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.

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.

Association Analysis of Quantitative Traits in F_1 Families Derived from Two Maize Landraces

[ Objective] The objective of this study was to evaluate the genetic diversity and characterization of special maize population consisting of 135 Fl fami- lies. [ Method ] In this study, association analysis was conducted in 135 F1 families derived from two maize landraces, and the efficiency of this method was evalua- ted through simulation. [ Result] Association analysis with different kinds of families showed that large population size and robust phenotypic data were required for association mapping. For all the phenotypic traits, the model controlling beth population structure and relative kinship （ Q ＋ K） performed better than the model controlling relative kinship （K）, and similarly to the model controlling population structure （Q）. Across 100 simulation runs in QULINE, the average power of QTL detection for the two models were 88.64% and 83.64% respectively, and the number of false QTL was reduced from 399 with GLM model to 199 with K mod- el. Our simulation results suggested that these F1 families can be used for association analysis, and the power of the QTL detection was related to the maximum al- lele frequency （MAF）and the phenotypic variation （PVE） explained by QTL. [ Conclusion] The results from this study suggest that association analysis using the F1 families is an effective approach to study maize landraces for discovering elite genes which we are interested in from these special populations.

Genome-wide Association Analysis of Maize Flowering Traits

Flowering regulation is important for maize to adapt to a variety of environments as well as associated with high yield.In this study,the genetic mechanism of three flowering traits of 310 maize inbred lines with rich genetic background was investigated in three years at three different environments such as days to tasseling(DTT),days to silking(DTS)and days to pollen shedding(DTP).Based on mean performance,the longest flowering time was observed in Zhanyi(2018),whereas the shortest in Shizong(2019).The coefficient of variance depicted the range from 3.62%to 9.06%for three flowering traits under all environments.Therefore,we have integrated these flowering traits corresponding to SNP molecular markers for genome-wide association study(GWAS).Results showed that 22 SNPs markers were significantly associated with DTT according to physical position and average linkage disequilibrium(LD)decay distance,and a total of 234 candidate genes were identified near these significantly associated SNP markers.Moreover,KEGG and GO analysis showed that these genes were enriched in the regulation of the physiological pathways for flowering.In more details,16 genes involved in development of floral organs are more worthy of our attention in future studies.

Association of neuroelectrophysiology and analysis of cerebrospinal fluid immunoglobulin with pathogenetic conditions of patients with Guillain-Barre syndrome

BACKGROUND： Guillain-Barre syndrome （GBS） is an autoimmune disease which is characterized by demyelination of peripheral nerve and nerve root, and inflammatory reaction of lymphocyte and macrophage. Neuroelectrophysiological examination and cerebrospinal fluid （CSF） analysis are of significance for its diagnosis. OBJECTIVE： To study the association of neuroelectrophysiology and cerebrospinal fluid immunoglobulin （CSF-lg） with pathogenetic conditions of patients with GBS. DESIGN： Case control study SETTING： Department of Neurology, Shenzhen Municipal Shekou Group Hospital; Department of Neuroelectrophysiology, People＇s Hospital of Guangdong Province. PARTICIPANTS： A total of 32 GBS patients including 18 males and 14 females who aged from 17 to 72 years were selected as experimental group from the Department of Neurology, People＇s Hospital of Guang- dong Province from January 2004 to December 2005. All cases conformed with GBS diagnostic criteria established by Asbury in 1990 and they were divided into three types according to neurological criteria established by Chinese Neurology and Psychology Journal in 1993： mild, moderate and severe types. Another 30 patients with vascular headache were selected as control group from the same hospital including 14 males and 16 females who aged from 17 to 79 years. METHODS： ① Neuroelectrophysiological examination： Multiple-functional electromyography device provided by Nicolet Company, USA was used to measure nerve conduction velocity （NCV）, including motor nerve conduction velocity （MCV） and sensory nerve conduction velocity （SCV）; meanwhile, electromyologram （EMG）, somatosensory evoked potential （SEP） and electroencephalogram （EEG） were also measured. ② Detection of CSF-lg： Concentrations of IgG, IgA and IgM were measured with immunofixation electrophoresis. ③Follow-up： Among 32 GBS patients, 14 cases received follow-up after treatment and the longest fol- low-up time was 1 year after onset. Among them, 8 cases were reexaminined with neuroelectrophysiological and CSF examinations. MAIN OUTCOME MEASURES： Results of NCV, EMG, SEP and EEG; comparison of CSF-lg content; results of follow-up examinations. RESULTS： All 32 GBS cases and 30 patients with vascular headache were involved in the final analysis. ① Abnormal rate of neuroelectrophysiological test： 75% of NCV, 88% of F-wave, 53% of MCV, 25% of SEP, 47% of EMG and 31% of EEG. There were no significant differences among various types （P 〉 0.05）. ② Results of CSF-lg test： There were no significant differences among various types （P 〉 0.05）; however, abnormalities in experimental group was higher than those in control group （P 〈 0.01）. CONCLUSION ： Results of follow-up study suggest that improvement of clinical symptom is earlier than neuroelectrophysiological recovery; MCV and EMG recoveries are faster than that of NCV; the earlier the abnormality of EMG, the poorer the recovery. CSF4g recovers normally along improvement of clinical symptoms. It is of significance for neuroelectrophysiology and abnormality of CSF-Ig to determine degree of peripheral nerve demyelination and prognosis.

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.

Structure of the Bovine ACAD8 Gene and the Association of Its Polymorphism with the Production Traits

Acyl-coenzyme A dehydrogenases （ACAD） are a family of nuclear-coded, mitochondrial flavoenzymes that catalyze the alpha, and beta-dehydrogenation of fatty acids. The eighth member of this family, ACAD8 catalyzes the valine catabolism. In this study, the bovine ACAD8 full-length mRNA and genomic DNA sequence were obtained and its gene structure was determined through alignment of the genomic DNA sequence to the mRNA sequence. The mRNA sequence consisted of a 1,251 bp open reading frame （ORF） flanked by a 37 bp 5＇-untranslated region （UTR） and a 444 bp 3＇-UTR; and its full-length genomic DNA sequence was 13,814 bp in length and included 11 exons and 10 introns. One A-G single nucleotide polymorphism （SNP） was revealed at nucleotide 13,408 （GenBank accession No. DQ435445） in the bovine ACAD8 gene by sequencing the polymerase chain reaction （PCR） products of 6 randomly selected individuals from the sample population. Different genotypes were determined by restriction fragment length polymorphism （RFLP）. The association analysis of this SNP in bovine ACAD8 with production traits in 178 unrelated steers from 5 breeds showed that it had a significant effect on the daily gain and the beef tenderness （P〈0.05）. Cattle with the G allele grew more rapidly and the beef they produced was more tender than those with the A allele. Thus, this SNP of the bovine ACAD8 gene can be used as an indicator to improve the growth rate and the beef tenderness.

Association of myostatin Variants with Growth Traits of Zhikong Scallop(Chlamys farreri)

Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservative regulator of muscle growth,and has become one of the most important target genes for genetic improvement of the production of farmed animals.In this study,four single nucleotide polymorphisms(SNPs) were identified in the 5' flanking region of MSTN gene(Cf MSTN) in Zhikong scallop(Chlamys farreri).The association of these SNPs with scallop growth traits,including shell length,shell height,body weight and striated muscle weight was analyzed.The SNP g-1162G>T was found to associate with shell length,shell height,and striated muscle weight.The TT type scallops showed significantly higher trait values than those of GT type,and the GG type individuals exhibited median values.On the contrary,significantly more Cf MSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones.Our results suggested that Cf MSTN might regulate the scallop muscle growth negatively,and SNP g-1162G>T can be used as a candidate marker for the selective breeding of high-yielding scallop.

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.