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Journal of Integrative Agriculture 2015年第10期14卷 1936-1948页

作者： ZHAO Jing-lan WANG Hong-wei ZHANG Xiao-cun DU Xu-ye LI An-fei KONG Ling-rang State Key Laboratory of Crop Biology College of Agronomy Shandong Agricultural University Taishan Polytechnic

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.

关键词： association analysis grain traits Aegilops tauschii Triticum aestivum SSR markers

association analysis of the Growth of Black Poplar (Populus Nigra L.) Under Contrasting Nitrogen Levels

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Phyton-International Journal of Experimental Botany 2019年第4期88卷 425-433页

作者： Xihua Liu Changjun Ding Xiaohua Su Fujian Provincial Key Laboratory of Resources and Environment Monitoring&Sustainable Management and Utilization Sanming UniversitySanming36504China Research Institute of Forestry Chinese Academy of ForestryKey Laboratory of Tree Breeding and CultivationState Forestry AdministrationBeijing100091China

The European black poplar(Populus nigra L.)has been used as a germplasm resource for the breeding of new poplar varieties around the *** identification and screening of its high nitrogen use efficiency genotypes could enable the breeding of new resource-efficient poplar *** 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 *** re-sequencing of seven genes related to root development was carried out using the minisequencing *** 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 *** 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 *** 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 ***,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.

关键词： Nitrogen Populus nigra SNP association analysis

Differential expression of FOXO1 during development and myoblast differentiation of Qinchuan cattle and its association analysis with growth traits

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Science China(Life Sciences) 2018年第7期61卷 826-835页

作者： Yujia Sun Kunpeng Liu Yongzhen Huang Xianyong Lan Hong Chen College of Animal Science and Technology Northwest A&F University Shaanxi Key Laboratory of Molecular Biology for Agriculture Institute of Cellular and Molecular Biology Jiangsu Normal University

Our previous work reported a relationship between FOXO1 mutations and growth of Qinchuan(QC) cattle. Here, we performed differential expression analysis of FOXO1 and its association analysis with growth traits in QC cattle. First, we measured the expression of the FOXO1 gene in nine tissues during three developmental stages. The results showed that FOXO1 was abundantly expressed in tissues of calves but was strongly repressed in adulthood, although there was significant transcription in skeletal muscle. FOXO1 expression showed gradual up-regulation during differentiation of primary bovine skeletal muscle *** also identified six SNPs of the bovine FOXO1 gene by sequencing DNA pools of samples from 488 individuals, and association analysis indicated that five SNPs were significantly associated with some growth traits in the QC population. We further analyzed four haplotype combinations of the six SNPs and found significant correlation with body length(P<0.01). In conclusion, FOXO1 participates in bovine myocyte differentiation and expression, and may be a strong candidate as a gene that affects growth traits that could be exploited in a QC cattle breeding program. More generally, our data provide a new theoretical basis for QC beef breeding and beef quality improvement.

关键词： tissues expression myoblast differentiation sequence variants association analysis Qinchuan cattle

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

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Journal of Integrative Agriculture 2017年第4期16卷 789-799页

作者： YUE Ai-qin LI Ang MAO Xin-guo CHANG Xiao-ping LI Run-zhi JING Rui-lian College of Agriculture Shanxi Agricultural University Institute of Crop Sciences Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Germplasm and UtilizationMinistry of Agriculture

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.

关键词： 1-FFT-A1 single nucleotide polymorphism association analysis haplotype marker development wheat

Genetic Diversity and association analysis for Salinity Tolerance, Heading Date and Plant Height of Barley Germplasm Using Simple Sequence Repeat Markers

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Journal of Integrative Plant Biology 2008年第8期50卷 1004-1014页

作者： Lilia Eleuch Abderrazek Jilal Stefania Grando Salvatore Ceccarelli Maria von Korff Schmising Hisashi Tsujimoto Amara Hajer Abderrazek Daaloul Michael Baum Laboratory of Genetics and Plant Breeding Department of Agronomy and Plant Biotechnology National Institute of Agronomy 1085 Tunis Tunisia International Centre for Agricultural Research in the Dry Areas (ICARDA) 5466 Aleppo Syria International Centre for Agricultural Research in the Dry Areas (ICARDA) 5466 Aleppo Syria Laboratory of Plant Genetics and Breeding Science Faculty of Agriculture Tottori UniversityTottori 680-8553 Japan

The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat （SSR） markers. Four of the 22 markers （Bmac316, scssr03907, HVM67 and Bmag770） were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 （2H, bin 13） in two different environments with common significant alleles （175, 177）, whereas the HVHOTR1 marker （2H, bin 3） was only significant in Sakhar Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398.

关键词： association analysis genetic variability plant height polymorphism salinity, heading date simple sequence repeat.

Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaea L.) mini-core collection

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Journal of Integrative Plant Biology 2014年第2期56卷 159-169页

作者： Huifang Jiang Li Huang Xiaoping Ren Yuning Chen Xiaojing Zhou Youlin Xia Jiaquan Huang Yong Lei Liying Yan Liyun Wan Boshou Liao Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of Agriculture Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Nanchong Academy of Agricultural Sciences

association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut （Arachis hypogaea L.） mini-core collection in China comprising 298 accessions was genotyped using lo9 simple sequence repeat （SSR） markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than o.05, indicating that there were no or weak relationships between accessions of the mini- core collection. For 15 agronomic traits in the peanut panel, generally the Q ＋ K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q＋K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection.

关键词： Arachis hypogaea L. association analysis mini-corecollection peanut

Molecular Diversity and association analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

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Journal of Integrative Agriculture 2014年第9期13卷 1845-1853页

作者： JIA Yin-hua SUN Jun-ling WANG Xi-wen ZHOU Zhong-li PAN Zao-e HE Shou-pu PANG Bao-yin WANG Li-ru DU Xiong-ming State Key Laboratory of Cotton Biology Institute of Cotton Research Chinese Academy of Agricultural Sciences

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.

关键词： cotton germplasm genetic diversity simple sequence repeats(SSR) markers linkage disequilibrium(LD) association analysis

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

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Journal of Integrative Agriculture 2016年第6期15卷 1198-1206页

作者： LI Qian WANG Jing-yi Nadia Khan CHANG Xiao-ping LIU Hui-min JING Rui-lian National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China College of Bioengineering Shanxi UniversityTaiyuan 030006P.R.China

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.

关键词： Triticum aesfivum L. TaLTP single nucleotide polymorphism association analysis plant height

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

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International Journal of Ophthalmology(English edition) 2016年第5期9卷 707-712页

作者： Nai-Jia Liu Qian Xiong Hui-Hui Wu Yan-Liang Li Zhen Yang Xiao-Ming Tao Yan-Ping Du Bin Lu Ren-Ming Hu Xuan-Chun Wang Jie Wen Department of Endocrinology and Metabolism Huashan Hospital Affiliated to Fudan University Department of Endocrinology and Metabolism Jing'an District Center Hospital of Shanghai Department of Endocrinology and Metabolism Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Department of Endocrinology and Metabolism Hua Dong Hospital Affiliated to Fudan University

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.

关键词： CDKAL1 polymorphism association analysis diabetic retinopathy Chinese Han population

A Developed Algorithm of Apriori Based on association analysis

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Geo-Spatial Information Science 2004年第2期7卷 108-112,116页

作者： LIPingxiang CHENJiangping BIANFuling professor StateKeyLaboratoryofInformationEngineeringinSurveyingMappingandRemoteSensingWuhanUniversity129LuoyuRoadWuhan430079China. 不详

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.

关键词： association rule algorithm apriori frequent itemset association analysis