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.

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.

Agronomic Performance, Stability Analysis and Evaluation of Anthracnose Disease Resistance of Common Bean Lines Derived by Marker-Assisted Backcrossing in Uganda

The present study focused on evaluating the agronomic performance, stability, and anthracnose resistance of common bean lines derived through Marker-Assisted Backcrossing in Uganda. Eight marker-assisted selection (MAS) backcross-derived bush bean lines with red seed types, alongside two checks, were evaluated in a randomized complete block design replicated two times in five locations for three consecutive crop-growing seasons in 2021 and 2022. The study aimed to identify lines with both high stable yields and enhanced resistance to anthracnose disease for potential release and utilization in future bean varietal development in Uganda. Agronomic traits, including days to 50% flowering, days to 90% physiological maturity, seed yield, seed yield components, and anthracnose disease reaction under natural infestation were assessed. The response to anthracnose disease was further assessed using six isolates of Colletotrichum lindemuthianum representing six different races. Results indicated that the agronomic performances of the MAS backcross-derived bush bean lines were statistically comparable to the recurrent parent NABE14. Specifically, six lines exhibited statistically equal to or higher performance than NABE14 in terms of seed yield, total number of seeds and number of pods per plant. The combined analysis of variance for seed yield showed significant (p Co-42 and Co-5 anthracnose resistance genes in the derived line. In conclusion, UGKT-B157-4, identified as the best-performing and stable genotype, demonstrates promise for release and use in future bean varietal development in Uganda, offering a combination of high yields and enhanced anthracnose disease resistance. The study provides valuable insights into the potential of Marker-Assisted Backcrossing in improving common bean varieties in the region.

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）.

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.

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 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.

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.

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

Variation and stability analysis of growth traits of poplar clones in the seedling stage in northeast China

Plant phenotypes are infl uenced by genetic and environmental factors.In this study,the growth traits of 43 one-year-old poplar clones grown at diff erent sites in northeast China(Dongling State-owned Forest Protection Center,DL;Baicheng State-owned forest farm,BC;and Cuohai Forest farm,CH)were evaluated and analyzed across clones and sites.Results show signifi cant diff erences in height and base diameter among sites and clones.Phenotypic and genetic variation coeffi cients ranged from 49.59%(BC)to 58.39%(DL)and from 49.33%(BC)to 58.06%(DL),respectively.Additive main eff ects and multiplicative interaction(AMMI)analysis showed that the eff ects of genotype,environment,and genotype×environment interaction were signifi cantly diff erent.Genetic variation was the main source of variation,accounting for 48.6%.AMMI biplot showed that clone 30 had high and stable yields at the three sites.From an evaluation of multiple traits and GGE biplot that clone 2,clone 30 and clone 25 had higher yield than the other clones at DL,CH and BC,respectively.These clones will provide material for forest regeneration in northeast China.

Growth variations and stability analyses of seven poplar clones at three sites in northeast China

Growth characteristics have complex inheritance patterns and genotype(G) by environment(E) interaction make predicting tree response to environmental changes difficult.In this study,the growth of seven poplar clones at three different sites was taken as the research focus,and heights and basal diameters were investigated in the second growing season.An ANOVA showed that all main effects,site,clone number and their interactions were highly significant in the overall F-tests.The coefficients of variation and repeatability of different traits ranged from 15.5 to 43.9%and from 0.549 to 0.912,respectively.AMMI(Additive Main Effects and Multiplicative Interaction) analysis results showed that genotype,environment and G × E interaction were significantly highly correlated.The stability analysis indicated that different clones showed different growth traits on different sites,which suggests that elite clones should be selected separately for different sites.Based on the growth traits,under a 10% selection rate,three clones were selected for different sites and the genetic gains of growth traits ranged from 4.7 to 11.2%.The three selected clones could be used to establish plantations in the future in different sites.

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.

Investigation on Pasting Characteristics of Spring-sown Chinese Bread Wheats

Forty-seven spring wheat Triticumaestivum cultivars and advanced lines from spring-sown spring wheat regions, at twelve locations in 1998 and 1999, were used to investigate pasting properties of Chinese spring wheats. Starch pasting properties were closely associated with noodle quality. Significant differences were observed for all pasting characteristics. Samples collected from Harbin, Shenyang, Beijing, Ba-meng, Yongning, and Urumqi had better pasting quality than those from other locations. Genotype, environment, and genotype by environment interaction had large effects on all pasting characteristics. Significant correlations among pasting characteristics were observed and peak viscosity was considered the most important pasting characteristics.

Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions

Plant height （PH） is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line （RIL） derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr （2013 and 2014）, respectively （regarded as four environments）, was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL^environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between genexgene interactions and genexenvironment interactions in specific growth period. A total of 26 additive QTLs （A-QTLs） and 37 epistatic QTLs （E-QTLs） associated with PH were detected by unconditional and conditional mapping over seven growth periods, qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses, qPH-4-3 and qPH-7-5 were detected in four stages （periods） to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects （A-QTLs） were mostly expressed in the period $3iS2 （the time interval from stages 2 to 3）, and QTLxenvironment interactions performed actively in the first three stages （periods） which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly influenced by environments as well. Many QTLs （qPH-1-2, qPH-3-5, qPH-4-1, qPH-2-3） coincident with previously identified drought resistance genes. The result of this study is helpful to elucidating the genetic mechanism and regulatory network underlying the development of PH in rice and providing references to marker assisted selection.

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.

Construction of SSR Linkage Map and Analysis of QTLs for Rolled Leaf in Japonica Rice

Genetic analysis of rolled leaf is important to rice ideotype breeding. To detect loci controlling rolled leaf of japonica restorer lines, SSR marker genotypes and phenotypes of flag leaf rolling index （LRI） were investigated in Xiushui 79 （P1, a japonica rice variety）, C Bao （P2, a japonica restorer line） and 254 recombinant inbred lines derived from the cross between P1 and P2 , and in two environments. A genetic map of this cross was constructed, QTLs for LRI were detected and their interactions with environments were analyzed. Among 818 pairs of SSR primers, 90 primers showed polymorphism between P1 and P2, and 12 markers showed highly significant correlation with LRI in both environments based on single marker regression analysis. The genetic map containing 74 information loci has a total distance of 744.6 cM, with an average of 10.1 cM between two adjacent loci. Three QTLs （qRL-1, qRL-7 and qRL-8-1） were detected with two softwares： WinQTLCart 2.5 and QTLNetwork2.0. qRL-8-1 was a new locus, accounting for 15.5% and 12.8% of phenotypic variations in the two environments, respectively. The phenotypic variation explained by additive effect was 6.6%. No interaction was found between qRL-8-1 genotype and environments.

Interactions between engineered nanoparticles and dissolved organic matter: A review on mechanisms and environmental effects

Dissolved organic matter（DOM） is ubiquitous in the environment and has high reactivity.Once engineered nanoparticles（ENPs） are released into natural systems, interactions of DOM with ENPs may significantly affect the fate and transport of ENPs, as well as the bioavailability and toxicity of ENPs to organisms. However, because of the complexity of DOM and the shortage of useful characterization methods, large knowledge gaps exist in our understanding of the interactions between DOM and ENPs. In this article, we systematically reviewed the interactions between DOM and ENPs, discussed the effects of DOM on the environmental behavior of ENPs, and described the changes in bioavailability and toxicity of ENPs caused by DOM. Critical evaluations of published references suggest further need for assessing and predicting the influences of DOM on the transport,transformation, bioavailability, and toxicity of ENPs in the environment.

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.

QTL Mapping of Chlorophyll Contents in Rice

The objectives of this study were to investigate the genetic factors controlling the chlorophyll content of rice leaf using QTL analysis. A linkage map consisting of 207 DNA markers was constructed by using 247 recombinant inbred lines （RILs） derived from an indica-indica rice cross of Zhenshan97B×Milyang 46. In 2002 and 2003, the contents of chlorophyll a and b of the parents and the 247 RILs were measured on the top first leaf, top second leaf, and top third leaf, respectively. The software QTLMapper 1.6 was used to detect quantitative trait loci （QTLs）, additive by environment （AE） interactions, and epistatic by environment （AAE） interactions. A total of eight QTLs in four intervals were detected to have significant additive effects on chlorophyll a and b contents at different leaf positions, with 1.96-9.77% of phenotypic variation explained by a single QTL, and two QTLs with significant AE interactions were detected. Epistasis analysis detected nine significant additive-by-additive interactions on chlorophyll a and b contents, and one pair of QTLs with significant AAE interactions was detected. On comparison with QTLs for yield traits detected in the same population, it was found in many cases that the QTLs for chlorophyll a and b contents and those for yield traits were located in the same chromosome intervals.

Estimation of genetic parameters on growth characteristics of a 35-year-old Pinus koraiensis progeny trial in South Korea

The effects of genetic and environmental factors on Pinus koraiensis growth were studied based on a35 year-old progeny trial composed of open-pollinated offspring of twenty-one plus trees.Height,DBH and volume of the offspring was analyzed using restricted maximum likelihood/best linear unbiased prediction in mixed model analysis.Significant site and family effects on the three traits were observed.The distinct growth of offspring by site with disparate climates corroborated the importance of planting species in suitable conditions.Growth differences by family was significant,emphasizing the importance of identifying families with either superior or inferior performance.The parental ranking was assigned in the sites,inferring the breeding value of each plus tree.The estimates of individual heritability(h_(i)^(2))of height,DBH and volume growth were 0.169-0.645,0.108-0.331 and 0.129-0.343 respectively,with higher h_(i)^(2) of the height than DBH on each site.Coefficient of variance of genetic effect was higher with DBH in some cases,indicating the scope for selection is larger for this trait despite the lower heritability compared to height.For the variation between families in terms of the performance stability across sites,consideration of the genotype by environment interaction is required in selecting materials to be used in reforestation with Korean pine.A few families with either superior or inferior performance retained their parental ranking for at least a decade.Other families with increased growth on a particular site were identified,indicating their high breeding value and low stability.Differences in the genetic performance of the families by site requires delineation of the breeding region of the species.