Grey associated analysis of the underground water quality effected by the leaching water of dumping area or hillock of coal mine

The underground water has been contaminated seriously by the leaching water of dumping area or hillock. To determine the pollution limits of underground water, author took samples in the study area, analyzed samples for water quality, assessed the water quality of each monitoring point by the grey associated analysis method, and gave out the classifications of the underground water quality of the study area. Comparing with fuzzy comprehensive appraisal method, it is demonstrated that grey associated analysis method is applied easily, because of its clear concept, simple and convenient calculation and excellently operation.

Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet

Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

Genetic transformation has been an effective technology for improving the agronomic traits of maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated variants.These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.These genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize

Soil salinization poses a threat to maize production worldwide,but the genetic mechanism of salt tolerance in maize is not well understood.Therefore,identifying the genetic components underlying salt tolerance in maize is of great importance.In the current study,a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related traits.In total,125 QTLs were detected using a high-density genetic bin map,with one to five QTLs explaining 6.05–32.02%of the phenotypic variation for each trait.The total phenotypic variation explained(PVE)by all detected QTLs ranged from 6.84 to 63.88%for each trait.Of all 125 QTLs,only three were major QTLs distributed in two genomic regions on chromosome 6,which were involved in three salt tolerance-related traits.In addition,10 pairs of epistatic QTLs with additive effects were detected for eight traits,explaining 0.9 to 4.44%of the phenotypic variation.Furthermore,18 QTL hotspots affecting 3–7 traits were identified.In one hotspot(L5),a gene cluster consisting of four genes(ZmNSA1,SAG6,ZmCLCg,and ZmHKT1;2)was found,suggesting the involvement of multiple pleiotropic genes.Finally,two important candidate genes,Zm00001d002090 and Zm00001d002391,were found to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association analyses.Zm00001d002090 encodes a calcium-dependent lipid-binding(CaLB domain)family protein,which may function as a Ca^(2+)sensor for transmitting the salt stress signal downstream,while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related subfamily.Our findings provide valuable insights into the genetic basis of salt tolerance-related traits in maize and a theoretical foundation for breeders to develop enhanced salt-tolerant maize varieties.

Analysis of Indian Monsoon and Associated Low-Level Circulation in 1980 and 1981

In this paper, Indian monsoon of 1980 and 1981 is analysed based on the seasonal and half-month averaged data of 850 hPa of ECMWF analysis. The results show that Indian monsoon is related to Somali jet, the low-latitude easterlies and the mid-latitude westerlies over southern Indian Ocean, which are associated with the stationary wave of Southern Hemisphere. The forces affecting on the low-level flow are diagnosed, which display the relationship between Indian monsoon and the associated low-level flow.

Carotenoid Analysis of Several Dark-Green Leafy Vegetables Associated With a Lower Risk of Cancers

We have examined the carotenoid contents of several dark green vegetables found to be associated with a lower risk of various epithelial cancers in our epidemiological study and animal study. Samples of these vegetables were quantitatively examined by highperformance liquid chromatography (HPLC) on a C-18 reversed-phase column for individual carotenoid content. Pure reference compounds (alpha-carotene, beta-carotent, lycopene, canthaxanthin, and lutein) and internal standard (beta-Apo-8'-carotenal) were employed to quantify xanthophylls and carotenes in these vegetables. The results indicated that fresh, dark-green, leafy vegetables were high in beta-carotene (0.94-9.36 mg/100 g) and oxygenated carotenoids or xanthophylls, primarily lutein (0.94-7.39 mg/100 g),whereas lycopene and alpha-carotene were not prominent and canthaxanthin was non existent in these vegetables. These analyses suggest that consumption of carotenoids such as lutein in addition to beta-carotene may be associated with a lower risk of cancers

Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism（PIC=0.53） was found, and three groups were detected（K=3） with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model（GLM） and mixed linear model（MLM）（P 0.01）. The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci（QTLs） information for marker-assisted selection.

Disagreement between symptom-reflux association analysis parameters in pediatric gastroesophageal reflux disease investigation

AIM: To assess the agreement within 3 commonly used symptom-reflux association analysis (SAA) parameters investigating gastroesophageal reflux disease (GERD) in infants. METHODS: Twenty three infants with suspected GERD were included in this study. Symptom index (SI), Symptom sensitivity index (SSI) and symptom association probability (SAP) related to cough and irritability were calculated after 24 h combined pH/multiple intraluminal impedance (MII) monitoring. Through defined cutoff values, SI, SSI and SAP values are differentiated in normal and abnormal, whereas abnormal values point towards gastroesophageal reflux (GER) as the origin of symptoms. We analyzed the correlation and the concordance of the diagnostic classification of these 3 SAA parameters.RESULTS: Evaluating the GER-irritability association, SI, SSI and SAP showed non-identical classification of normal and abnormal cases in 39.2% of the infants. When irritability was taken as a symptom, there was only a poor inter-parameter association between SI and SSI, and between SI and SAP (Kendall’s tau b = 0.37, P < 0.05; Kendall’s tau b = 0.36, P < 0.05, respectively). Evaluating the GER-cough association, SI, SSI and SAP showed non-identical classification of normal and abnormal cases in 52.2% of the patients. When cough was taken as a symptom, only SI and SSI showed a poor inter-parameter association (Kendall’s tau b = 0.33, P < 0.05). CONCLUSION: In infants investigated for suspected GERD with pH/MII-monitoring, SI, SSI and SAP showed a poor inter-parameter association and important dis-agreements in diagnostic classification. These limitations must be taken into consideration when interpreting the results of SAA in infants.

The association analysis polymorphism of CDKAL1 and diabetic retinopathy in Chinese Han population

AIM： To identify the contribution of CDKAL1 to the development of diabetic retinopathy（DR） in Chinese population.·METHODS： A case-control study was performed to investigate the genetic association between DR and polymorphic variants of CDKAL1 in Chinese Han population with type 2 diabetes mellitus（T2DM）. A welldefined population with T2 DM, consisting of 475 controls and 105 DR patients, was recruited. All subjects were genotyped for the genetic variant（rs10946398） of CDKAL1. Genotyping was performed by i PLEX technology. The association between rs10946398 and T2 DM was assessed by univariate and multivariate logistic regression（MLR） analysis.· RESULTS： There were significant differences in C allele frequencies of rs10946398（CDKAL1） between control and DR groups（45.06% versus 55.00%, P 〈0.05）.The rs10946398 of CDKAL1 was found to be associated with the increased risk of DR among patients with diabetes.·CONCLUSION： Our findings suggest that rs10946398 of CDKAL1 is independently associated with DR in a Chinese Han population.

Single-nucleotide polymorphisms,mapping and association analysis of 1-FFT-A1 gene in wheat

Fructans are major nonstructural carbohydrates in wheat （Triticum aestivum L.）. Fructan 1-fructosyltransferase （1-FFT） is the key enzyme in fructan biosynthesis. In the present study, 96 sequence variants were detected in the 1-FFT-A 1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes. Two markers M39 and M2164 were developed based on the InDe121-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-AI. 1-FFT-A1 was located on chromosome 4A using marker M2164 and was flanked by markers Xcwm27 and 6-SFT-A 1. By association analysis using a natural wheat population consisted of 154 accessions, the results showed that the two markers were significantly associated with water-soluble carbohydrate （WSC） content in the lower internode stem and total stem at the early and middle grain filling stages, 1 000-grain weight （TGW） at different grain filling stages and peduncle length （PLE）. Comparison of the effects of three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike （TNSS）were significantly influenced by haplotypes. Haplll showed a significant positive effect on TGW, PLE and TNSS.

Association analysis of grain traits with SSR markers between Aegilops tauschii and hexaploid wheat(Triticum aestivum L.)

Seven important grain traits, including grain length（GL）, grain width（GW）, grain perimeter（GP）, grain area（GA）, grain length/width ratio（GLW）, roundness（GR）, and thousand-grain weight（TGW）, were analyzed using a set of 139 simple sequence repeat（SSR） markers in 130 hexaploid wheat varieties and 193 Aegilops tauschii accessions worldwide. In total, 1 612 alleles in Ae. tauschii and 1 360 alleles in hexaploid wheat（Triticum aestivum L.） were detected throughout the D genome. 197 marker-trait associations in Ae. tauschii were identified with 58 different SSR loci in 3 environments, and the average phenotypic variation value（R2） ranged from 0.68 to 15.12%. In contrast, 208 marker-trait associations were identified in wheat with 66 different SSR markers in 4 environments and the average phenotypic R2 ranged from 0.90 to 19.92%. Further analysis indicated that there are 6 common SSR loci present in both Ae. tauschii and hexaploid wheat, which are significantly associated with the 5 investigated grain traits（i.e., GA, GP, GR, GL, and TGW） and in total, 16 alleles derived from the 6 aforementioned SSR loci were shared by Ae. tauschii and hexaploid wheat. These preliminary data suggest the existence of common alleles may explain the evolutionary process and the selection between Ae. tauschii and hexaploid wheat. Furthermore, the genetic differentiation of grain shape and thousand-grain weight were observed in the evolutionary developmental process from Ae. tauschii to hexaploid wheat.

A Developed Algorithm of Apriori Based on Association Analysis

A method for mining frequent itemsets by evaluating their probability of supports based on association analysis is presented. This paper obtains the probability of every 1\|itemset by scanning the database, then evaluates the probability of every 2\|itemset, every 3\|itemset, every k \|itemset from the frequent 1\|itemsets and gains all the candidate frequent itemsets. This paper also scans the database for verifying the support of the candidate frequent itemsets. Last, the frequent itemsets are mined. The method reduces a lot of time of scanning database and shortens the computation time of the algorithm.

An approach to incorporate linkage disequilibrium structure into genomic association analysis

In this study, we propose to use the principal component analysis （PCA） and regression model to incorporate linkage disequilibrium （LD） in genomic association data analysis. To accommodate LD in genomic data and reduce multiple testing, we suggest performing PCA and extracting the PCA score to capture the variation of genomic data, after which regression analysis is used to assess the association of the disease with the principal component score. An empirical analysis result shows that both genotype-based correlation matrix and haplotype-based LD matrix can produce similar results for PCA. Principal component score seems to be more powerful in detecting genetic association because the principal component score is quantitatively measured and may be able to capture the effect of multiple loci.

A dCAPS marker developed from a stress associated protein gene TaSAP7-B governing grain size and plant height in wheat

Stress associated proteins（SAPs） are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants. In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat（Triticum aestivum L.）. Sequencing analysis on TaSAP7-B illustrated one In Del（insertion-deletion） and one SNP（single nucleotide polymorphism） in the promoter region while no diversity was observed in the coding region. On the basis of SNP in the promoter region（–260 bp）, a dCAPS（derived cleaved amplified polymorphic sequences） marker SNP-260 was developed for TaSAP7-B. Using a natural population consisting of 262 wheat accessions, significant associations were detected between the marker SNP-260 and agronomic traits, such as plant height（PH）, peduncle length（PL）, length of penultimate internode（LPI）, number of spike per plant（NSP）, and 1 000-grain weight（TGW）. Two genotypes were identified using marker SNP-260 in the natural population. Among them, the genotypes possessing C allele exhibited a higher TGW and shorter PH than the T genotypes. Hence, base C was considered as the superior allele. The dCAPS marker of TaSAP7-B can be instrumental for marker-assisted selection for high grain size and short plant height.

Polymorphism and association analysis of a drought-resistant gene TaLTP-s in wheat

Lipid transfer protein （LTP） is a kind of small molecular protein, which is named for its ability to transfer lipid between cell membranes. It has been proved that the protein is involved in the responding to abiotic stresses. In this study, TaLTP-s, a genomic sequence of TaLTP was isolated from A genome of wheat （Triticum aestivum L）. Sequencing analysis exhibited that there was no diversity in the coding region of TaLTP-s, but seven single nucleotide polymorphisms （SNPs） and 1 bp insertion/deletion （InOel） were detected in the promoter regions of different wheat accessions. Nucleotide diversity （T1） in the region was 0.00033, and linkage disequilibrium （LD） extended over almost the entire TaLTP-s region in wheat. The dCAPS markers based on sequence variations in the promoter regions （SNP-207 and SNP-1696） were developed, and three haplotypes were identified based on those markers. Association analysis between the haplotypes and agronomic traits of natural population consisted of 262 accessions showed that three haplotypes of TaLTP-s were significantly associated with plant height （PH）. Among the three haplotypes, Haplll is considered as the superior haplotype for increasing plant height in the drought stress environments. The G variance at the position of 207 bp could be a superior allele that significantly increased number of spikes per plant （NSP）. The functional marker of TaLTP-s provide a tool for marker-assisted selection regarding to plant height and number of spikelet per plant in wheat.

Association Analysis of the Growth of Black Poplar (Populus Nigra L.) Under Contrasting Nitrogen Levels

The European black poplar(Populus nigra L.)has been used as a germplasm resource for the breeding of new poplar varieties around the world.The identification and screening of its high nitrogen use efficiency genotypes could enable the breeding of new resource-efficient poplar varieties.The accessions were screened using MALDI-TOF MS genotyping technology for ammonium transporter(AMT)and nitrate transporters(NRT)genes against phenotypic data for seedling height and ground diameter traits,in both low and high nitrogen environments.Allele re-sequencing of seven genes related to root development was carried out using the minisequencing method.By cluster analysis,101 accessions of black poplar were divided into 4 populations,and it was concluded that Central Europe is the origin of the evolution of low-nitrogen and high-efficiency populations of European black poplar.Association study between SNP typing and seedling height and ground diameter traits showed that there were significant correlations between four SNP loci and growth traits under the contrasting N levels.We found that SNP3 and SNP4 in the PttAMT1;3 gene were significantly associated with seedling height traits,and that SNP2 and SNP7 in the PttAMT1;2 and PttAMT1;5 genes,respectively,were significantly associated with ground diameter traits.Thus,considerable allelic diversity is present within the candidate genes studied and can be utilized to develop functional markers to select for poplars with improved growth under N stress conditions.

Association Analysis of SP-SNPs and Avirulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Puccinia striiformis f. sp. tritici (Pst) is one of the pathogenic fungi on wheat, caused stripe rust that is a great threat for wheat production all over the world. Intensive efforts have been made to study genetics of wheat resistance to this disease, but few on avirulence of the pathogen due mainly to the nature of obligate biotrophism and the lack of systems for studying its genetics and molecular manipulations. To overcome these limitations, a natural Pst population comprising 352 isolates representative of a diverse virulence spectrum was genotyped using 97 secreted protein-single nucleotide polymorphism (SP-SNP) markers to identify candidate avirulence genes using association analysis. Among avirulence genes corresponding to 19 resistance genes, significantly associated SP-SNP markers were detected for avirulence genes AvYr1, AvYr2, AvYr6, AvYr7, AvYr8, AvYr44, AvYrExp2, AvYrSP, and AvYrTye. These results indicate that association analysis can be used to identify markers for avirulence genes. This study has laid the foundation for developing more SP-SNPs for mapping avirulence genes using segregating populations that can be generated through sexual reproduction on alternate hosts of the pathogen.

Genome-wide Association Analysis of Fast Chlorophyll Fluorescence Parameters in Maize

Fast chlorophyll fluorescence parameters are widely used to characterize the photosynthetic efficiency of plants. In this study, a genome-wide association analysis was used to detect key single-nueleotide polymorphisms （SNPs） associated with fast chlorophyll fluorescence parameters using more than 560 000 SNPs in a maize panel consisting of 404 inbred lines. In four fidd environments, 41 SNPs were detected to be associated with five fast chlorophyll fluorescence parameters, including ABS/CS0, ET0/CS0, TR0/ABS, ET0/TR0 and Pies. Among these identified SNPs, 8, 6, 18, 4 and 5 were significantly associated with ET0/TR0, ABS/ CS0, TR0/ABS, ET0/CS, and Plcs, respectively. These SNPs will help to discover genes for chlorophyll fluorescence parameters, better understand the genetic basis of photosynthesis, and assist in developing marker-assisted selection breeding programs in maize.

Spatial pattern analysis and associations of different growth stages of populations of Abies georgei var.smithii in Southeast Tibet,China

Abies georgei var.smithii is an important plant species in Southeast Tibet,China.It has high ecological value in terms of biodiversity protection,as well as soil and water conservation.We analyzed the spatial pattern and associations of A.georgei var.smithii populations at different growth stages by using Ripley's L function for point pattern analysis.The diameter structure was a nearly reverse 'J' shape.The amount of saplings and medium-sized trees accounts for a large part of the entire population,suggesting a high regeneration rate and an expanding population.In the transition from saplings to medium trees or to large trees,saplings show a significant aggregation distribution at small scales,while medium trees and large trees show a random distribution.There are significant inverse associations between saplings and medium trees and large trees at small scales,while there are no obvious associations between medium trees and large trees.The natural regeneration was affected by interspecific competition,and it was also affected by intraspecific competition.The joint effects of biological characteristics and environmental factors contribute to the spatial distribution pattern and associations of this A.georgei var.sm ithii population.

Molecular Cloning and Characterization of an Allene Oxide Cyclase Gene Associated with Fiber Strength in Cotton

Allene oxide cyclase （AOC） is one of the most important enzymes in the biosynthetic pathway of the plant hormone jasmonic acid （JA）. AOC catalyzes the conversion ofallene oxide into 12-oxo-phytodienoic acid （OPDA）, a precursor of JA. Using 28K cotton genome array hybridization, an expressed sequence tag （EST; GenBank accession no. ES792958） was investigated that exhibited significant expression differences between lintless-fuzzless XinWX and linted-fuzzless XinFLM isogenic lines during fiber initiation stages. The EST was used to search the Gossypium EST database （http：//www.ncbi.nlm.nih.gov/） for corresponding cDNA sequences encoding full-length open reading frames （ORFs）. Identified ORFs were confirmed using transcriptional and genomic data. As a result, a novel gene encoding AOC in cotton （Gossypium hirsutum AOC; GenBank accession no. KF383427） was cloned and characterized. The 741-bp GhAOC gene comprises three exons and two introns and encodes a polypeptide of 246 amino acids. Two homologous copies were identified in the tetraploid cotton species G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124, and one copy in the diploid cotton species G. herbaceum and G. raimondii, qRT-PCR showed that the GhAOC transcript was abundant in cotton fiber tissues from 8 to 23 days post anthesis （DPA）, and the expression profiles were similar in the two cultivated tetraploid cotton species G. hirsutum acc. TM- 1 and G. barbadense cv. Hai7124, with a higher level of transcription in the former. One copy of GhAOC in tetraploid cotton was localized to chromosome 24 （Chr. D8） using the subgenome-specific single nucleotide polymorphism （SNP） marker analysis, which co-localized GhAOC to within 10 cM of a fiber strength quantitative trait locus （QTL） reported previously. GhAOC was highly correlated with fiber quality and strength （P=0.014） in an association analysis, suggesting a possible role in cotton fiber development, especially in secondary cell wall thickening.