polymerized on the polypropylene membranes is a good method which not only improved human hepatocytes cytocompatibility but also found a new simple culture method with spheroidal aggregate culture of human hepatocyte.

[Study on the interface of human hepatocyte/micropore polypropylene ultrafiltration membrane].

OBJECTIVE: To found a new interface of human hepatocyte/micropore polypropylene ultrafiltration membrane (MPP) with good cytocompatibility so as to construct bioartificial bioreactor with polypropylene hollow fibers in future. METHODS: MPP ultrafiltration membrane underwent chemical grafting modification through ultraviolet irradiation and Fe(2+) reduction. The contact angles of MPP and the modified MPP membranes were measured. Human hepatic cells L-02 were cultured. MPP and modified MPP membranes were spread on the wells of culture plate and human hepatic cells and cytodex 3 were inoculated on them. Different kinds of microscopy were used to observe the morphology of these cells. RESULTS: The water contact angle of MPP and the modified MPP membranes decreased from 78 degrees +/- 5 degrees to 27 degrees +/- 4 degrees (P < 0.05), which indicated that the hydrophilicity of the membrane was improved obviously after the grafting modification. Human hepatocyte L-02 did not adhere to and spread on the modified MPP membrane surface, and only grew on the microcarrier cytodex 3 with higher density and higher proliferation ratio measured by MTT. CONCLUSION: Grafting modification of acrylamide on MPP membrane is a good method to improve the human hepatocyte cytocompatibility with MPP ultrafiltration membrane.

[Retrospective analysis on 682 cases of liver cancer after surgical treatment].

OBJECTIVE: To investigate the factors of long-turn survival of liver cancer after surgical treatment. METHODS: Five hundred and twenty-two cases of liver cancer that received surgical treatment in 14 years were analyzed retrospectively. RESULTS: Comparison between the small liver cancer (< 5 cm) and the greater one (> 10 cm) revealed that the small liver cancer had a higher survival rates than the greater one [3 year (61.25 +/- 4.41)% versus (45.90 +/- 6.98)%; 5 year (53.84 +/- 5.68)% versus (30.21 +/- 10.23)%]. There were same results between single-nodule and two or more than two nodule [3 year (61.86 +/- 3.69)% versus (38.31 +/- 4.97)%; 5 year (55.40 +/- 4.91)% versus (28.01 +/- 6.31)%], between child I and child II or more than II [3 year (60.68 +/- 3.68)% versus (49.88 +/- 4.13)%; 5 year (50.99 +/- 5.10)% versus (36.39 +/- 7.58)%], and between single segmentectomy of the liver and two or more than two segmentectomy [3 year (68.65 +/- 4.95)% versus (49.88 +/- 4.13)%; 5 year (65.38 +/- 5.69)% versus (37.98 +/- 5.70)%]. CONCLUSIONS: Small liver cancer, single-nodule, good hepatic function and minor resection were important factors to prolong survival further.