Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

Association Mapping for Drought Tolerance of Rice (Oryza sativa L.) at Vegetative Stage

[Objective] This study aimed to identify possible quantitative trait loci (QTL) for vegetative drought tolerance traits of rice (Oryza sativa L.). [Method] A total of 184 rice genotypes were field screened and 156 SSR markers randomly distributed at each 3 Mb bin were used through genome-wide scanning method and association analysis to detect QTLs for vegetative drought tolerance traits leaf rolling (LER), leaf drying (LED) and drought recovery rate (DRR). [Result] The experimental rice genotypes showed varied response under vegetative drought, LER, LED and DRR were highly correlated. Population structure was detected at K=3 and K=7, certain extent of admixture existed in the experimental rice genotypes, relative kinship of the rice genotypes ranged from 0 to 0.924 5. Significant linkage disequilibrium among SSR markers was detected. Sixteen SSR markers have been detected to be associated with vegetative drought tolerance traits, four for LER, eight for LED and four for DDR. Most of the markers were associated with more than one trait, indicating a single mechanism might involve in expression of several related traits, i.e. osmotic adjustment. RM107 (Chr.9) was associated with all the three traits and fell exactly within or closely nearby to previous reported regions, was a major QTL for vegetative drought tolerance, RM477 (Chr.8) was significantly associated with DRR and extremely significantly associated with LER was probably another major QTL for vegetative drought tolerance. [Conclusion] Association mapping is a very effective method for describing complex traits like drought tolerance.

QTL Identification of the Insensitive Response to Photoperiod and Temperature in Soybean by Association Mapping

The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 275 accessions of soybean [Glycine max （L.） Merrill] from China. Genome-wide association mapping, based on population structure analysis, was carried out using 118 SSR markers by the TASSEL GLM （general linear model） program. Nine SSR markers （P〈0.01） were associated with the value of the response to photoperiod and temperature （VRPT） caused by days to flowering （DF）, among which, Satt308 （LG M）, Sattl50 （LG M） and Satt440 （LG l）, were identified in both 2006 and 2007. Twelve SSR markers （P〈0.01） were associated with VRPT caused by days to maturity （DM）, among which three markers, Satt387 （LG N）, Satt307 （LG C2） and AW310961 （LG J）, were detected in both 2006 and 2007. In addition, a total of 20 elite alleles were screened out over 2006 and 2007 for being associated with an insensitive response to photoperiod and temperature （IRPT） caused by DF and a total of seven different elite alleles were screened out for being associated with IRPT caused by DM. Among these elite alleles, five alleles, Satt150-244, Satt308-164, Satt308-206, Satt440-176, and Satt440-206, were associated with IRPT caused by DF and were identified in both years, but only one allele, Satt307-170, was identified as being associated with an IRPT caused by DM. Based on these elite alleles, a set of typical accessions were screened out. The result about the genetic basis of IRPT is meaningful for soybean wide adaption breeding.

Genotype × Environment Interactions for Agronomic Traits of Rice Revealed by Association Mapping

Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment （G × E） interaction effects. The G × E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G × E interaction effects for all the agronomic traits were at highly significant levels （P〈0.01）, accounting for 3.4%-22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci （QTLs）, including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G × E effects with association mapping.

Association Mapping and Marker Development of Genes forStarch Lysophospholipid Synthesis in Rice

Phospholipids are a major kind of lipids in rice grains and have fundamental nutritional andfunctional benefits to the plant. Their lyso forms （lysophospholipids, LPLs） often form inclusion complexeswith amylose or independently influence the physicochemical and functional properties of rice starch.However, the genetic basis for LPL synthesis in rice endosperm is largely unknown. Here, we performeda preliminary association test of 13 LPL compositions among 20 rice accessions, and identified 22putative main-effect quantitative trait loci responsible for all LPLs except for LPC14：0 and LPE14：0. Fivederived cleaved amplified polymorphic sequences and one insertion/deletion marker for threeLPL-synthesis-related candidate genes were developed. Association analysis revealed two markerssignificantly associated with starch LPL traits. These results provide an insight into the genetic basis ofphospholipid biosynthesis in rice and may contribute to the rice quality breeding programs usingfunctional markers.

Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza rufipogon

Grain size is one of the critical agronomic traits governing grain yield and quality in rice.However,the underlying genetic mechanisms that control grain size in rice are poorly understood.We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff.This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size.Genome-wide association study(GWAS)was performed using 28193 SNPs through a general linear model,and 56 significant SNPs on different loci associated with the 4 grain size traits were detected.Cloned genes including GS3 and q GL3 showed substantial effects on grain length and size.Seven new stable loci were identified with pleiotropic effects on grain size.Haplotype,gene expression analyses,combined gene-based associations,and functional annotations permitted the shortlisting of important dominant genes including GS3 and q GL3.

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration （GD） and productive panicle number per plant （PN） were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height （PH） in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat （SSR） marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

Customer Requirements Mapping Method Based on Association Rule Mining for Mass Customization

Customer requirements analysis is the key step for product variety design of mass customiza-tion(MC). Quality function deployment (QFD) is a widely used management technique for understanding the voice of the customer (VOC), however, QFD depends heavily on human subject judgment during extracting customer requirements and determination of the importance weights of customer requirements. QFD pro-cess and related problems are so complicated that it is not easily used. In this paper, based on a general data structure of product family, generic bill of material (GBOM), association rules analysis was introduced to construct the classification mechanism between customer requirements and product architecture. The new method can map customer requirements to the items of product family architecture respectively, accomplish the mapping process from customer domain to physical domain directly, and decrease mutual process between customer and designer, improve the product design quality, and thus furthest satisfy customer needs. Finally, an example of customer requirements mapping of the elevator cabin was used to illustrate the proposed method.

Population structure and association mapping to detect QTL controlling tomato spotted wilt virus resistance in cultivated peanuts

Tomato spotted wilt(TSW)is a serious virus disease of peanut in the United States.Breeding for TSWV resistance would be facilitated by the implementation of marker-assisted selection in breeding programs;however,genes associated with resistance have not been identified.Association mapping is a type of genetic mapping that can exploit relationships between markers and traits in many lineages.The objectives of this study were to examine genetic diversity and population structure in the U.S.peanut mini-core collection using simple sequence repeat(SSR)markers,and to conduct association mapping between SSR markers and TSWV resistance in cultivated peanuts.One hundred and thirty-three SSR markers were used for genotyping 104 accessions.Four subpopulations,generally corresponding to botanical varieties,were classified by population structure analysis.Association mapping analysis indicated that five markers:pP GPseq5D5,GM1135,GM1991,TC23C08,and TC24C06,were consistently associated with TSW resistance by the Q,PCA,Q+K,and PCA+K models.These markers together explained 36.4%of the phenotypic variance.Moreover,pP GPseq5D5 and GM1991 were associated with both visual symptoms of TSWV and ELISA values with a high R^2.The potential of these markers for use in a marker-assisted selection program to breed peanut for resistance to TSWV is discussed.

Combined linkage and association mapping reveals two major QTL for stripe rust adult plant resistance in Shaanmai 155 and their haplotype variation in common wheat germplasm

The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.

Genetic and Association Mapping Study of English Grain Aphid Resistance and Tolerance in Bread Wheat Germplasm

English grain aphid （EGA） is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistance and tolerance traits at two locations, and genotyped with 51 SSR markers. Totally, three accessions showed high or moderate levels resistance and 17 genotypes displayed highly or moderately tolerate to EGA. Genetic diversity of these lines was investigated also. After 97 SSR loci which evenly covered all wheat chromosomes were scanned for association, four SSR loci were significantly associated with EGA resistance and four with EGA tolerance. After association analysis was conducted with dynamic aphid densities, we found four loci Xgwm192b, Xgwm391, Xbarc98, and Xgwm613b were detected continuously at different growing stages of wheat. In addition, the loci of EGA resistance/tolerance and Russian wheat aphid resistance were compared. The results generated in this study would be helpful for utilization of the EGA resistance/tolerance germplasm, and for development of mapping populations in EGA resistance breeding programs.

Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

Deep-sowing is an important method for avoiding drought stress in crop species,including maize.Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.This study evaluated four traits(mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12)related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms(SNPs).The genomewide association study detected that 273 SNPs were in linkage disequilibrium(LD)with the genetic basis of maize deep-sowing tolerance.The RNA-sequencing analysis identified 1944 and 2098 differentially expressed genes(DEGs)in two comparisons,which shared 281 DEGs.By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs,we identified seven candidate genes,of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length,auxin,or light response.Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.These results suggest that GRMZM2G119769 is the most likely candidate gene.This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes,which would be useful for further research on maize deep-sowing tolerance.

Association mapping of quantitative trait loci for yield-related agronomic traits in rice(Oryza sativa L.)

High yield in rice mainly depends on large grain weight, ideal plant architecture and proper flowering time adapting to various geographic regions. To help achieve higher yield, phenotype variations of heading date（HD）, plant architecture and grain shape in a panel of 416 rice accessions were investigated in this study. A total of 143 markers including 100 simple sequence repeat（SSR） markers and 43 gene-tagged markers were employed in association mapping to detect quantitative trait loci（QTL） responsible for these variations. Among the 7 subpopulations, POP5 in japonica group showed the largest values of HD and grain width（GW）, but the smallest values of grain length（GL） and grain length to width ratio（GLW）. Among the six indica groups, POP7 had the largest values of HD, GL, GLW, and 1 000-grain weight（TGW）. A total of 27 QTLs were detected underlying these phenotypic variations in single year, while 12 of them could be detected in 2006 and 2007. GS3 marker was closely associated with GL, GW and GLW, and widely distributed in different groups. The starch synthesis related gene markers, SSI, SSIIa, SBE1, AGPL4, and ISA1, were linked to plant height（PH）, panicle length（PL）, flag leaf length（FLL）, GW, and GLW. The SSR markers, RM267, RM340 and RM346, were linked to at least two traits. Therefore, these new markers will probably be used to improve rice grain yield or plant architecture when performing marker-assisted selection of proper alleles.

Association Mapping, QTL Mapping and Positional Cloning in Maize: Applications in Molecular Breeding

Natural variation is at the core of plant breeding. Genetic or linkage mapping is the traditional method for identifying loci/genes responsible for variati on in complex traits. More recently, association mapping or

T2 mapping眼外肌定量测量在甲状腺相关眼病诊断和分期中的应用价值

目的:探讨T2 mapping眼外肌定量测量在甲状腺相关眼病(thyroid-associated ophthalmopathy,TAO)诊断和分期中的价值。方法:对36例TAO患者及28例健康志愿者行眼眶T2 mapping检查,测量眼外肌的T2弛豫时间(T2 relaxation time,T2RT)值。比较病例组与正常对照组、活动期组与非活动期组眼外肌T2RT值的差异。采用受试者工作特征曲线(ROC曲线)法评估其判断TAO活动性的诊断价值。结果:病例组眼外肌的T2RT值明显大于正常对照组(P<0.001)。活动期组眼外肌的T2RT值明显大于非活动期组(P<0.001)。ROC结果显示以眼外肌T2RT值≥116.5 ms判断TAO处于活动期的诊断效能最优(曲线下面积0.863,敏感度75.0%,特异度93.8%)。结论:基于T2 mapping的眼外肌定量测量可辅助TAO的诊断和分期。

基质诱导的自体软骨移植术后3T磁共振T2mapping成像对移植软骨的分层定量评价

目的评估磁共振T2mapping成像技术在基质诱导自体软骨移植(MACT)术后的定量分析价值。方法纳入6例膝关节MACT术后患者(9处软骨损伤),分别在术后3月、6月及12月进行磁共振动态随访检查,测量软骨修复区与正常对照区深浅两个区域及全层T2值,横向比较同一时间点修复区与正常区T2值差异,纵向评估术后3、6、12个月修复区T2值的变化。结果MACT术后3、6月移植区全层T2值显著高于邻近正常软骨(P均<0.05),术后12月修复区全层T2值变化较正常对照区无明显统计学差异(P=0.063)。术后6、12个月修复区浅层软骨T2值显著高于深层(P均<0.05)。术后3、6、12个月修复区深浅层T2值纵向变化均有统计学差异(P均<0.05)。结论 MACT术后磁共振T2mapping成像可作为评估关节软骨修复效果的重要依据。

MR T_(1)-mapping技术在甲状腺相关眼病临床分期中的初步探索

目的:探讨T_(1)-mapping技术在甲状腺相关眼病(TAO)临床分期中的应用价值。方法:回顾性分析50例TAO患者的临床和影像资料,测量每例患者4条眼外肌中信号强度最高(“热点”)和最低区域(“冷点”)的T_(1)弛豫时间(T_(1)RT),比较活动期组和非活动期组之间热点和冷点T_(1)RT值的差异,并采用受试者工作特征曲线评估T_(1)RT在TAO分期中的诊断效能。结果:活动期组眼外肌T_(1)RT的冷点值显著高于非活动期组(P<0.001),而两组间眼外肌的T_(1)RT热点值的差异无统计学意义(P=0.122)。T_(1)RT冷点值与临床活动性评分呈正相关(r=0.501,P<0.001)。以T_(1)RT冷点值≥1000 ms判断TAO处于活动期的效能最优(曲线下面积为0.815,敏感度为80.6%,特异度为71.1%)。结论:T_(1)-mapping技术在甲状腺相关眼病分期中具有临床应用价值,眼外肌T_(1)RT冷点值可作为预测甲状腺相关眼病分期的指标。

Genome-wide association study for starch content and constitution in sorghum(Sorghum bicolor(L.) Moench)

Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.

Mapping epistasis and environment × QTX interaction based on four-omics genotypes for the detected QTX loci controlling complex traits in tobacco

Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four-omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP(QTS) loci, quantitative trait transcript(QTT) differences,quantitative trait protein(QTP) variability, and quantitative trait metabolite(QTM) changes,which can be summarized as QTX locus variation. The total heritabilities of the four-omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction.Epistasis and environment × treatment interaction had important impacts on complex traits at all-omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

Genetic dissection of hexanol content in soybean seed through genome-wide association analysis

Hexanol is a major compound contributing to the off-flavors(the bean-like odor)of soybean derived soymilk.The most effective way to reduce the off-flavors of soymilk is the screening and utilization of soybean cultivars with improved hexanol content.However,no genome-wide genetic analysis for this particular trait has been conducted to date.The objective of the present study was to dissect the genetic basis of hexanol content in soybean seed through genome-wide association analysis(GWAS).A total of 105 soybean accessions were analyzed for hexanol content in a three-year experiments and genotyped by sequencing using the specific locus amplified fragment sequencing(SLAF-seq)approach.A total of 25 724 single nucleotide polymorphisms(SNPs)were obtained with minor allele frequencies(MAF)>5%.GWAS showed that 25 quantitative trait nucleotides(QTNs)were significantly associated with the hexanol concentration in soybean seed.These identified QTNs distributed on different genomic regions of the 15 chromosomes.A total of 91 genes were predicted as candidate genes underlying the seed hexanol level and six candidates were predicted possibly underlying the seed hexanol by gene based association.In this study,GWAS has been proven to be an effective way to dissect the genetic basis of the hexanol concentration in multiple genetic backgrounds.The identified beneficial alleles and candidate genes might be valuable for the improvement of marker-assisted breeding efficiency for low hexanol level and help to explore possible molecular mechanisms underlying hexanol content in soybean seed.