Influence of Epistasis and QTL×Environment Interaction on Heading Date of Rice(Oryza sativa L.)

QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.

Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai＇an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions （QEs）. Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rhtl and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection （MAS）.

Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTL on the Genetic Basis of Plant Height and Heading Date in Rice

Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plantheight and heading date, using a doubled-haploid ( DH) population consisting of 190 lines from the cross between anindica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A geneticlinkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach wasapplied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactionsinvolving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactionswere detected between the digenic interaction and environment. The amounts of variations explained by QTLs of maineffect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not bedisregarded.

Genetic and Genotype × Environment Interaction Effects for Appearance Quality of Rice

This study was conducted to generate genetic information in rice varieties based on a complete diallel crosses over two years. The results indicated that genotype effect was significant for all traits. Genotype × environment interaction effects were significant only for cooked grain length （CGL） and cooked grain shape （CGSH）. General combining ability （GCA） and specific combining ability （SCA） effects were significant for entire traits, which indicated the important roles of both additive and non-additive gene actions. GCA x environment interaction effects were significant for CGL, CGSH and grain elongation index （GEI）. In the controlling of the inheritance of milled grain shape （GSH）, milled grain width （MGW）, GEI, milled grain length （MGL）, CGSH and cooked grain width （CGW）, the additive gene effects were more important than non-additive one. The average degree of dominance was within the range of partial dominance for all of the traits. The narrow-sense heritability was ranged from 0.65 （GSH） to 0.36 （CGL）. GCA effects were significant for all of the parents in milled grain length and it was significant for some of the parents in other traits. The crosses of Deilmani × IRFAON-215 exhibited significant SCA for GEI. The positive mean of heterosis was observed for CGW. The highest maximum values of heterosis were revealed in GEI, flowed by GSH, MGW and CGW. GCA and MPV were significantly and positively correlated together for all traits.

Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia

To explore the effect of genotype and genotype x environment interaction on Fe concentration in rice grains, Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007-2008 using the AMMI-biplot method. Experiments were conducted using a randomized completely block design with three replications in eight environments. Results indicated that environment （E）, genotype （G） and genotype x environment interaction （GE） significantly affected Fe concentration in rice grains. Environment explained 74.43 % of total （G＋E＋GE） variation, whereas G and GE captured 5.60% and 19.67%, respectively. Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains. Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.

Effects of erect panicle genotype and environment interactions on rice yield and yield components

The dense and erect panicle (EP) genotype conferred by DEP1 has been widely used in the breeding of high-yield Chinese japonica rice varieties.However,the breeding value of the EP genotype has rarely been determined at the plant population level.Therefore,the effects of the interaction of EP genotype and the environment at different locations and times on rice yield and its various components were investigated in this study.Two sets of near-isogenic lines (NILs)of EP and non-EP (NEP) genotypes with Liaojing 5 (LG5) and Akitakomachi (AKI) backgrounds were grown in the field in 2016 and 2017 in Shenyang,China,and Kyoto,Japan.In 2018,these sets were grown only in Kyoto,Japan.The average yields of the EP and NEP genotypes were 6.67 and 6.13 t ha^(-1)for the AKI background,and 6.66 and 6.58 t ha^(-1)for the LG5 background,respectively.The EP genotype positively affected panicle number (PN) and grain number per square meter (GNPM),mostly resulting in a positive effect on harvest index (HI).In contrast,the EP genotype exerted a negative effect on thousand-grain weight (KGW).The ratio of the performance of the EP genotype relative to the NEP genotype in terms of yield and total biomass correlated positively with mean daily solar radiation during a 40-day period around heading.These results indicate that the effectiveness of the EP genotype depends on the availability of solar radiation,and the effect of this genotype is consistently positive for sink formation,conditional in terms of source capacity,and positive in a high-radiation environment.

Gene environment interaction in periphery and brain converge to modulate behavioral outcomes:Insights from the SP1 transient early in life interference rat model

It is generally assumed that behavior results from an interaction between susceptible genes and environmental stimuli during critical life stages.The present article reviews the main theoretical and practical concepts in the research of gene environment interaction,emphasizing the need for models simulating real life complexity.We review a novel approach to study gene environment interaction in which a brief post-natal interference with the expression of multiple genes,by hindering the activity of the ubiquitous transcription factor specificity protein 1(Sp1) is followed by later-in-life exposure of rats to stress.Finally,this review discusses the role of peripheral processes in behavioral responses,with the Sp1 model as one example demonstrating how specific behavioral patterns are linked to modulations in both peripheral and central physiological processes.We suggest that models,which take into account the tripartite reciprocal interaction between the central nervous system,peripheral systems and environmental stimuli will advance our understanding of the complexity of behavior.

A Method for Assessing the Interaction Environment of Organizations

This paper presents a method for assessing the influence of the interaction environment of an organization. The interaction environment of an organization is composed of three elements： （1） the physical structure of the organization, including numbers of buildings, floors, common gathering areas, size, industry, and physical layout; （2） the information structure, consisting of the numbers and types of communication channels in the organization; and （3） the social structure, consisting of both individual-level assessments of the social environment of the organization as well as the organizational attempts to create a more social environment. This assessment tool has been tested in a large-scale study of organ donation campaigns in 46 organizations. Findings from this earlier test of the assessment tool demonstrate that interaction environment influences the way people communicate about, seek information about, and make decisions about health-related topics in organizations. Additionally, the individual elements of the interaction environment work in complex ways and also influence communication patterns and knowledge about health information. This paper details the procedures for using this assessment tool, methods for analyzing the findings, limitations of the tool, and areas in need of refinements and further researches.

Gene×environment interaction in major depressive disorder

Major depressive disorder(MDD)is a multifactorial disorder,where multiple susceptibility genes interact with environmental factors,predisposing individuals to the development of the illness.In this article,we reviewed different gene×environment interaction(G×E)studies shifting from a candidate gene to a genome-wide approach.Among environmental factors,childhood adversities and stressful life events have been suggested to exert crucial impacts on MDD.Importantly,the diathesis-stress conceptualization of G×E has been challenged by the differential susceptibility theory.Finally,we summarized several limitations of G×E studies and suggested how future G×E studies might reveal complex interactions between genes and environments in MDD.

Study on the Priority and Interaction of Food Security,Food Safety and Environmental Protection

Food security, food safety and environmental protection are major livelihood issues in front of the Chinese people. The priorities of the three are different, and there is mutually dependent and contradictory relationship among them. Facing the triple pressures of food security, food safety, and environmental protection, this paper analyzes the priority of the three from the historical development, then further analyzes the interaction between food security,food safety and environmental protection and finally puts forward the healthy development of food security, food safety and environmental protection, and the proper settlement of the three problems.

Genotype x Environment Interaction of Carotene Content of Yellow-Fleshed Cassava Genotypes in Nigeria

Cassava is an important starchy root crop and a major staple for more than 70 million people in Nigeria. New yellow-fleshed genotypes are being developed to combat vitamin A deficiency. Trials of 18 yellow-fleshed genotypes and two officially released white-fleshed clones, used as checks for 2008/2009 and 2009/2010 seasons in five major cassava growing agroecological zones of Nigeria. The trial locations were Ikenne （humid forest）, Ibadan （forest-savanna transition）, Ubiaja （subhumid forest）, Mokwa （southern Guinea savanna） and Zaria （northern Guinea savanna）. At each location, the trial was established in a randomized complete block design with four replications. The objective of the study was to assess genotype performance and genotype ~ environment interaction for total carotene concentration （TCC）, total carotene content per root （TC-R）, and total carotene content per plant （TC-P）. Significant differences （P 〈 0.001） among genotypes, environments and genotype x environment interaction for all the traits evaluated were observed. For TCC, TC-R and TC-P, the best genotypes across the 10 environments were TMS I051601, TMS 1050311, and TMS 1050998. Variation among genotypes accounted for most of the Total Sum of Squares for TCC （67.9%）, TC-R （39.0%） and TC-P （35.9%）. These characteristics of total carotene were also highly correlated. This study revealed that cassava with total carotene concentration can be assessed using either the TCC, or the TC-R, or the TC-P.

Study on the interaction between polymorphisms of FOXO3A gene and environmental factors in longevity at Bama county,Guangxi province

Objective: To study the interaction between the polymorphisms of FOXO3A and the environmental factors in the longevity district of Bama county.Methods: Using Taqmaq probe,genotyping of FOXO3A gene was performed for 200 longevous elderly(aged 90-110)and 288 healthy controls(aged 48-89).The interaction between the polymorphisms of gene and environmental factors were analyzed by using conditional logistic regression.Results: Minor allele frequencies(MAF)of five known SNPs in FOXO3A gene were higher in cases than in controls(P<0.05).There was a positive interction between minority alleles of rs2764264 in FOXO3A gene and the environment factors in the longevity district(OR=11.08,γ=1.075).Conclusion: Five SNPs of FOXO3A gene would be closely correlated with human longevity in Bama.The interaction between the polymorphisms of FOXO3A genes rs2764264 and the environment factors in the longevity district had synergy to longevity.The longevity phenomenon in Bama probably was the result of the interaction between gene and environmental factors.

Modeling the Effects of Interactions between Environmental Variables on the State of an Environmental Issue: The Case of the Morelos State in Mexico

An important use of environmental indicators is oriented to know their individual impact on the whole environment quality. Nevertheless, most of the important causes of environment affectations are derived from multiple interactions between indicators which correspond more specifically to the environmental reality. The affectations derived from interactions should be analyzed and interpreted through numerical expressions representing a relevant challenge for developers of environmental indicators. To cope with the analysis and interpretation problem, we propose in this work a methodology in two senses: in a bottom-up sense a directed graph is built representing interactions between environmental indicators as behavioral relations, which exert an effect on the state of an environmental issue of a site over time (10 years);in a top-down sense to assist users in the analysis and interpretation of interactions through a computer interface that provides users with the capacity of knowing how and what relational behaviors between indicators are affecting, the most or the least, the performance of the environmental issue being studied. This methodology was applied to the analysis an interpretation of interactions between environmental variables that affect the state of an environmental quality issue related with the State of Morelos in Mexico. The results showed the adequate expressivity of a directed graph to represent interactions allowed to verify the coherence of the numerical values associated with their behaviors during a period of time and with their effects on the environmental issue under study.

AMMI analysis of interaction of genotype and environment in chalkiness of indica rice

Chalkiness is an unpleasant trait for rice con-sumer,which is known to be controlled geneti-cally and affected by environment during grainmaturing.We used the model of Additive Main

One compound approach combining factor-analytic model with AMMI and GGE biplot to improve multi-environment trials analysis

To improve multi-environmental trial(MET)analysis,a compound method—which combines factor analytic(FA)model with additive main effect and multiplicative interaction(AMMI)and genotype main effect plus genotype-by-environment interaction(GGE)biplot—was conducted in this study.The diameter at breast height of 36 open-pollinated(OP)families of Pinus taeda at six sites in South China was used as a raw dataset.The best linear unbiased prediction(BLUP)data of all individual trees in each site was obtained by fitting the spatial effects with the FA method from raw data.The raw data and BLUP data were analyzed and compared by using the AMMI and GGE biplot.BLUP results showed that the six sites were heterogeneous and spatial variation could be effectively fitted by spatial analysis with the FA method.AMMI analysis identified that two datasets had highly significant effects on the site,family,and their interactions,while BLUP data had a smaller residual error,but higher variation explaining ability and more credible stability than raw data.GGE biplot results revealed that raw data and BLUP data had different results in mega-environment delineation,test-environment evaluation,and genotype evaluation.In addition,BLUP data results were more reasonable due to the stronger analytical ability of the first two principal components.Our study suggests that the compound method combing the FA method with the AMMI and GGE biplot could improve the analysis result of MET data in Pinus teada as it was more reliable than direct AMMI and GGE biplot analysis on raw data.

Performance and yield stability of maize hybrids in stress-prone environments in eastern Africa

Identification and deployment of high-yielding and stress-tolerant maize hybrids adapted to stress-prone agro-ecologies is important for improving the food security and livelihoods of smallholder farmers in eastern Africa.The objectives of this study were to(i)assess the performance of maize hybrids under well-watered and drought stress conditions;(ii)evaluate grain yield stability of 65 intermediate-maturing and 55 early-maturing hybrids in 24 well-watered locations and seven drought stress locations;and(iii)identify representative and/or discriminative testing locations for increasing genetic gains for the target traits.There were significant differences for grain yield among early-and intermediatematuring hybrids tested under well-watered and drought stress environments.Among the early-maturing hybrids,the top 10 hybrids produced 46.8%–73.9%and 31.2%–42.1%higher mean grain yields than the best commercial check under drought and well-watered conditions,respectively.Among the intermediate-maturing hybrids,the top 10 hybrids produced 25.2%–47.7%and 8.5%–13.5%higher grain yield than commercial checks under drought stress and well-watered conditions,respectively,suggesting improvement in the levels of drought tolerance in both early-and intermediate-maturing hybrids.GGE biplot analysis and a bi-segmented regression linear method identified specific early-maturing and intermediate-maturing hybrids that performed well under both well-watered and drought stress conditions.These hybrids could be recommended for commercial production in eastern Africa.Kakamega in Kenya was found to be the most representative and highly discriminating site among well-watered testing locations,while Kabuku in Tanzania was the least representative of test locations.For testing under drought stress conditions,Kiboko in Kenya was identified as the most representative location.This information could be useful for allocating resources and streamlining CIMMYT maize hybrid testing in eastern Africa.

QTL mapping for leaf area in maize (Zea mays L.) under multienvironments

Leaves are the main organs of photosynthesis in green plants. Leaf area plays a vital role in dry matter accumulation and grain yield in maize （Zea mays L.）. Thus, investigating the genetic basis of leaf area will aid efforts to breed maize with high yield. In this study, a total of 150 F7 recombinant inbred lines （RILs） derived from a cross between the maize lines Xu 178 and K12 were used to evaluate three ear-leaves area （TELA） under multi-environments. Inclusive composite interval map- ping （ICIM） was used to identify quantitative trait loci （QTLs） for TELA under a single environment and estimated breeding value （EBV）. A total of eight QTLs were detected under a single environmental condition, and four QTLs were identified for EBV which also can be detected in single environment. This indicated that the EBV-detected QTLs have high genetic stability. A major QTL （qTELA_2-9） located in chromosome bin 2.04/2.05 could be detected in four environments and has a high phenotypic contribution rate （ranging from 10.79 to 16.51%） that making it a good target for molecular breeding. In addition, joint analysis was used to reveal the genetic basis of leaf area in six environments. In total, six QTLxenvironment interactions and nine epistatic interactions were identified. Our results reveal that the genetic basis of the leaf area is not only mainly determined by additive effects, but also affected by epistatic effects environmental interaction effects.

A holistic framework for facilitating environmental and human health

In the Anthropocene,health is necessary to achieve global sustainable development.This is a challenge because health issues are complex and span from humans to ecosystems and the environment through dynamic interac-tions across scales.We find that the health issues have been mainly addressed by disciplinary endeavors which unfortunately will not result in panoramic theories or effective solutions.We recommend focusing on the intri-cate interactions between humans,ecosystems and the environment for developing common theoretical under-standings and practical solutions for safeguarding planetary health,with human health as the key indicator and endpoint.To facilitate this paradigm shift,a holistic framework is formulated that incorporates disturbances from inner Earth and our solar system,and accommodates interactions between humans,ecosystems and the environ-ment in a nested hierarchy.An integrative and transdisciplinary health science is advocated along with holistic thinking to resolve our current health challenges and to achieve the health-related sustainable development goals.

Genotype × environment interaction patterns of dry matter yield in meadow brome, orchardgrass, tall fescue, and timothy evaluated at harsh winter sites

Background:Genotype×environment interaction(GEI)slows genetic gains and complicates selection decisions in plant breeding programs.Forage breeding program seed sales often encompass large geographic regions to which the cultivars may not be adapted.An understanding of the extent of GEI in perennial,cool-season forage grasses will facilitate improved selection decisions and end-use in areas with harsh winters.Methods:We evaluated the dry matter yield of nine meadow brome(Bromus biebersteinii Roemer&J.A.Schultes),nine orchardgrass(Dactylis glomerata L.),seven tall fescue(Lolium arundinaceum(Schreb.)Darbysh.),and 10 timothy(Phleum pratense L.)cultivars or breeding populations at seven high latitude and/or elevation locations in Canada and the United States from 2019 to 2021.Results:For each of the species,we found significant differences among the genotypes for dry matter yield across environments and found significant levels of GEI.Using site regression analysis and GGE biplot visualizations,we then characterized the extent of the interactions in each species.Except for tall fescue,there was little evidence for the broad adaptation of genotypes across locations.Conclusions:This research adds further evidence to the limitations of perennial,forage breeding programs to develop widely adapted cultivars and the need to maintain regional breeding efforts.

Dynamics of Quantum Discord in Asymmetric and Local Non-Markovian Environments

The non-Markovian decoherence of quantum and classical correlations is analytically obtained when two qubits are asymmetrically subjected to the bit flip channel and phase flip channel. For one class of initial mixed states, quantum correlations quantified by quantum discord decay synchronously with classical correlations. The discovery that the decaying rates of quantum and classical correlations suddenly change at the characteristic time is physically interpreted by the distance from quantum state to the closest classical states. In a large time interval, quantum correlations are greater than classical correlations. The quantum and classical correlations can be preserved over a longer period of time via the kernel characterizing the environment memory effects.