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 pheno...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.展开更多
The phosphorus uptake (PU) in above-ground parts of plant,root characteristics and root exudations as well as the quantitative trait loci (QTLs) associated with these characteristics were determined for a F2:3 populat...The phosphorus uptake (PU) in above-ground parts of plant,root characteristics and root exudations as well as the quantitative trait loci (QTLs) associated with these characteristics were determined for a F2:3 population derived from the cross of two contrasting maize (Zea mays L.) genotypes,082 and Ye107.A total of 241 F2:3 families were evaluated in replicated trials under deficient phosphorus conditions in 2007 at two sites (Kaixian County and Southwest University,Chongqing,P.R.China).The results show pleiotropy and close linkage among QTLs.Four common regions in different environments were in bnlg100bnlg1268b (bins 1.02) for QTL of H+,bnlg1268a-umc1290a (bins 1.09) for QTL of AP (acid phosphatase activity),dupssr15-P1M7/a (bins 6.06) for QTLs of PU (phosphorus uptake) and RW (root weight),and P1M3/d-P1M3/g (bins9.04) for QTLs of PU and AP.These QTLs are non-environment or minor QTLs × environment.By epistatic analysis,three main QTLs and eighteen QTLs × QTLs interactions were detected for the seven measured characteristics.These QTLs may affect trait expression by epistatic interaction with the other loci,and make a substantial contribution to phosphorus utilization efficiency,which should be considered when breeding maize varieties with high P efficiency.Two regions were detected in dupssr15-P1M7/a (bins 6.06) for QTL of RW and P1M3/d-P1M3/g (bins 9.04) for QTL of PU and AP.They were detected in two different environments and by two methods of QTL analysis,which were useful for marker-assisted selection.展开更多
Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator-prey relationship. The resulting model allows ...Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator-prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.展开更多
The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many appr...The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.展开更多
The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many appr...The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.展开更多
Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut products.In order to determine the genetic control of pod shape,six component traits of pod shape(pod length,pod width,pod l...Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut products.In order to determine the genetic control of pod shape,six component traits of pod shape(pod length,pod width,pod length/width ratio,pod roundness,beak degree and constriction degree)were measured using an image-based phenotyping method.A recombinant inbred line(RIL)population consisting of 181 lines was phenotyped across three environments.Continuous distributions and transgressive segregations were demonstrated in all measured traits and environments.Significant correlations were found among most component traits with broad-sense heritability ranging from 0.87 to 0.95.Quantitative trait locus(QTL)analysis yielded 26 additive QTLs explaining 3.79 to 52.37%phenotypic variations.A novel,stable and major QTL region conditioning multiple shape features was detected on chromosome 2,which spans a 10.81-Mb genomic region with 543 putative genes.Bioinformatics analysis revealed several candidate genes in this region.In addition,73 pairs of epistatic interactions involving 92 loci were identified for six component traits explaining 0.94–6.45%phenotypic variations.These results provide new genetic loci to facilitate genomics-assisted breeding of peanut pod shape.展开更多
Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified ...Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene(named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene,GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis,also has potential breeding value by engineering GaPC to develop colored petals or fibers for multifunctional utilization of cotton.展开更多
Malnutrition is one of the prevailing health problems worldwide, affecting a large proportion of the populations in rice-consuming countries. Breeding rice varieties with increased concentrations of elements in the gr...Malnutrition is one of the prevailing health problems worldwide, affecting a large proportion of the populations in rice-consuming countries. Breeding rice varieties with increased concentrations of elements in the grain is considered the most cost-effective approach to alleviate malnutrition. Development of molecular markers for high grain concentrations of essential elements, particularly Zn, for use in marker-assisted selection (MAS) can hasten breeding efforts to develop rice varieties with nutrient-dense grain. We performed QTL mapping for four agronomic traits: days to 50% flowering, plant height, number of tillers, grain yield, and 13 grain elements: As, B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn, in two doubled-haploid populations derived from the crosses IR64 × IR69428 and BR29 × IR75862. These populations were phenotyped during 2015DS and 2015WS at IRRI, Los Ba os, The Philippines, and genotyped them with a 6 K SNP chip. Inclusive composite interval mapping revealed 15 QTL for agronomic traits and 50 QTL for grain element concentration. Of these, eight QTL showed phenotypic variance of >25% and 11 QTL were consistent across seasons. There were seven QTL co-localization regions containing QTL for more than two traits. Twenty five epistatic interactions were detected for two agronomic traits and seven mineral elements. Several DH lines with high Fe and Zn in polished rice were identified. These lines can be used as donors for breeding high-Zn rice varieties. Some of the major QTL can be further validated and used in MAS to improve the concentrations of nutritive elements in rice grain.展开更多
Wheat(Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci(QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits i...Wheat(Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci(QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content(GPC); test weight(TW); single kernel characterization system(SKCS)-estimated kernel weight(SKW); kernel diameter(KD);kernel hardness measured by near-infrared reflectance spectroscopy(NIRS) hardness index(NHI); and SKCS-hardness index(SHI), a high-density genetic map with single nucleotide polymorphism(SNP) and simple sequence repeat(SSR) markers was developed using recombinant inbred lines(RILs) derived from Ning7840 × Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes,excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive × additive effects(AA), four QTL were involved in additive × environment(AE)effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.展开更多
Genetic variability in the base population plays an important role in crop⁃breeding program.A comprehensive assessment on the quantitative signs of white lupin genotypes was performed to be included in the selection p...Genetic variability in the base population plays an important role in crop⁃breeding program.A comprehensive assessment on the quantitative signs of white lupin genotypes was performed to be included in the selection process.Two limits of the environment were applied,i.e.,dense and sparse sowing.Positive true heterosis was established in PI533704×Zuter and PI533704×Lucky801 crosses by using the traits of the weight of nodules and fresh root mass weight at both limits of the environment.In more favorable growing conditions,the number and weight of nodules,as well as fresh aboveground mass weight had greater influence on the inheritance of epistatic gene interactions.In the case of dense sowing,the dominant gene actions for the weight of seeds were found more significant.With a high coefficient of inheritance in both environments,the hybrids of PI533704×Zuter and Lucky801×PI533704 were characterized by number and weight of nodules,Zuter×PI533704 by fresh root and aboveground mass weight,and almost all hybrids by seed weight per plant.The assessment of the initial material makes it highly likely to speed up the process of creating new varieties of white lupin.展开更多
Stochastic epistasis that is one of the characteristics of epistatic gene modules can have an important role in the maintenance of intraspecific population diversity. The effect of an epistatic modifier variant can va...Stochastic epistasis that is one of the characteristics of epistatic gene modules can have an important role in the maintenance of intraspecific population diversity. The effect of an epistatic modifier variant can vary in size and direction among the modifier careers on the basis of stochastic genetic individuality and the entire module effect can be also individually stochastic. This stochastic genetic contribution under a genetic background may be conditional upon the presence of a monomorphic switch locus in the gene module. The genetic background includes multiple modifier variants and the gene module is composed of the switch and the modifiers. The bell-shaped distribution of quantitative traits can be well simulated by the involvement of multiple stochastic epistatic modules. The phenotypic stochasticity makes the presence of switch and modifiers cryptic or missing in the research field and this cryptic gene networks can maintain and innovate in the phenotypic diversity under selection as a process of the evolution of complexity.展开更多
Psychiatric disorders have traditionally been segregated from medical disorders in terms of drugs,treatment,insurance coverage and training of clinicians.This segregation is consistent with the long-standing observati...Psychiatric disorders have traditionally been segregated from medical disorders in terms of drugs,treatment,insurance coverage and training of clinicians.This segregation is consistent with the long-standing observation that there are inherent differences between psychiatric disorders(diseases relating to thoughts,feelings and behavior)and medical disorders(diseases relating to physical processes).However,these differences are growing less distinct as we improve our understanding of the roles of epistasis and pleiotropy in medical genetics.Both psychiatric and medical disorders are predisposed in part by genetic variation,and psychiatric disorders tend to be comorbid with medical disorders.One hypothesis on this interaction posits that certain combinations of genetic variants(epistasis)influence psychiatric disorders due to their impact on the brain,but the associated genes are also expressed in other tissues so the same groups of variants influence medical disorders(pleiotropy).The observation that psychiatric and medical disorders may interact is not novel.Equally,both epistasis and pleiotropy are fundamental concepts in medical genetics.However,we are just beginning to understand how genetic variation can influence both psychiatric and medical disorders.In our recent work,we have discovered gene networks significantly associated with psychiatric and substance use disorders.Invariably,these networks are also significantly associated with medical disorders.Recognizing how genetic variation can influence both psychiatric and medical disorders will help us to understand the etiology of the individual and comorbid disease phenotypes,predict and minimize side effects in drug and other treatments,and help to reduce stigma associated with psychiatric disorders.展开更多
Many human diseases involve multiple genes in complex interactions.Large Genome-Wide Association Studies (GWASs) have been considered to hold promise for unraveling such interactions.However,statistic tests for high-o...Many human diseases involve multiple genes in complex interactions.Large Genome-Wide Association Studies (GWASs) have been considered to hold promise for unraveling such interactions.However,statistic tests for high-order epistatic interactions (≥2 Single Nucleotide Polymorphisms (SNPs)) raise enormous computational and analytical challenges.It is well known that the block-wise structure exists in the human genome due to Linkage Disequilibrium (LD) between adjacent SNPs.In this paper,we propose a novel Bayesian method,named BAM,for simultaneously partitioning SNPs into LD-blocks and detecting genome-wide multi-locus epistatic interactions that are associated with multiple diseases.Experimental results on the simulated datasets demonstrate that BAM is powerful and efficient.We also applied BAM on two GWAS datasets from WTCCC,i.e.,Rheumatoid Arthritis and Type 1 Diabetes,and accurately recovered the LD-block structure.Therefore,we believe that BAM is suitable and efficient for the full-scale analysis of multi-disease-related interactions in GWASs.展开更多
More and more studies demonstrate that a great deal of interactions among the quantitative trait loci (QTLs) are far more than those detected by single markers. A correlation method was proposed for estimating the int...More and more studies demonstrate that a great deal of interactions among the quantitative trait loci (QTLs) are far more than those detected by single markers. A correlation method was proposed for estimating the interactions of multiple QTLs detected by multi-markers in several mapping populations. Genetic implication of this method and usage were discussed.展开更多
基金supported by the National Basic Research Program of China (2011CB109306 and 2009CB118404)the Program of Introducing Talents of Discipline to Universities of China ("111" Project, B06014)Research Programs (CNTC-D2011100, CNTC-[2012]146, NY-[2011]3047, QKHRZ [2013] 02)
文摘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.
基金Funded by Chongqing Key Scientific and Technological Project (No. CSTC2007AB1045)Chinese Key Scientific and Technological Project (No. 2006BAD13B03)
文摘The phosphorus uptake (PU) in above-ground parts of plant,root characteristics and root exudations as well as the quantitative trait loci (QTLs) associated with these characteristics were determined for a F2:3 population derived from the cross of two contrasting maize (Zea mays L.) genotypes,082 and Ye107.A total of 241 F2:3 families were evaluated in replicated trials under deficient phosphorus conditions in 2007 at two sites (Kaixian County and Southwest University,Chongqing,P.R.China).The results show pleiotropy and close linkage among QTLs.Four common regions in different environments were in bnlg100bnlg1268b (bins 1.02) for QTL of H+,bnlg1268a-umc1290a (bins 1.09) for QTL of AP (acid phosphatase activity),dupssr15-P1M7/a (bins 6.06) for QTLs of PU (phosphorus uptake) and RW (root weight),and P1M3/d-P1M3/g (bins9.04) for QTLs of PU and AP.These QTLs are non-environment or minor QTLs × environment.By epistatic analysis,three main QTLs and eighteen QTLs × QTLs interactions were detected for the seven measured characteristics.These QTLs may affect trait expression by epistatic interaction with the other loci,and make a substantial contribution to phosphorus utilization efficiency,which should be considered when breeding maize varieties with high P efficiency.Two regions were detected in dupssr15-P1M7/a (bins 6.06) for QTL of RW and P1M3/d-P1M3/g (bins 9.04) for QTL of PU and AP.They were detected in two different environments and by two methods of QTL analysis,which were useful for marker-assisted selection.
文摘Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator-prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.
基金The work reported in this paper was partially supported by two National Natural Science Foundation of China projects 61363025,61751314a key project of Natural Science Foundation of Guangxi 2017GXNSFDA198033a key research and development plan of Guangxi AB17195055.
文摘The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.
基金partially supported by two National Natural Science Foundation of China projects 61363025,61751314a key project of Natural Science Foundation of Guangxi 2017GXNSFDA198033a key research and development plan of Guangxi AB17195055.
文摘The interaction between gene loci,namely epistasis,is a widespread biological genetic phenomenon.In genome-wide association studies(GWAS),epistasis detection of complex diseases is a major challenge.Although many approaches using statistics,machine learning,and information entropy were proposed for epistasis detection,the privacy preserving for single nucleotide polymorphism(SNP)data has been largely ignored.Thus,this paper proposes a novel two-stage approach.A fusion strategy assists in combining and sorting the SNPs importance scores obtained by the relief and mutual information,thereby obtaining a candidate set of SNPs.This avoids missing some SNPs with strong interaction.Furthermore,differentially private decision tree is applied to search for SNPs.This achieves the efficient epistasis detection of complex diseases on the basis of privacy preserving compared with heuristic methods.The recognition rate on simulation data set is more than 90%.Also,several susceptible loci including rs380390 and rs1329428 are found in the real data set for Age-related Macular Degeneration(AMD).This demonstrates that our method is promising in epistasis detection.
基金supported by the National Natural Science Foundation of China(32001584)the Natural Science Foundation of Shandong Province,China(ZR202111290099)+2 种基金the Breeding Project from Department Science&Technology of Shandong Province,China(2020LZGC001)the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(CXGC2022A21,CXGC2022A03,and CXGC2023A06(A39 and A46))the Qingdao People’s Livelihood Science and Technology Program,China(20-3-4-26-nsh)。
文摘Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut products.In order to determine the genetic control of pod shape,six component traits of pod shape(pod length,pod width,pod length/width ratio,pod roundness,beak degree and constriction degree)were measured using an image-based phenotyping method.A recombinant inbred line(RIL)population consisting of 181 lines was phenotyped across three environments.Continuous distributions and transgressive segregations were demonstrated in all measured traits and environments.Significant correlations were found among most component traits with broad-sense heritability ranging from 0.87 to 0.95.Quantitative trait locus(QTL)analysis yielded 26 additive QTLs explaining 3.79 to 52.37%phenotypic variations.A novel,stable and major QTL region conditioning multiple shape features was detected on chromosome 2,which spans a 10.81-Mb genomic region with 543 putative genes.Bioinformatics analysis revealed several candidate genes in this region.In addition,73 pairs of epistatic interactions involving 92 loci were identified for six component traits explaining 0.94–6.45%phenotypic variations.These results provide new genetic loci to facilitate genomics-assisted breeding of peanut pod shape.
基金supported by the Fundamental Research Funds for the Central Universities(KYZZ2022003)Jiangsu Collaborative Innovation Center for Modern Crop Production project (No.10)。
文摘Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene(named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene,GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis,also has potential breeding value by engineering GaPC to develop colored petals or fibers for multifunctional utilization of cotton.
基金HarvestPlus for funding development of high Zinc rice
文摘Malnutrition is one of the prevailing health problems worldwide, affecting a large proportion of the populations in rice-consuming countries. Breeding rice varieties with increased concentrations of elements in the grain is considered the most cost-effective approach to alleviate malnutrition. Development of molecular markers for high grain concentrations of essential elements, particularly Zn, for use in marker-assisted selection (MAS) can hasten breeding efforts to develop rice varieties with nutrient-dense grain. We performed QTL mapping for four agronomic traits: days to 50% flowering, plant height, number of tillers, grain yield, and 13 grain elements: As, B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn, in two doubled-haploid populations derived from the crosses IR64 × IR69428 and BR29 × IR75862. These populations were phenotyped during 2015DS and 2015WS at IRRI, Los Ba os, The Philippines, and genotyped them with a 6 K SNP chip. Inclusive composite interval mapping revealed 15 QTL for agronomic traits and 50 QTL for grain element concentration. Of these, eight QTL showed phenotypic variance of >25% and 11 QTL were consistent across seasons. There were seven QTL co-localization regions containing QTL for more than two traits. Twenty five epistatic interactions were detected for two agronomic traits and seven mineral elements. Several DH lines with high Fe and Zn in polished rice were identified. These lines can be used as donors for breeding high-Zn rice varieties. Some of the major QTL can be further validated and used in MAS to improve the concentrations of nutritive elements in rice grain.
基金partly funded by the National Research Initiative Competitive Grants CAP Project 2011-68002-30029 from the USDA National Institute of Food and AgricultureScience and Technology Innovation Team Plan (2014KCT-25) from Shaanxi province, China
文摘Wheat(Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci(QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content(GPC); test weight(TW); single kernel characterization system(SKCS)-estimated kernel weight(SKW); kernel diameter(KD);kernel hardness measured by near-infrared reflectance spectroscopy(NIRS) hardness index(NHI); and SKCS-hardness index(SHI), a high-density genetic map with single nucleotide polymorphism(SNP) and simple sequence repeat(SSR) markers was developed using recombinant inbred lines(RILs) derived from Ning7840 × Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes,excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive × additive effects(AA), four QTL were involved in additive × environment(AE)effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.
文摘Genetic variability in the base population plays an important role in crop⁃breeding program.A comprehensive assessment on the quantitative signs of white lupin genotypes was performed to be included in the selection process.Two limits of the environment were applied,i.e.,dense and sparse sowing.Positive true heterosis was established in PI533704×Zuter and PI533704×Lucky801 crosses by using the traits of the weight of nodules and fresh root mass weight at both limits of the environment.In more favorable growing conditions,the number and weight of nodules,as well as fresh aboveground mass weight had greater influence on the inheritance of epistatic gene interactions.In the case of dense sowing,the dominant gene actions for the weight of seeds were found more significant.With a high coefficient of inheritance in both environments,the hybrids of PI533704×Zuter and Lucky801×PI533704 were characterized by number and weight of nodules,Zuter×PI533704 by fresh root and aboveground mass weight,and almost all hybrids by seed weight per plant.The assessment of the initial material makes it highly likely to speed up the process of creating new varieties of white lupin.
文摘Stochastic epistasis that is one of the characteristics of epistatic gene modules can have an important role in the maintenance of intraspecific population diversity. The effect of an epistatic modifier variant can vary in size and direction among the modifier careers on the basis of stochastic genetic individuality and the entire module effect can be also individually stochastic. This stochastic genetic contribution under a genetic background may be conditional upon the presence of a monomorphic switch locus in the gene module. The genetic background includes multiple modifier variants and the gene module is composed of the switch and the modifiers. The bell-shaped distribution of quantitative traits can be well simulated by the involvement of multiple stochastic epistatic modules. The phenotypic stochasticity makes the presence of switch and modifiers cryptic or missing in the research field and this cryptic gene networks can maintain and innovate in the phenotypic diversity under selection as a process of the evolution of complexity.
文摘Psychiatric disorders have traditionally been segregated from medical disorders in terms of drugs,treatment,insurance coverage and training of clinicians.This segregation is consistent with the long-standing observation that there are inherent differences between psychiatric disorders(diseases relating to thoughts,feelings and behavior)and medical disorders(diseases relating to physical processes).However,these differences are growing less distinct as we improve our understanding of the roles of epistasis and pleiotropy in medical genetics.Both psychiatric and medical disorders are predisposed in part by genetic variation,and psychiatric disorders tend to be comorbid with medical disorders.One hypothesis on this interaction posits that certain combinations of genetic variants(epistasis)influence psychiatric disorders due to their impact on the brain,but the associated genes are also expressed in other tissues so the same groups of variants influence medical disorders(pleiotropy).The observation that psychiatric and medical disorders may interact is not novel.Equally,both epistasis and pleiotropy are fundamental concepts in medical genetics.However,we are just beginning to understand how genetic variation can influence both psychiatric and medical disorders.In our recent work,we have discovered gene networks significantly associated with psychiatric and substance use disorders.Invariably,these networks are also significantly associated with medical disorders.Recognizing how genetic variation can influence both psychiatric and medical disorders will help us to understand the etiology of the individual and comorbid disease phenotypes,predict and minimize side effects in drug and other treatments,and help to reduce stigma associated with psychiatric disorders.
文摘Many human diseases involve multiple genes in complex interactions.Large Genome-Wide Association Studies (GWASs) have been considered to hold promise for unraveling such interactions.However,statistic tests for high-order epistatic interactions (≥2 Single Nucleotide Polymorphisms (SNPs)) raise enormous computational and analytical challenges.It is well known that the block-wise structure exists in the human genome due to Linkage Disequilibrium (LD) between adjacent SNPs.In this paper,we propose a novel Bayesian method,named BAM,for simultaneously partitioning SNPs into LD-blocks and detecting genome-wide multi-locus epistatic interactions that are associated with multiple diseases.Experimental results on the simulated datasets demonstrate that BAM is powerful and efficient.We also applied BAM on two GWAS datasets from WTCCC,i.e.,Rheumatoid Arthritis and Type 1 Diabetes,and accurately recovered the LD-block structure.Therefore,we believe that BAM is suitable and efficient for the full-scale analysis of multi-disease-related interactions in GWASs.
基金This research was supported by the National Natural Science Foundation of China (Grant No. 30070425).
文摘More and more studies demonstrate that a great deal of interactions among the quantitative trait loci (QTLs) are far more than those detected by single markers. A correlation method was proposed for estimating the interactions of multiple QTLs detected by multi-markers in several mapping populations. Genetic implication of this method and usage were discussed.
