Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important role. This paper investigates the effect of model choice on the set and magnitude of detected root QTL in rice. Published studies on QTLs for root traits indicate that different results are obtained if varying genetic populations are used and also if different environmental conditions are included. An experiment was conducted with 168 RILs of the Bala × Azucena mapping population plus parents as checks under four environmental conditions (low light, low nitrogen, drought and a control environment). We propose a model that incorporates all relevant experimental information into a composite interval mapping approach based on a mixed model, which especially considers the correlation of genotypes in different environments. An extensive sequential model selection procedure was applied based on the phenotypic model, using the AIC to determine an appropriate random structure and Type 3 Wald F-tests for selection of fixed effects. In a first step we checked whether any of the fixed effects and random (nested) design effects could be dropped. Secondly, an appropriate covariance structure was chosen for genotype × environment interaction. In a third step Box-Cox transformations were applied based on residual analysis. We compared profiles of composite interval mapping scans with and without the inclusion of genotype × environment interaction and the experimental design information. Some distinct differences in profiles indicate that insufficient modeling of the non-QTL part can lead to an overly optimistic interpretation of QTL main effects in interval mapping. It is concluded that mixed model QTL mapping offers a reasonable way to separate environmental and genetic influences in the evaluation of quantitative genes and especially enables a more realistic assessment of QTL and QTL × environment effects than standard approaches by including all relevant effects.     

Comparison and analysis of main effects,epistatic effects,and QTL × environment interactions of QTLs for agronomic traits using DH and RILs populations in rice

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross ‘Samgang × Nagdong’, were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population, respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).     

QTL × genetic background interaction: predicting inbred progeny value

Failures of the additive infinitesimal model continue to provide incentive to study other modes of gene action, in particular, epistasis. Epistasis can be modeled as a QTL by genetic background interaction. Association mapping models lend themselves to fitting such an interaction because they often include both main marker and genetic background factors. In this study, I review a model that fits the QTL by background interaction as an added random effect in the now standard mixed model framework of association analyses. The model is applied to four-generation pedigrees where the objective is to predict the genotypic values of fourth-generation individuals that have not been phenotyped. In particular, I look at how well epistatic effects are estimated under two levels of inbreeding. Interaction detection power was 8% and 65% for pedigrees of 240 randomly mated individuals when the interaction generated 6% and 20% of the phenotypic variance, respectively. Power increased to 21% and 94% for these conditions when evaluated individuals were inbred by selfing four times. The interaction variance was estimated in an unbiased way under both levels of inbreeding, but its mean squared error was reduced by 40% to 70% when estimated in inbred relative to randomly mated individuals. The performance of the epistatic model was also enhanced relative to the additive model by inbreeding. These results are promising for the application of the model to typically self-pollinating crops such as wheat and soybean. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Quantitative trait loci for dry matter digestibility and particle size traits in two-rowed × six-rowed barley population

More than half of the barley grown in the USA is used for livestock feed, with the remaining stocks diverted for human food and malting purposes. The use of barley grain as a major source of cattle feed has been criticized because of its rapid digestion in the rumen, which can result in digestive disorders in cattle. In sacco dry matter digestibility (ISDMD) and particle size (PS) after dry rolling have been found to play a role in the feedlot performance of barley as a feed grain. Reducing the rate of ISDMD is predicted to result in significantly improved animal health and average daily gain. A recombinant inbred line population derived from a cross between a high ISDMD, two-rowed barley cultivar (Valier) and a six-rowed Swiss landrace line (PI370970) exhibiting far slower ISDMD has been developed for studying the underlying genetic locations and mechanisms of these traits. To detect associated quantitative trait loci (QTLs), we collected and analyzed data from irrigated and rain-fed environments. A significant negative correlation was observed between ISDMD and PS. High heritability estimates for ISDMD and PS suggest that early selection for these traits during breeding would be achievable. Four QTLs were identified on chromosomes 2H, 6H, and 7H, explaining 73–85% of ISDMD phenotypic variation, while three QTLs on 2H and 7H were associated with variation in PS and explained 58–77% of its variation. A major QTL on chromosome 2H tightly linked to the morphology-modifying gene vrs1 was found to dramatically control 35–62% of the phenotypic variation of ISDMD and 26–53% of that of PS. The impact of the vrs1 locus on ISDMD was validated in two populations representing different genetic backgrounds. Our results suggest that it may also be advantageous to simultaneously overlap these QTLs around the vrs1 locus.     

QTL analysis for eating quality-related traits in an F2:3 population derived from waxy corn × sweet corn cross

In order to identify quantitative trait loci (QTL) for the eating quality of waxy corn and sweet corn (Zea mays L.), QTL analysis was conducted on an F₂ population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. Ten QTLs for pericarp thickness (PER), amylose content (AMY), dextrose content (DEX) and sucrose content (SUC) were found in the 158 F₂ families. Among them, four QTLs, qAMY4 (10.43%), qAMY9 (19.33%), qDEX4 (21.31%) and qSUC4 (30.71%), may be considered as major QTLs. Three of these, qAMY4, qDEX4 and qSUC4, were found to be located within a region flanked by two adjacent SSR markers on chromosome 4 (umc1088 and bnlg1265), making this SSR marker pair a useful selection tool for screening the eating quality traits of AMY, DEX and SUC. The QTL for amylose content was found to be located between markers phi027 and umc1634, raising the possibility of its identity being the Wx1 gene, which encodes a granule-bound amylose synthase. The new QTLs identified by the present study could serve as useful molecular markers for selecting important eating quality traits in subsequent waxy corn breeding studies.     

Mapping QTLs with epistatic effects and QTL × treatment interactions for salt tolerance at seedling stage of wheat

Quantitative trait loci (QTLs) with additive (a), additive × additive (aa) epistatic effects, and their treatmental interactions (at and aat) were studied under salt stress and normal conditions at seedling stage of wheat (Triticum aestivum L.). A set of 182 recombinant inbred lines (RILs) derived from cross Xiaoyan 54 × Jing 411 were used. A total of 29 additive QTLs and 17 epistasis were detected for 12 traits examined, among which eight and seven, respectively, were identified to have QTL × treatment effects. Physiological traits rather than biomass traits were more likely to be involved in QTL × treatment interactions. Ten intervals on chromosomes 1A, 1D, 2A (two), 2D, 3B, 4B, 5A, 5B and 7D showed overlapping QTLs for different traits; some of them represent a single locus affecting different traits and/or the same trait under both treatments. Eleven pairs of QTLs were detected on seemingly homoeologous positions of six chromosome groups of wheat, showing synteny among the A, B and D genomes. Ten pairs were detected in which each pair was contributed by the same parent, indicating a strong genetic plasticity of the QTLs. The results are helpful for understanding the genetic basis of salt tolerance in wheat and provide useful information for genetic improvement of salt tolerance in wheat by marker-assisted selection.     

Phenotypic segregation and relationships of agronomic traits in Monastrell × Syrah wine grape progeny

The aim of this work was to study the phenotypic segregation of different agronomic and fruit quality traits, and their relationships, in Monastrell × Syrah wine grape progeny. Twenty-two agronomic traits were evaluated and compared for three consecutive years in this progeny. The results show the phenotypic diversity existing in a cross between two different wine grape cultivars. Most of the phenological, productive, morphological, and enological parameters evaluated displayed continuous variation within the progeny, suggesting a polygenic inheritance. Some correlations between traits were detected by the Spearman correlation test, although high coefficients were not found for most of them. Cluster analysis of the progeny grouped the hybrids based on criteria with significance for wine grape breeding. Also, we investigated the relationship between the skin color and total content of anthocyanins with the VvmybA genotype, using the CAPS (Cleaved Amplified Polymorphic Sequence) marker 20D18CB9. The results show that hybrids with two copies of the functional color allele tend to have increased anthocyanins content. Based on this study, 14 genotypes were pre-selected from the breeding population for additional quality studies.     

Genotype × environment interaction and genetic improvement for yield and yield stability of rainfed durum wheat in Iran

The genotype × environment (GE) interaction influences genotype selection and recommendations. Consequently, the objectives of genetic improvement should include obtaining genotypes with high potential yield and stability in unpredictable conditions. The GE interaction and genetic improvement for grain yield and yield stability was studied for 11 durum breeding lines, selected from Iran/ICARDA joint program, and compared to current checks (i.e., one durum modern cultivar and two durum and bread wheat landraces). The genotypes were grown in three rainfed research stations, representative of major rainfed durum wheat-growing areas, during 2005–09 cropping seasons in Iran. The additive main effect and multiplicative interaction (AMMI) analysis, genotype plus GE (GGE) biplot analysis, joint regression analysis (JRA) (b and S²di), six stability parameters derived from AMMI model, two Kang’s parameters [i.e., yield-stability (YSi) statistic and rank-sum], GGE distance (mean performance + stability evaluation), and two adaptability parameters [i.e., TOP (proportion of environments in which a genotype ranked in the top third) and percentage of adaptability (Ad)] were used to analyze GE interaction in rainfed durum multi-environment trials data. The main objectives were to (i) evaluate changes in adaptation and yield stability of the durum breeding lines compared to modern cultivar and landraces (ii) document genetic improvement in grain yield and analyze associated changes in yield stability of breeding lines compared to checks and (iii) to analyze rank correlation among GGE biplot, AMMI analysis and JRA in ranking of genotypes for yield, stability and yield-stability. The results showed that the effects due to environments, genotypes and GE interaction were significant (P < 0.01), suggesting differential responses of the genotypes and the need for stability analysis. The overall yield was 2,270 kg ha^?1 for breeding lines and modern cultivar versus 2,041 kg ha^?1 for landraces representing 11.2 % increase in yield. Positive genetic gains for grain yield in warm and moderate locations compared to cold location suggests continuing the evaluation of the breeding material in warm and moderate conditions. According to Spearman’s rank correlation analysis, two types of associations were found between the stability parameters: the first type included the AMMI stability parameters and joint regression parameters which were related to static stability and ranked the genotypes in similar fashion, whereas the second type consisted of the rank-sum, YSi, TOP, Ad and GGED which are related to dynamic concept of stability. Rank correlations among statistical methods for: (i) stability ranged between 0.27 and 0.97 (P < 0.01), was the least between AMMI and GGE biplot, and highest for AMMI and JRA and (ii) yield-stability varied from 0.22 (between GGE and JRA) to 0.44 (between JRA and AMMI). Breeding lines G8 (Stj3//Bcr/Lks4), G10 (Ossl-1/Stj-5) and G12 (modern cultivar) were the best genotypes in terms of both nominal yield and stability, indicating that selecting for improved yield potential may increase yield in a wide range of environments. The increase in adaptation, yield potential and stability of breeding lines has been reached due to gradual accumulation of favorable genes through targeted crosses, robust shuttle breeding and multi-locational testing.     

Genetic variation,genotype × environment interaction,and selection for tipburn resistance in lettuce in multi-environments

Tipburn is a calcium related and environmentally induced physiological disorder causing economic damage in all lettuce (Lactuca sativa L.) production regions. The objectives of this research were to determine (1) the genetic variation for tipburn incidence, (2) the genotype (G) × environment (E) interaction (GE) for tipburn incidence, and (3) the efficiency of field selection for tipburn resistance. Tipburn incidence was recorded over 2 years in Salinas, CA, and Yuma, AZ, for 55 romaine, crisphead, green leaf, and red leaf type cultivars, and over 3 years in Quebec for 15 romaine cultivars. Analysis revealed that G, E, and GE affected tipburn incidence, including crossover interactions that were not repeatable over years. This indicates that cultivar/breeding line evaluations should be based on mean performance and stability over multiple environments. Among lettuce types, only crisphead had significant genetic variability for tipburn resistance, reflecting the greater breeding effort applied to this type compared romaine, green and red leaf types. Analysis of a dataset with five romaine cultivars in eight environments in California, Arizona, and Quebec for 2 years revealed that Yuma in 2006 and Saint-Blaise in 2005 were highly correlated (r = 0.923, P < 0.05), and were the most discriminating and most representative environments for tipburn evaluation. Single plant selection for tipburn resistance in three F₂ romaine populations was ineffective. Further, the degree of head closure was significantly associated with tipburn incidence. Identification and selection of morphological characters associated with resistance in conjunction with direct selection against tipburn may be an effective method for genetic improvement of tipburn resistance.     

Parental effects on the performance of cultivated × wild species hybrids in potato

Valuable genetic diversity in diploid wild Solanum species can be accessed through crosses to haploids (2n = 2×) of the tetraploid cultivated potato, Solanum tuberosum. Haploid-wild species hybrids segregate for the ability to tuberize in the field. In addition, they vary in male fertility, vine size, stolon length, and tuber size. In this study, three haploids were crossed with nine diploid wild Solanum species and 27 hybrid families were evaluated in the field for two years. The proportion of male fertile hybrid clones varied depending on the wild species parent. A large effect of the female parent was detected for vine size, stolon length, tuber size, percent tuberization, and percent plants selected for agronomic quality. An exceptional haploid (US-W4) was identified for the production of agronomically desirable haploid-wild species hybrids. In hybrids derived from US-W4, differences among wild species parents were observed for agronomic quality. Superior hybrids were produced by S. berthaultii and S. microdontum. Reciprocal crosses were evaluated for a subset of families. When the wild species was used as the female parent, male fertility was restored, but tuberization and tuber size were reduced. Careful selection of both haploid and wild species parents can result in a large proportion of fertile, agronomically desirable hybrid offspring.     

Impact of epistasis and QTL × environmental interaction on the oil filling rate of soybean seed at different developmental stages

The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities at different phases affected by both genotype and environment. The objective of the present study was to investigate additive, epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development. A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil filling rate in soybean seed were under genetic, developmental and environmental control.     

Phenotypic diversity and relationships of fruit quality traits in inter-specific almond × peach backcrosses breeding progenies

Nineteen agrochemical traits of 20 almond inter-specific backcrosses progenies were evaluated and compared for three consequence years to find out their phenotypic diversity and determine the relationships of fruit quality traits in almond × peach backcrosses breeding progenies. The variation was observed for traits of phenology parameters (blooming time, ripening time), Physical parameters (fruit weight, width, height, shape, thickness, skin pubescences, colour and flower type), chemical parameters (total sugar content, soluble solids content and acidity) and sensory parameters (attractiveness, taste, and flavor) and yield. Many fruit characteristics that are important to breeders are present in this collection. A high variability was found in the evaluated almond progenies and significant differences were found among them in all studied quality attributes. Year-by-year variations were observed for majority of traits. A significant correlation was found among the fruit height, fruit width, skin pubescences and yield. Fruit height showed a significant positive correlation with fruit weight and fruit thickness and some other traits and a negative correlation with the titratable acidity, skin pubescences and fruit flavour. A high negative correlation was found between the fruit weight and titratable acidity (?0.8). Low coefficients were got between the flower colour and skin pubescences. In addition, principal component analysis it possible to established similar groups of genotypes depending on their quality characteristics and to study relationships among pomological traits in almond progenies evaluated.     

Genotype × environment interaction for yield and reaction to leaf spot infections in groundnut in semiarid West Africa

Capitalizing on the yield potential in available groundnut germplasm, and high stability of kernel yield are important requirements for groundnut producers in semiarid environments. Forty-seven groundnut genotypes were evaluated from 2003 to 2005 at 4 locations representative of the Guinea and Sudan savanna ecologies in Ghana. The objectives were to assess genotypic differences in reaction to early and late leaf spot infections under natural field conditions, assess the extent of genotype × environment (G × E) interaction for kernel yield, and determine the relationship between yield potential and yield stability. Genotypes differed significantly in their reaction to leaf spot infections indicated by the area under disease progress curve (AUDPC). Genotypic AUDPC was negatively correlated with maturity period (P < 0.01), with kernel yield (P < 0.05) at each of the 3 locations in the Guinea savanna ecology but not in the Sudan savanna ecology and with each of four stability parameters (P < 0.05). High or low yielding genotypes were grouped based on Dunnett’s test at P < 0.10. High yielding groups had significantly low AUDPC, high biomass, high partitioning of dry matter for kernel growth, and were later in maturity compared to low yielding genotypes. Significant G × E interaction effect for kernel yield was dominated mainly by the lack of correlation among environments variance (76–78%) relative to the heterogeneity of genotypic variance component (22–24%). Stability of yield assessed through the among-environment variance, Wricke’s ecovalence, and Finlay-Wilkinson regression coefficient revealed that genotypes in the higher yielding group were relatively unstable compared to the low yielding group. Indicated by the Kataoka’s index of yield reliability, however, relatively unstable genotypes in the high yielding group are expected to be more productive even under assumptions of high risk aversion (P = 0.75–0.95) compared to the more stable, low yielding genotypes. The findings indicate that deploying these recently developed germplasm in semiarid regions in West Africa provides a better match to farmers’ risk-averse strategies compared with the use of existing earlier maturing cultivars.     

Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population

Cultivated barley is the major livestock feed grain in the Northern Plains and Northwestern United States due to the fact that its short growing season and limited rainfall limit the planting and production of corn. Starch and fiber content play a significant role in feedlot performance of animals raised on barley feed. To study the underlying genetic locations and mechanisms for these traits, a recombinant inbred line population was derived from a cross between the hulled barley cultivar Valier and a hull-less Swiss landrace line, PI370970. Valier has a high acid detergent fiber content (ADF) and low starch and protein while PI370970 contains low ADF and high starch and protein content. To detect associated QTLs, data were collected and analyzed from irrigated and rain-fed environments. A total of 30 main effect QTLs and four epistatic QTLs were identified which conditioned ADF, starch and protein content under rain-fed, irrigated and combined analyses. These QTLs were located on chromosomes 2H, 3H, 5H, 6H and 7H. Major ADF and starch QTL were identified on chromosome 7H near the nud locus (the locus controlling hulled vs. hull-less caryopsis). High heritability estimates for both ADF and starch content suggest that early selection for these traits during breeding would be productive. Low ADF-QTL were independently verified in a second population in a different genetic background.     

Genetic effects and genotype × environment interactions for cooking quality traits in Indica-japonica crosses of rice (Oryza sativa L.)

Indica-japonica hybridization is an important approach for developing superior performing hybrids in rice (Oryza sativa L.). In view of the scanty information available on cooking quality characters in indica-japonica crosses, an investigation was undertaken to estimate genetic and genotype × environment variance and covariance components of amylose content, gel consistency and alkali digestion value, and to determine the relative importance of direct genetic effects, maternal genetic effects and cytoplasmic effects in the genetic variations of the three quality characters. Two indica photo-sensitive genic male sterile (PGMS) lines and four japonica varieties were used as parents to make crosses. Genetic model with genotype × environment interactions for triploid endosperm was used for genetic studies of the three cooking quality characters. Variance component analysis revealed that genetic variations of the three characters were mainly attributable to direct additive and maternal additive effects, and the three traits had significant direct and maternal heritabilities. Genotype × environment interactions were mainly dominance × environment (including direct dominance × environment and maternal dominance × environment) and cytoplasm × environment interactions. Environment factors could only affect the expression extent of dominant genes, without changing their directions. Predicted values of genetic effects indicated that the parental lines, ‘VI-70’ and ‘H9304-1’, appeared to be best for amylose content, ‘T 1950’ and ‘Suxuan’ appeared to be best for gel consistency and alkali digestion value. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population

Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology^®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.     

Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L.

Plant height is an important plant architecture trait that determines the canopy structure, photosynthetic capacity and lodging resistance of upland cotton populations. To understand the genetic basis of plant height for marker-assisted breeding, quantitative trait loci (QTL) analysis was conducted based on the genetic map of recombinant inbred lines (RILs) derived from the cross “CRI12 × J8891” (Gossypium hirsutum L.). Three methods, including composite interval mapping, multiple interval mapping and multi-marker joint analysis, were used to detect QTL across multiple environments in the RILs and in the immortalized F₂ population developed through intermating between RILs. A total of 19 QTL with genetic main effects and/or genetic × environment interaction effects were identified on 15 chromosomes or linkage groups, each explaining 5.8–14.3 % of the phenotypic variation. Five digenic epistatic QTL pairs, mainly involving additive × additive and/or dominance × dominance, were detected in different environments. Seven out of eight interacting loci were main-effect QTL, suggesting that these loci act as major genes as well as modifying genes in the expression of plant height. The results demonstrate that additive effects, dominance and epistasis are all important for the genetic constitution of plant height, with additive effects playing a more important role in reducing plant height. QTL showing stability across environments that were repeatedly detected by different methods can be used in marker-assisted breeding.