Combining association with linkage mapping to dissect the phenolamides metabolism of the maize kernel.

Phenolamides are important secondary metabolites in plant species. They play important roles in plant defense responses against pathogens and insect herbivores, protection against UV irradiation and floral induction and development. However, the accumulation and variation in phenolamides content in diverse maize lines and the genes responsible for their biosynthesis remain largely unknown. Here, we combined genetic mapping, protein regulatory network and bioinformatics analysis to further enhance the understanding of maize phenolamides biosynthesis. Sixteen phenolamides were identified in multiple populations, and they were all significantly correlated with one or several of 19 phenotypic traits. By linkage mapping, 58, 58, 39 and 67 QTLs, with an average of 3.9, 3.6, 3.6 and 4.2 QTLs for each trait were mapped in BBE1, BBE2, ZYE1 and ZYE2, explaining 9.47%, 10.78%, 9.51% and 11.40% phenotypic variation for each QTL on average, respectively. By GWAS, 39 and 36 significant loci were detected in two different environments, 3.3 and 2.8 loci for each trait, explaining 10.00% and 9.97% phenotypic variation for each locus on average, respectively. Totally, 58 unique candidate genes were identified, 31% of them encoding enzymes involved in amine and derivative metabolic processes. Gene Ontology term analysis of the 358 protein-protein interrelated genes revealed significant enrichment in terms relating to cellular nitrogen metabolism, amine metabolism. GRMZM2G066142, GRMZM2G066049, GRMZM2G165390 and GRMZM2G159587 were further validated involvement in phenolamides biosynthesis. Our results provide insights into the genetic basis of phenolamides biosynthesis in maize kernels, understanding phenolamides biosynthesis and its nutritional content and ability to withstand biotic and abiotic stress.

Multi-omics assists genomic prediction of maize yield with machine learning approaches.

With the improvement of high-throughput technologies in recent years, large multi-dimensional plant omics data have been produced, and big-data-driven yield prediction research has received increasing attention. Machine learning offers promising computational and analytical solutions to interpret the biological meaning of large amounts of data in crops. In this study, we utilized multi-omics datasets from 156 maize recombinant inbred lines, containing 2496 single nucleotide polymorphisms (SNPs), 46 image traits (i-traits) from 16 developmental stages obtained through an automatic phenotyping platform, and 133 primary metabolites. Based on benchmark tests with different types of prediction models, some machine learning methods, such as Partial Least Squares (PLS), Random Forest (RF), and Gaussian process with Radial basis function kernel (GaussprRadial), achieved better prediction for maize yield, albeit slight difference for method preferences among i-traits, genomic, and metabolic data. We found that better yield prediction may be caused by various capabilities in ranking and filtering data features, which is found to be linked with biological meaning such as photosynthesis-related or kernel development-related regulations. Finally, by integrating multiple omics data with the RF machine learning approach, we can further improve the prediction accuracy of grain yield from 0.32 to 0.43. Our research provides new ideas for the application of plant omics data and artificial intelligence approaches to facilitate crop genetic improvements. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01454-z.

Two teosintes made modern maize.

The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.

Genome sequencing reveals evidence of adaptive variation in the genus Zea.

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

A pan-Zea genome map for enhancing maize improvement.

BACKGROUND: Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking. RESULTS: Here, we construct an approximately 6.71-Gb pan-Zea genome that contains around 4.57-Gb non-B73 reference sequences from fragmented de novo assemblies of 721 pan-Zea individuals. We annotate a total of 58,944 pan-Zea genes and find around 44.34% of them are dispensable in the pan-Zea population. Moreover, 255,821 common structural variations are identified and genotyped in a maize association mapping panel. Further analyses reveal gene presence/absence variants and their potential roles during domestication of maize. Combining genetic analyses with multi-omics data, we demonstrate how structural variants are associated with complex agronomic traits. CONCLUSIONS: Our results highlight the underexplored role of the pan-Zea genome and structural variations to further understand domestication of maize and explore their potential utilization in crop improvement.

ScCO2-assisted fabrication and compressive property of poly (lactic acid) foam reinforced by in-situ polytetrafluoroethylene fibrils.

As an effective alternative for petrochemical-based polymers, bio-based poly (lactic acid) (PLA) foam has been anticipated to alleviate enormous environmental pollution caused by microplastics. However, some difficulties involved in PLA foaming process due to the inherently poor melt strength and crystallization properties. In this context, a small amount of polytetrafluoroethylene (PTFE) was incorporated into PLA matrix to solve the aforementioned issues. Scanning electron microscopy measurement exhibited that PTFE fibrils and their physical networks were formed in molten PLA after blending. Due to these PTFE networks, approximately 2 orders of magnitudes increment in the storage modulus and more than 20% improvement in crystallinity of PLA were obtained. Diverse PLA samples were successfully foamed by a cost-effective, green and supercritical CO2-assisted foaming method. The PLA/PTFE foam with the PTFE content of 5 wt% (PLA/PTFE5) possessed the smallest pore size (9.51 µm) and the highest pore density (2.60 × 108 pores/cm3). In addition, the average specific compressive strength of PLA/PTFE5 foam was enhanced 30% in comparison with that of pure PLA foam. Overall, this study could provide a prospective strategy for developing bioderived and biodegradable polymer foams with controllable pore structures and high compression property.

Target-oriented prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding.

Genomic prediction in crop breeding is hindered by modeling on limited phenotypic traits. We propose an integrative multi-trait breeding strategy via machine learning algorithm, target-oriented prioritization (TOP). Using a large hybrid maize population, we demonstrate that the accuracy for identifying a candidate that is phenotypically closest to an ideotype, or target variety, achieves up to 91%. The strength of TOP is enhanced when omics level traits are included. We show that TOP enables selection of inbreds or hybrids that outperform existing commercial varieties. It improves multiple traits and accurately identifies improved candidates for new varieties, which will greatly influence breeding.

Facile Fabrication of PBS/CNTs Nanocomposite Foam for Electromagnetic Interference Shielding.

In order to reduce the pollutants of environment and electromagnetic waves, environment friendly polymer foams with outstanding electromagnetic interference shielding are imminently required. In this paper, a kind of electromagnetic shielding, biodegradable nanocomposite foam was fabricated by blending poly (butylene succinate) (PBS) with carbon nanotubes (CNTs) followed by foaming with supercritical CO2 . The crystallization temperature and melting temperature of PBS/CNTs nanocomposites with 4 wt % of CNTs increased remarkably by 6 °C and 3.1 °C compared with that of pure PBS and a double crystal melting peak of various PBS samples appeared in DSC curves. Increasing the CNT content from 0 to 4 wt % leads to an increase of approximately 3 orders of magnitude in storage modulus and nearly 9 orders of magnitude in enhancement of electrical properties. Furthermore, CNTs endowed PBS nanocomposite foam with adjustable electromagnetic interference (EMI) shielding property, giving a specific EMI shielding effectiveness of 28.5 dB cm3 /g. This study provides a promising methodology for preparing biodegradable, lightweight PBS/CNTs foam with outstanding electromagnetic shielding properties.

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.

ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era.

As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP, a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures, and populational DNA methylation signals within maize inbred lines. ZEAMAP is user friendly, with the ability to interactively integrate, visualize, and cross-reference multiple different omics datasets.

MaizeCUBIC: a comprehensive variation database for a maize synthetic population.

MaizeCUBIC is a free database that describes genomic variations, gene expression, phenotypes and quantitative trait locus (QTLs) for a maize CUBIC population (24 founders and 1404 inbred offspring). The database not only includes information for over 14M single nucleotide polymorphism (SNPs) and 43K indels previously identified but also contains 660K structure variations (SVs) and 600M novel sequences newly identified in the present study, which represents a comprehensive high-density variant map for a diverse population. Based on these genomic variations, the database would demonstrate the mosaic structure for each progeny, reflecting a high-resolution reshuffle across parental genomes. A total of 23 agronomic traits measured on parents and progeny in five locations, where are representative of the maize main growing regions in China, were also included in the database. To further explore the genotype-phenotype relationships, two different methods of genome-wide association studies (GWAS) were employed for dissecting the genetic architecture of 23 agronomic traits. Additionally, the Basic Local Alignment Search Tool and primer design tools are developed to promote follow-up analysis and experimental verification. All the original data and corresponding analytical results can be accessed through user-friendly online queries and web interface dynamic visualization, as well as downloadable files. These data and tools provide valuable resources on genetic and genomic studies of maize and other crops.

Metabolomics analysis reveals differences in evolution between maize and rice.

Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.

CUBIC: an atlas of genetic architecture promises directed maize improvement.

BACKGROUND: Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders. RESULTS: Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width. CONCLUSIONS: Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.

Modified kissing balloon inflation associated with better results after Culotte stenting for bifurcation lesions: A bench test.

BACKGROUND: Main vessel (MV) stent deformation and overstretch caused by classical kissing balloon inflation (C-KBI) using two balloons with a longer overlapping in the MV for bifurcation lesions has caused a widespread concern. PURPOSE: This bench study tested our hypothesis that mini-KBI (M-KBI) with a shorter protrusion of side branch (SB) balloon would ascertain a better result after Culotte stenting. METHODS: Twenty-four coronary stents were deployed using Culotte approach in twelve bifurcation models with a bifurcation angle of 45°, 3.5 mm in MV diameter, and 3.0 mm in SB diameter. After stent implantation, the final KBI were assigned to C-KBI (two kissing balloons juxtaposed within the MV stent, at least overlap for 3 mm; n = 6) and M-KBI (the proximal marker of SB balloon just sited at the level of upper edge of SB ostium; n = 6). Proximal optimization technique (POT) was performed after KBI. Stent geometry was visually evaluated based on bench photos, microscopy, videoscopy, micro-CT, and scanning electron microscopy. Stent deformation index, minimal lumen diameter, and cross-sectional area at either carina level of MV and ostium of SB were measured from optical coherence tomography (OCT). RESULTS: In Culotte technique, C-KBI was associated with visually significant stent deformation, overexpansion and the "bottleneck" effect of the MV stent, which could not be effectively rectified by POT, while M-KBI could keep the circle shape of MV stent with good stent apposition in both MV and SB stent. By quantitative measurements, deformation index of MV was 0.06 ± 0.01 after M-KBI, significantly lower than 0.25 ± 0.02 if C-KBI was performed. In the line in carina, compared to C-KBI, M-KBI has smaller CSA-stent/CSA-reference, which indicated a less overstretch of MV stent. However, minimal lumen diameter and cross-sectional area of SB ostium was not different in the mini-KBI group (3.0958 ± 0.0285 mm and 7.9667 ± 0.1741 mm), when compared those after C-KBI (3.1217 ± 0.0772 mm and 7.9083 ± 0.3115 mm, p > .05). CONCLUSIONS: Followed by POT, M-KBI is preferable than C-KBI in preventing stent deformation, overexpansion in MV stent and could get well apposed of MV stent and well-opened SB stent as expected in a Culotte technique.

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement.

Maize is one of the most important crops globally, and it shows remarkable genetic diversity. Knowledge of this diversity could help in crop improvement; however, gold-standard genomes have been elucidated only for modern temperate varieties. Here, we present a high-quality reference genome (contig N50 of 15.78 megabases) of the maize small-kernel inbred line, which is derived from a tropical landrace. Using haplotype maps derived from B73, Mo17 and SK, we identified 80,614 polymorphic structural variants across 521 diverse lines. Approximately 22% of these variants could not be detected by traditional single-nucleotide-polymorphism-based approaches, and some of them could affect gene expression and trait performance. To illustrate the utility of the diverse SK line, we used it to perform map-based cloning of a major effect quantitative trait locus controlling kernel weight-a key trait selected during maize improvement. The underlying candidate gene ZmBARELY ANY MERISTEM1d provides a target for increasing crop yields.

Contributions of Zea mays subspecies mexicana haplotypes to modern maize.

Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

The genetic architecture of amino acids dissection by association and linkage analysis in maize.

Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signalling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5.1 and 4.4 loci for each trait, explaining 7.44% and 7.90% phenotypic variation for each locus in average, respectively. By linkage mapping, 89, 150 and 165 QTLs were identified in B73/By804, Kui3/B77 and Zong3/Yu87-1 RIL populations, 2.0, 2.7 and 2.8 QTLs for each trait, explaining 13.6%, 16.4% and 21.4% phenotypic variation for each QTL in average, respectively. It implies that the genetic architecture of amino acids is relative simple and controlled by limited loci. About 43.2% of the loci identified by GWAS were verified by expression QTL, and 17 loci overlapped with mapped QTLs in the three RIL populations. GRMZM2G015534, GRMZM2G143008 and one QTL were further validated using molecular approaches. The amino acid biosynthetic and catabolic pathways were reconstructed on the basis of candidate genes proposed in this study. Our results provide insights into the genetic basis of amino acid biosynthesis in maize kernels and may facilitate marker-based breeding for quality protein maize.

Maize orthologs of rice GS5 and their trans-regulator are associated with kernel development.

Genome information from model species such as rice can assist in the cloning of genes in a complex genome, such as maize. Here, we identified a maize ortholog of rice GS5 that contributes to kernel development in maize. The genome-wide association analysis of the expression levels of ZmGS5, and 15 of its 26 paralogs, identified a trans-regulator on chromosome 7, which was a BAK1-like gene. This gene that we named as ZmBAK1-7 could regulate the expression of ZmGS5 and three of the paralogs. Candidate-gene association analyses revealed that these five genes were associated with maize kernel development-related traits. Linkage analyses also detected that ZmGS5 and ZmBAK1-7 co-localized with mapped QTLs. A transgenic analysis of ZmGS5 in Arabidopsis thaliana L. showed a significant increase in seed weight and cell number, suggesting that ZmGS5 may have a conserved function among different plant species that affects seed development.

Effect of Intracoronary Plus Low-Dose Intravenous Tirofiban in Elderly Patients with Acute Myocardial Infarction.

BACKGROUND: To investigate the efficacy and safety of low-dose tirofiban in elderly patients undergoing primary percutaneous coronary intervention (PPCI) for acute myocardial infarction (AMI). METHODS: One hundred and four patients aged 70 years and above undergoing PPCI for AMI were divided into control (n=52) and study (n=52) groups. All patients received bolus intracoronary injection of tirofiban (10µg/kg), which was followed by intravenous infusion at 0.15µg/kg/min in the control group and at 0.075µg/kg/min in the study group for 24h. RESULTS: There was no statistically significant difference between the study group and the control group in patients with complete ST segment resolution (84.2% vs. 85.7%, P=0.851), peak high-sensitive cardiac troponin T level (5.1±1.9 vs. 5.8±2.6µg/L, P=0.123), scores of thrombus in the infarct-related artery (0.98±0.51 vs. 1.12±0.59, P=0.214), and patients with TIMI grade 3 flow (86.0% vs. 88.2%, P=0.737) after PPCI. There were no statistically significant differences between the two groups in left ventricular ejection fraction (57.1±6.3 vs. 57.7±6.1, P=0.611) and composite major adverse cardiovascular events rate (P =0.778) at 90 days after PCI. The total bleeding rate in the study group was lower than in the control group (P=0.048). CONCLUSION: In elderly patients with AMI undergoing primary PCI, low and standard dose of tirofiban exerts similar effects on platelet aggregation, coronary flow, infarct size, left ventricular systolic function and short-term clinical outcomes. Low dose regimen is associated with a lower bleeding rate than the standard dose.

Enhanced external counterpulsation inhibits endothelial apoptosis via modulation of BIRC2 and Apaf-1 genes in porcine hypercholesterolemia.

OBJECTIVES: Enhanced external counterpulsation (EECP) could improve endothelium-dependent vasodilatation of carotid artery and restore imbalance of nitric oxide and endothein-1 in patients with coronary artery disease. Our study was designed to test the hypothesis that long-term EECP may protect vascular endothelial cells from apoptosis by modifying apoptosis-related gene expression. METHODS: Eighteen male Yorkshire pigs were randomly assigned to three groups: usual diet (Normal), high cholesterol diet (HC) and high cholesterol diet plus EECP (HC+EECP). Vascular endothelial cells were isolated from the aortic endothelium and identified by CD31 staining and DiI-Ac-LDL reaction. Morphological changes were observed by both scanning and transmission electronic microscopes. TUNEL technique was applied to detect the apoptotic index of vascular endothelial cells. Two genes, Apaf-1 and BIRC2, were chosen for exploring the potential mechanisms of action at the molecular level. RESULTS: EECP brought a certain degree of alleviation from ultrastructural changes such as shrinking and blebbing of cytomembrane, marginalization, degeneration, and fragmentation of the nucleus. EECP also significantly reduced apoptotic indices while compared with that of control (177±12‰ vs. 237±23‰, P<0.05). The Apaf-1 expression at both protein and mRNA level in pigs of HC+EECP group was significantly decreased than those of the HC group (P<0.05), whereas the BIRC2 expression was significantly enhanced after EECP treatment, documented by immunostaining and semi-quantitative RT-PCR analysis, respectively (P<0.05). CONCLUSIONS: EECP could protect vascular endothelial cells from apoptosis, thereby delaying the progression of early atherosclerotic lesions possibly through transcriptional down-regulation of pro-apoptotic gene Apaf-1, and up-regulation of anti-apoptotic gene BIRC2.