Identification of candidate genes for drought tolerance by whole-genome resequencing in maize.

BACKGROUND: Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance. RESULTS: A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient. CONCLUSIONS: Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

Ultraflexible Ultrathin 3D/1D Hierarchical Interpenetrating Ni-MOF/CNT Buckypaper Composites: Microstructures and Microwave Absorption Properties.

Metal-organic frameworks (MOFs) have attracted attention due to their designable structures. However, recently reported MOF microwave-absorbing materials (MAMs) are dominated by powders. It remains a challenge to design MOF/carbon nanotube (CNT) composite structures that combine the mechanical properties of self-supporting flexibility with excellent microwave absorption. This work involves the hydrothermal approach to grow Ni-MOF of different microstructures in situ on the CNT monofilament by adjusting the molar ratio of nickel ions to organic ligands. Subsequently, an ultraflexible self-supporting Ni-MOF/CNT buckypaper (BP) is obtained by directional gas pressure filtration technology. The BP porous skeleton and the Ni-MOF with a unique porous structure provide effective impedance matching. The CNTs contribute to the conduction loss, the cross-scale heterogeneous interface generated by Ni-MOF/CNT BP provides rich interfacial polarization loss, and the porous structure complicates the microwave propagation path. All factors work together to give Ni-MOF/CNT BP an excellent microwave absorption capacity. The minimum reflection losses of Ni-MOF/CNT BPs decorated with granular-, hollow porous prism-, and porous prism-shaped Ni-MOFs reach -50.8, -57.8, and -43.3 dB, respectively. The corresponding effective absorption bandwidths are 4.5, 6.3, and 4.8 GHz, respectively. Furthermore, BPs show remarkable flexibility as they can be wound hundreds of times around a glass rod with a diameter of 4 mm without structural damage. This work presents a new concept for creating ultraflexible self-supported MOF-based MAMs with hierarchical interpenetrating porous structures, with potential application advantages in the field of flexible electronics.

Effect of Sodium Gluconate on Properties and Microstructure of Ultra-High-Performance Concrete (UHPC).

The properties of concrete can be significantly affected by sodium gluconate (SG) at very small dosages. In this paper, the effects of SG on the fluidity, setting time, heat of hydration, and strength of ultra-high-performance concrete (UHPC) were studied. The results show that (1) in the plastic stage, SG inhibited the formation of early ettringite (AFt) and delayed the hydration of tricalcium silicate (C3S) and dicalcium silicate (C2S). SG increased the initial fluidity of UHPC without decreasing within 1 h. When the SG dosage was ≥0.06%, the slumps at 30 min and 60 min increased slightly. (2) In the setting hardening stage, the addition of SG inhibited the formation of calcium hydroxide (CH), which significantly extended the setting time of UHPC. When the dosage of SG was 0.15%, the initial and final setting times were 5.0 times and 4.5 times that of the blank group, respectively. SG had no obvious effect on the hydration rate of cement in the accelerated period, but the peak hydration temperature of UHPC was increased when the SG dosage was 0.03~0.12%. (3) In the strength development stage, the 1 d and 3 d strength of UHPC decreased significantly with the increase in the SG dosage. However, SG could promote the formation of AFt at the pores and aggregate interface in the later stage, reduce the porosity of cementite, and improve the compressive strength of UHPC in 28 d, 60 d, and 90 d. When the SG dosage was 0.12%, the 90d strength increased by 13%.

Genomic Prediction of Resistance to Tar Spot Complex of Maize in Multiple Populations Using Genotyping-by-Sequencing SNPs.

Tar spot complex (TSC) is one of the most important foliar diseases in tropical maize. TSC resistance could be furtherly improved by implementing marker-assisted selection (MAS) and genomic selection (GS) individually, or by implementing them stepwise. Implementation of GS requires a profound understanding of factors affecting genomic prediction accuracy. In the present study, an association-mapping panel and three doubled haploid populations, genotyped with genotyping-by-sequencing, were used to estimate the effectiveness of GS for improving TSC resistance. When the training and prediction sets were independent, moderate-to-high prediction accuracies were achieved across populations by using the training sets with broader genetic diversity, or in pairwise populations having closer genetic relationships. A collection of inbred lines with broader genetic diversity could be used as a permanent training set for TSC improvement, which can be updated by adding more phenotyped lines having closer genetic relationships with the prediction set. The prediction accuracies estimated with a few significantly associated SNPs were moderate-to-high, and continuously increased as more significantly associated SNPs were included. It confirmed that TSC resistance could be furtherly improved by implementing GS for selecting multiple stable genomic regions simultaneously, or by implementing MAS and GS stepwise. The factors of marker density, marker quality, and heterozygosity rate of samples had minor effects on the estimation of the genomic prediction accuracy. The training set size, the genetic relationship between training and prediction sets, phenotypic and genotypic diversity of the training sets, and incorporating known trait-marker associations played more important roles in improving prediction accuracy. The result of the present study provides insight into less complex trait improvement via GS in maize.

In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth.

The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.

Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding.

Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput genotyping method that relies on restriction enzymes to reduce genome complexity. GBS is being widely used for various genetic and breeding applications. In the present study, 2240 individuals from eight maize populations, including two association populations (AM), backcross first generation (BC1), BC1F2, F2, double haploid (DH), intermated B73 × Mo17 (IBM), and a recombinant inbred line (RIL) population, were genotyped using GBS. A total of 955,120 of raw data for SNPs was obtained for each individual, with an average genotyping error of 0.70%. The rate of missing genotypic data for these SNPs was related to the level of multiplex sequencing: ~ 25% missing data for 96-plex and ~ 55% for 384-plex. Imputation can greatly reduce the rate of missing genotypes to 12.65% and 3.72% for AM populations and bi-parental populations, respectively, although it increases total genotyping error. For analysis of genetic diversity and linkage mapping, unimputed data with a low rate of genotyping error is beneficial, whereas, for association mapping, imputed data would result in higher marker density and would improve map resolution. Because imputation does not influence the prediction accuracy, both unimputed and imputed data can be used for genomic prediction. In summary, GBS is a versatile and efficient SNP discovery approach for homozygous materials and can be effectively applied for various purposes in maize genetics and breeding.

The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication.

Coix is a grass crop domesticated as early as the Neolithic era. It is still widely cultivated for both highly nutritional food and medicinal use. However, the genetic study and breeding of this crop are hindered by the lack of a sequenced genome. Here, we report de novo sequencing and assembly of the 1619-Mb genome of Coix, and annotation of 75.39% repeats and 39 629 protein-coding genes. Comparative genomics analysis showed that Coix is more closely related to sorghum than maize, but intriguingly only Coix and maize had a recent genome duplication event, which was not detected in sorghum. We further constructed a genetic map and mapped several important traits, especially the strength of hull. Selection of papery hull (thin: easy dehulling) from the stony hull (thick: difficult dehulling) in wild progenitors was a key step in Coix domestication. The papery hull makes seed easier to process and germinate. Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis. We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci (QTLs), which are associated with hull thickness and color, respectively. The two QTLs were further fine mapped within intervals of 250 kb and 146 kb, respectively. These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

Genome-Wide Association Study of 13 Traits in Maize Seedlings under Low Phosphorus Stress.

CORE IDEAS: Low P stress is a global issue for grain production. Significant phenotypic differences were detected among 13 traits in 356 maize lines under P-sufficient and P-deficient conditions. Significant single nucleotide polymorphisms (SNPs) and low-P stress-responsive genes were identified for 13 maize root traits based on a genome-wide association study. Hap5, harboring 12 favorable SNPs, could enhance strong root systems and P absorption under low-P stress. Phosphorus is an essential macronutrient required for normal plant growth and development. Determining the genetic basis of root traits will enhance our understanding of maize's (Zea mays L.) tolerance to low-P stress. Here, we identified significant phenotypic differences for 13 traits in maize seedlings subjected to P-sufficient and P-deficient conditions. Six extremely sensitive and seven low-P stress tolerant inbreds were selected from 356 inbred lines of maize. No significant differences were observed between temperate and tropical-subtropical groups with respect to trait ratios associated with the adaptation to low-P stress. The broad-sense heritability of these traits ranged from relatively moderate (0.59) to high (0.90). Through genome-wide association mapping with 541,575 informative single nucleotide polymorphisms (SNPs), 551, 1140 and 1157 significant SNPs were detected for the 13 traits in 2012, 2016 and both years combined, respectively, along with 23 shared candidate genes, seven of which overlapped with reported quantitative trait loci and genes for low-P stress. Five haplotypes located in candidate gene GRMZM2G009544 were identified; among these, Hap5, harboring 12 favorable SNP alleles, showed significantly greater values for the root traits studied than the other four haplotypes under both experimental conditions. The candidate genes and favorable haplotypes and alleles identified here provide promising resources for genetic studies and molecular breeding for improving tolerance to abiotic stress in maize.

Genomic Selection Outperforms Marker Assisted Selection for Grain Yield and Physiological Traits in a Maize Doubled Haploid Population Across Water Treatments.

To increase genetic gain for tolerance to drought, we aimed to identify environmentally stable QTL in per se and testcross combination under well-watered (WW) and drought stressed (DS) conditions and evaluate the possible deployment of QTL using marker assisted and/or genomic selection (QTL/GS-MAS). A total of 169 doubled haploid lines derived from the cross between CML495 and LPSC7F64 and 190 testcrosses (tester CML494) were evaluated in a total of 11 treatment-by-population combinations under WW and DS conditions. In response to DS, grain yield (GY) and plant height (PHT) were reduced while time to anthesis and the anthesis silking interval (ASI) increased for both lines and hybrids. Forty-eight QTL were detected for a total of nine traits. The allele derived from CML495 generally increased trait values for anthesis, ASI, PHT, the normalized difference vegetative index (NDVI) and the green leaf area duration (GLAD; a composite trait of NDVI, PHT and senescence) while it reduced trait values for leaf rolling and senescence. The LOD scores for all detected QTL ranged from 2.0 to 7.2 explaining 4.4 to 19.4% of the observed phenotypic variance with R2 ranging from 0 (GY, DS, lines) to 37.3% (PHT, WW, lines). Prediction accuracy of the model used for genomic selection was generally higher than phenotypic variance explained by the sum of QTL for individual traits indicative of the polygenic control of traits evaluated here. We therefore propose to use QTL-MAS in forward breeding to enrich the allelic frequency for a few desired traits with strong additive QTL in early selection cycles while GS-MAS could be used in more mature breeding programs to additionally capture alleles with smaller additive effects.

Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize.

Drought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection.

Genome-Wide Analysis of Tar Spot Complex Resistance in Maize Using Genotyping-by-Sequencing SNPs and Whole-Genome Prediction.

Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Association mapping revealed four quantitative trait loci (QTL) on chromosome 2, 3, 7, and 8. All the QTL, except for the one on chromosome 3, were further validated by linkage mapping in different genetic backgrounds. Additional QTL were identified by linkage mapping alone. A major QTL located on bin 8.03 was consistently detected with the largest phenotypic explained variation: 13% in association-mapping analysis and 13.18 to 43.31% in linkage-mapping analysis. These results indicated that TSC resistance in maize was controlled by a major QTL located on bin 8.03 and several minor QTL with smaller effects on other chromosomes. Genomic prediction results showed moderate-to-high prediction accuracies in different populations using various training population sizes and marker densities. Prediction accuracy of TSC resistance was >0.50 when half of the population was included into the training set and 500 to 1,000 SNPs were used for prediction. Information obtained from this study can be used for developing functional molecular markers for marker-assisted selection (MAS) and for implementing genomic selection (GS) to improve TSC resistance in tropical maize.

[Significances of COX-2, p21, Ki-67 expression and HPV infection in nasal inverted papilloma].

OBJECTIVE: To investigate the significance of expression of COX-2, p21, Ki67 and HPV in nasal inverted papilloma. METHOD: Detecting COX-2, p21, Ki-67 in 30 cases of nasal inverted papilloma (NIP), 20 cases of nasal polyps (NP) and 10 cases of normal nasal mucosa (NM) by two step immunohistochemical method, and HPV virus by flow-through hybridization method. RESULT: The positive expression rate of COX-2 and Ki-67 in NIP, NP and NM group was decreased in turn, COX-2 had significant difference in the groups(χ2 = 30.00, P< 0. 05); the positive expression rate of Ki-67 had significant differences between NIP and NM group (χ2 = 8. 533, P<0. 05). The expression of COX-2 in NIP tissues was positively correlate with that of Ki-67 by using Spearman rank correlation analysis (r=0.78, P<0.05). Expression of p21 were not observed in NIP group. The positive rate of HPV was 26. 67% in 30 cases of NIP, all of HPV16 type. CONCLUSION: COX-2, Ki-67 and HPV infection have certain correlation with the occurrence of NIP. The occurrence of NIP has relationship with inflammatory reaction mediated by COX-2. Ki-67 can well reflect the proliferation activity of tumor cells, and can be used to measure the proliferation rate of nasal inverted papilloma. The COX-2 and Ki-67 have a synergistic role in the pathogenesis of NIP. p21 has no significant relationship with the incidence of NIP. HPV infection is related to the pathogenesis of NIP, but not as a;major factor in the pathogenesis of NIP.

[The management of sinonasal inverted papilloma by endoscopic surgery: an analysis of 54 cases].

OBJECTIVE: The study is to evaluate our results of patients with sinonasal inverted papilloma (SIP) undergoing endoscopic sinus surgery and to investigate the recurrence relative factors of SIP. METHOD: A retrospec- tive analysis was performed of medical records for 54 cases SIP treated with endoscopic resection. Compared to pre operation imaging evaluation and intraoperative observation, efficacy assessments included endoscopy during follow-up after operation and combined with CT examination results. RESULT: The incidence of 54 cases with ethmoid sinus, part of the lateral wall of the nasal cavity was higher. The recurrence rate was higher in the cases invaded front and/or inferior wall of maxillary sinus, frontal recess. There was no case with middle turbinate. Canceration with the same time accounted for 1.85%. CONCLUSION: Misdiagnosis as polyps, the lesion sites of tumour, involving the frontal recess, front and inferior wall of maxillary sinus are the risk factors of recurrence. The preoperative accurate judgment of the primary tumor site and surgical resection completly are the most effective means of preventing recurrence. Postoperative endoscopy examination combined with CT examination is an effective means for the evaluation of recurrence.