GENOTYPE-ENVIRONMENT INTERACTION FOR JUVENILE GROWTH IN THE HARD CLAM MERCENARIA MERCENARIA (L.)

Offspring from half-sib and full-sib families of the hard clam, Mercenaria mercenaria were reared in five locations along the Atlantic Coast to test for the presence of genotype-environment interaction for juvenile growth rate. Location effects upon growth rate variation were prevalent; of the genetic effects, the additive genetic by location variance was predominant with the nonadditive genetic by location component contributing to a lesser degree to the interaction variance. The additive and nonadditive variation over all environments was negligible. Genotype-environment interaction was found to be at least partially due to a change in the amount of genetic variation expressed at each location; with significant additive variation detected at Charleston and Georgetown, SC sites and significant nonadditive variation at Millsboro, DE. Genetic covariance/correlation analysis indicated that reversals in relative family performance across locations were prevalent, implying the possibility of habitat specialization among genotypes. In addition, graphical analysis produced no evidence of a ubiquitously superior genotype. These analyses suggest that genotype-environment interaction should act to constrain the evolution of juvenile growth rate in Mercenaria, preserve any heritable variation associated with this trait and may lead to the development of phenotypic plasticity for growth.     

甘蔗品种主要性状的基因型与环境及其互作效应分析

用AMMI模型双标图对国家第六轮甘蔗品种区域试验5个试点的12个甘蔗品种试验数据进行分析,研究甘蔗区试中不同品种的产量稳定性问题。结果表明,参试品种的6个产量性状在品种间和地点间差异显著,品种与地点的互作效应差异显著;FN30、YG16蔗茎产量和含糖量高,稳定性强,属于高产、稳产性较好的品种。AMMI模型很好地解释了甘蔗品种产量性状的基因型效应、环境效应和GE互作效应。     

Assessment of yield stability in sorghum using univariate and multivariate statistical approaches

The experiment was carried out to estimate GEI in sorghum for grain yield using univariate and multivariate statistical approaches based on two sets of performance trials (T1 and T2). While T1 consisted of 15 genotypes and tested in 8 environments, T2 that consisted of 13 genotypes was carried out in 13 environments. Because the combined ANOVA of each trial revealed significant differences among the genotypes, among the environments and GEI, the five univariate stability estimates: CV(i), S(i)(2), W(i)(2), sigma(i)(2), b(i) and Sd(i)(2) were evaluated for ranking the genotypes. There was positive rank-correlation between CVi and S(i)(2) and among W(i)(2), sigma(i)(2), b(i). Sd(i)(2) had significant positive rank-correlation with sigma(i)(2) and bi in T1 but weak rank-correlation with the remaining parameters in both trials. The three types of univariate stability estimates and the only multivariate stability estimate, the AMMI analysis declared genotypes 2 and 5 to be the most stable in T1, but they gave quite unrelated ranking in T2. Because of the lack of correspondence among the tested stability estimates in the two trials, it was difficult to reach a conclusion on producing genotype recommendation based on the univariate statistical approach. However, as GEI has multivariate nature, the multivariate approach is believed to give more robust inference. Hence, some stable genotypes were suggested using the AMMI model for sorghum growing dry lowlands of the country.     

Mapping and validation of a major QTL for yellow pigment content on 7AL in durum wheat (<Emphasis Type="Italic">Triticum turgidum</Emphasis> L. ssp. <Emphasis Type="Italic">durum</Emphasis>)

Yellow pigment content in durum wheat (Triticum turgidum L. ssp. durum) is an important criterion for both pasta bright yellow color and human health because of antioxidant properties of carotenoids involved in this pigmentation. In the present study, QTLs for yellow pigment content in durum wheat were mapped in a population of 140 RILs developed from a intraspecific cross between a released variety (PDW 233) and a landrace (Bhalegaon 4). This trait was evaluated in one location for 3 years and in two more locations for one additional year (five different year × location combinations further called “environments”). Yellow pigment content was highly heritable across the five different environments. Analysis of variance showed the significant effect of genotype, environment and genotype × environment interaction on the trait. Five different QTLs linked to yellow pigment content were identified on chromosome 1A, 3B, 5B, 7A and 7B across five different environments. The strongest one located on the distal part of the long arm of chromosome 7A, QYp.macs-7A, explained 55.22% of the variation in the trait, while, remaining four QTLs explained 5–8.75% of phenotypic variation in yellow pigment content. Marker analysis revealed significant association of one ISSR and one AFLP fragment with the trait. These two markers were linked to the major QTL QYp.macs-7A and were converted into SCAR markers. These SCAR markers were further validated on another population as well as 38 diverse genotypes so as to prove their potential in marker assisted selection. These markers will be very useful for the marker assisted breeding of durum wheat for higher yellow pigment content.     

Stability analysis of grain yield in barley (Hordeum vulgare) in the US mid-Atlantic Region

Stability of grain yield performance is an important characteristic in the selection of new crop cultivars. Information from cultivar trials, however, is seldom fully analysed for genotype by environment interactions and, therefore, information on stability of current crop cultivars is lacking. The objectives of this study were to investigate the stability of agronomic traits among genotypes of barley (Hordeum vulgare) across 17 environments (location‐years) in Maryland (USA) from 1994 through 1997 and to examine the effect of locations and years of testing on grain yield performance in this region. Significant differences were observed among barley cultivars and experimental lines for grain yield, plant height, and heading date. Grain yield was positively correlated with plant height and negatively correlated with heading date. Genotype x environment interactions measured through regression analysis were significant for grain yield, heading date and plant height, with the environmental component having the largest effect. Most barley genotypes tested (90%) had regression slopes for grain yield that did not differ from 1.0, indicating good potential for yield response under improving environmental conditions. The most widely grown cultivar in the mid‐Atlantic region, ‘Nomini’, had a regression slope that was higher than 1.0 for grain yield. This indicates that it tends to respond with increasingly higher yields under favorable conditions. In this study, the slope and the standard error of the slope were moderately correlated with grain yield. The genotype's coefficient of variation was not a good indicator of stability for this region. Grain yields of genotype entries common to all years and locations were correlated with corresponding yields at each of the locations and years to assess the relative performance of each location and year. Correlation coefficients across locations were relatively high (r=0.64) within each year of testing. Correlations between years for the same and across locations were generally much lower. The data presented here supports a testing program over more years rather than increased locations to fully characterise the performance of new cultivars.     

Genotype X environment interaction and simultaneous selection for high yield and stability in soybeans (Glycine max (L.) Merr.)

Eighteen genotypes of soybean were grown in five locations in Nigeria. The heritability estimates for seed yield were generally low, ranging from 22.6% to 45.3%. Joint regression analysis indicated the presence of genotype x environment, although a large proportion was non-linear. The genotypes responded differently to environments, highlighting the possibility of breeding for specific environments. The correlation of regression coefficients with mean yield indicated that high yielding genotypes were responsive to changing environments. The simultaneous selection parameters Pi, S³ and rank-sums gave somewhat similar results but Pi produced higher yielding genotypes than others. The correlation between Pi and rank-sum indicated that either of the techniques could be employed during selection.     

Heritability of male attractiveness persists despite evidence for unreliable sexual signals in Drosophila simulans

Sexual signals can be used to attract mates, but to be honest indicators of signaller quality they need to convey information reliably. However, environmental variation and genotype‐by‐environment (G × E) interactions have the potential to compromise the reliability of sexual signals. Here, we test the reliability of cuticular hydrocarbons (CHCs) as signals of heritable aspects of male attractiveness in Drosophila simulans. We examined the heritability of male attractiveness and a measure of the difference between fathers' and sons' CHC profiles across dietary and temperature environments. Our results show that environmental heterogeneity disrupts the similarity of some components of father and son CHC profile. However, overall male attractiveness is heritable within and across environments, so that sire attractiveness is a good predictor of son attractiveness even with environmental heterogeneity. This suggests that although some male CHC signals are unreliable, attractive genotypes retain their attractiveness across environments on average.     

Mendelian Factors Underlying Quantitative Traits in Tomato: Comparison across Species, Generations, and Environments

As part of ongoing studies regarding the genetic basis of quantitative variation in phenotype, we have determined the chromosomal locations of quantitative trait loci (QTLs) affecting fruit size, soluble solids concentration, and pH, in a cross between the domestic tomato (Lycopersicon esculentum Mill.) and a closely-related wild species, L. cheesmanii. Using a RFLP map of the tomato genome, we compared the inheritance patterns of polymorphisms in 350 F2 individuals with phenotypes scored in three different ways: (1) from the F2 progeny themselves, grown near Davis, California; (2) from F3 families obtained by selfing each F2 individual, grown near Gilroy, California (F3-CA); and (3) from equivalent F3 families grown near Rehovot, Israel (F3-IS). Maximum likelihood methods were used to estimate the approximate chromosomal locations, phenotypic effects (both additive effects and dominance deviations), and gene action of QTLs underlying phenotypic variation in each of these three environments. A total of 29 putative QTLs were detected in the three environments. These QTLs were distributed over 11 of the 12 chromosomes, accounted for 4.7-42.0% of the phenotypic variance in a trait, and showed different types of gene action. Among these 29 QTLs, 4 were detected in all three environments, 10 in two environments, and 15 in only a single environment. The two California environments were most similar, sharing 11/25 (44%) QTLs, while the Israel environment was quite different, sharing 7/20 (35%) and 5/26 (19%) QTLs with the respective California environments. One major goal of QTL mapping is to predict, with maximum accuracy, which individuals will produce progeny showing particular phenotypes. Traditionally, the phenotype of an individual alone has been used to predict the phenotype of its progeny. Our results suggested that, for a trait with low heritability (soluble solids), the phenotype of F3 progeny could be predicted more accurately from the genotype of the F2 parent at QTLs than from the phenotype of the F2 individual. For a trait with intermediate heritability (fruit pH), QTL genotype and observed phenotype were about equally effective at predicting progeny phenotype. For a trait with high heritability (mass per fruit), knowing the QTL genotype of an individual added little if any predictive value, to simply knowing the phenotype. The QTLs mapped in the L. esculentum X L. cheesmanii F2 appear to be at similar locations to many of those mapped in a previous cross with a different wild tomato (L. chmielewskii).(ABSTRACT TRUNCATED AT 400 WORDS)     

Genotype by environment interactions for fitness in hybrid genotypes of Avena barbata

We examined genotype (G) by environment (E) interactions for fitness in mesic and xeric ecotypes of the self-fertilizing annual grass, Avena barbata and their recombinant inbred hybrid progeny. Fitness was assayed (1) in experimental water and nutrient treatments in the greenhouse and (2) in common gardens in each ecotype's native habitat. G x E interactions were significant in the greenhouse. Nevertheless, the same recombinant genotypes tended to have high fitness across all water and nutrient treatments. G x E interactions were less pronounced in the field, and were driven by the contrast between the uniformly low survivorship at the mesic site in 2004 and genetic variation in fitness at the other years/site combinations. Moreover, the mesic ecotype consistently outperformed the xeric in both field and greenhouse. Several of the recombinant genotypes outperformed the parents in the novel greenhouse treatments, but these genotypes did not outperform the mesic parent in field trials. Indeed, it is only in the comparison between field and greenhouse environments that there was a noticeable change in the identity of the most-fit genotype. The results provide evidence that hybridization can create genotypes that are better adapted to newer environments such as those imposed in our greenhouse experiments.     

Use of the additive main effects and multiplicative interaction model in QTL mapping for adaptation in barley

The additive main effects and multiplicative interaction (AMMI) model has emerged as a powerful analytical tool for genotype x environment studies. The objective of the present study was to assess its value in quantitative trait locus (QTL) mapping. This was done through the analysis of a large two-way table of genotype-by-environment data of barley (Hordeum vulgare L.) grain yields, where the genotypes constituted a genetic population suitable for mapping studies. Grain yield data of 150 doubled haploid lines derived from the Steptoe x Morex cross, and the two parental lines, were taken by the North American Barley Genome Mapping Project (NABGMP) at 16 environments throughout the barley production areas of the USA and Canada. Four regions of the genome were responsible for most of the differential genotypic expression across environments. They accounted for approximately 50% of the genotypic main effect and 30% of the genotype x environment interaction (GE) sums of squares. The magnitude and sign of AMMI scores for genotypes and sites facilitate inferences about specific interactions. The parallel use of classification (cluster analysis of environments) and ordination (principal component analysis of GE matrix) techniques allowed most of the variation present in the genotype x environment matrix to be summarized in just a few dimensions, specifically four QTLs showing differential adaptation to four clusters of environments. Thus, AMMI genotypic scores, when the genotypes constituted a population suitable for QTL mapping, could provide an adequate way of resolving the magnitude and nature of QTL x environment interactions.Ignacio Romagosa was on sabbatical leave from the University of Lleida and the Institut de Recerca i Tecnologia Agroalimentàries, Lleida, Spain, when this study was conducted     

Apolipoprotein E gene polymorphism,hypercholesterolemia and glomerular filtration rate in type 2 diabetic subjects: A 9-year follow-up study

OBJECTIVE: To study the association between apolipoprotein E (apoE) genotype and the rate of decline in glomerular filtration rate (GFR) in type 2 diabetic patients in a 9-year prospective study. METHODS: GFR was determined in 84 type 2 diabetic patients by plasma clearance of (51)Cr-EDTA at baseline and after 9 years of follow-up. ApoE genotypes were determined by polymerase chain reaction and restriction enzyme HHAI digestion and designated as epsilon4 allele group (apoE4/2, 4/3 and 4/4 genotypes; n = 20) and non-epsilon4 allele group (apoE3/3 and E3/2 genotypes; n = 64). We focused our analysis on those patients who were more likely to progress to diabetic renal disease, i.e. whose GFR fell more than expected in the normal course of ageing [1 ml x min(-1) x (1.73 m(2))(-1) per year]. RESULTS: In the whole population, the decline in the GFR did not differ statistically significantly between the apoE genotype groups [p = 0.65 with analysis of variance for repeated variables (RANOVA) for interaction between apoE genotype group and time point]. However, among patients whose GFR changed more than 9 ml x min(-1) x (1.73 m(2))(-1), GFR showed a statistically significantly greater decline in the epsilon4 allele group (n = 11) than in the non-epsilon4 allele group (n = 43) [from 116 +/- 36 to 80 +/- 29 ml x min(-1) x (1.73 m(2))(-1) vs. from 119 +/- 20 to 96 +/- 18 ml x min(-1) x (1.73 m(2))(-1); p = 0.005 with RANOVA]. CONCLUSION: ApoE allele epsilon4 may speed up the rate of decline of the GFR in patients with progressive diabetic renal disease.     

AMMI adjustment for statistical analysis of an international wheat yield trial

Summary Multilocation trials are important for the CIMMYT Bread Wheat Program in producing high-yielding, adapted lines for a wide range of environments. This study investigated procedures for improving predictive success of a yield trial, grouping environments and genotypes into homogeneous subsets, and determining the yield stability of 18 CIMMYT bread wheats evaluated at 25 locations. Additive Main effects and Multiplicative Interaction (AMMI) analysis gave more precise estimates of genotypic yields within locations than means across replicates. This precision facilitated formation by cluster analysis of more cohesive groups of genotypes and locations for biological interpretation of interactions than occurred with unadjusted means. Locations were clustered into two subsets for which genotypes with positive interactions manifested in high, stable yields were identified. The analyses highlighted superior selections with both broad and specific adaptation.     

Alternative partitioning of the genotype-by-environment interaction

Summary Alternative methods for partitioning the genotype-by-environment interaction, for an arbitrary number of genotypes or environments, were examined. Partitioning of the interaction is important in order to determine the nature of the interaction. Two methods of partitioning were examined; both separated the interaction into two types: (1) due to heterogeneous variances or (2) due to imperfect correlations. Method 1 was based on heterogeneity among environments in the scaling of differences among genotypes. Method 2 was based on heterogeneity among genotypes in the scaling of differences among environments. Any remaining interaction arises from deviations from the perfect positive correlation of genotypic rankings among environments (Method 1) or of environmental rankings among genotypes (Method 2). Method 1 is more appropriate for random genotypes that are to be tested in either fixed or random environments. With Method 1, the interactions that arise mainly from heterogeneity of genotypic scaling among environments are generally unimportant. However, if environments are fixed and interactions are mainly due to imperfect correlations of rankings, specialized lines may be indicated for each environment. Method 2 is more useful in evaluating fixed genotypes for sensitivity to random environments. A partitioning of the interaction into that due to the type of interaction within each genotype was shown to be useful in that situation.Journal Paper No. 123737 of the Purdue University Agricultural Experiment Station     

Stability of Sweet Potato Cultivars to Alternaria Leaf and Stem Blight Disease

Alternaria leaf petiole and stem blight is an economically important disease of sweet potato ( Ipomoea batatus L.) in tropical and sub-tropical environments. Published research on cultivar resistance to the sweet potato disease is limited. To evaluate cultivar reaction and stability to the disease, multi-location and replicated experiments were established in 12 environments in Uganda. Disease severity (area under disease progress curves – AUDPC), and cultivar root yield were also assessed. Significant differences (P < 0.001) in AUDPC were detected among cultivars. Mean AUDPC ranged from 46.3 (Araka Red) to 78.4 (New Kawogo) across locations and seasons and the genotypes Araka Red and Tanzania had the lowest disease values. The location and season effects accounted for 67.1% and 7.5% of the total variance of AUDPC recorded among cultivars. The ranking of cultivars based on predicted AUDPC from Additive Main Effect and Multiplicative Interactive model (AMMI) showed that the NASPOT 1, the susceptible check, and New Kawogo were most susceptible to the disease in 11 of the 12 environments. Low and stable disease was consistently recorded and predicted on NASPOT 3 and the landrace cultivars Tanzania, Dimbuca, and Araka Red across environments. These results suggest that landrace cultivars had relative stability to the disease and wide adaptation across environments. These results suggest that AMMI statistical model and other multivariate techniques can be utilized for prediction of Alternaria disease stability in these locations.     

Seedling and adult stage resistance to net form of net blotch (NFNB) in spring barley and stability of adult stage resistance to NFNB in Morocco

This study was conducted to identify stable resistance to net form of net blotch (NFNB) in spring barley in Moroccan environments. Seedling resistance to NFNB was evaluated by inoculating 336 barley genotypes with two NFNB isolates LDNH04Ptt-19 and TD-10 in the greenhouse. These genotypes were evaluated for adult plant resistance to NFNB under seven environments in Morocco in 2015 and 2016. The disease severity was estimated at GS 77–87 on barley leaves using a double-digit scale. To investigate stability of resistance, 149 barley genotypes were subjected to AMMI analysis. At the seedling stage, differential responses of barley genotypes to different NFNB isolates were identified, whereas genotypes had variable stability to NFNB resistance at the adult stages. Five genotypes, AM-68, AM-95, AM-250, AM-267 and AM-322, were resistant to both NFNB isolates at the seedling stage. There were significant (p < .001) effects of genotype (G) and G × E interaction on NFNB severity for barley genotypes at the adult stage. The principal components, IPCA1 and IPCA2, accounted for 48.4% and 18.7% variation for NFNB severity, respectively. The AMMI stability values (ASVs) ranged from 0.01 to 15.5, and fifty-nine barley genotypes had stable responses (ASV ≤ 0.05) across all seven environments. Specifically, two stable genotypes, AM-187 and AM-244, had lower mean NFNB severities across all environments, suggesting a quantitative resistance in these genotypes. Divergent environmental responses of NFNB severity were measured in Sidi El Ayedi 2015 and Sidi Allal Tazi 2016, suggesting that these environments may be suitable to capture resistance to diverse pathotypes. These stable genotypes are valuable resources for introgression of both qualitative resistance and quantitative resistance to NFNB in future.     

An unusual genotype of Toxoplasma gondii is common in California sea otters (Enhydra lutris nereis) and is a cause of mortality

Toxoplasma gondii-associated meningoencephalitis is a significant disease of California sea otters (Enhydra lutris nereis), responsible for 16% of total mortality in fresh, beachcast carcasses. Toxoplasma gondii isolates were obtained from 35 California otters necropsied between 1998 and 2002. Based on multi-locus PCR-restriction fragment length polymorphism and DNA sequencing at conserved genes (18S rDNA, ITS-1) and polymorphic genes (B1, SAG1, SAG3 and GRA6), two distinct genotypes were identified: type II and a novel genotype, here called type x, that possessed distinct alleles at three of the four polymorphic loci sequenced. The majority (60%) of sea otter T. gondii infections were of genotype x, with the remaining 40% being of genotype II. No type I or III genotypes were identified. Epidemiological methods were used to examine the relationship between isolated T. gondii genotype(s) and spatial and demographic risk factors, such as otter stranding location and sex, as well as specific outcomes related to pathogenicity, such as severity of brain inflammation on histopathology and T. gondii-associated mortality. Differences were identified with respect to T. gondii genotype and sea otter sex and stranding location along the California coast. Localised spatial clustering was detected for both type II (centred within Monterey Bay) and x (centred near Morro Bay)-infected otters. The Morro Bay cluster of type x-infected otters overlaps previously reported high-risk areas for sea otter infection and mortality due to T. gondii. Nine of the 12 otters that had T. gondii-associated meningoencephalitis as a primary cause of death were infected with type x parasites.     

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice

Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.     

Longevity and metabolism in Drosophila melanogaster: genetic correlations between life span and age-specific metabolic rate in populations artificially selected for long life

We measured age-specific metabolic rates in 2861 individual Drosophila melanogaster adult males to determine how genetic variation in metabolism is related to life span. Using recombinant inbred (RI) lines derived from populations artificially selected for long life, resting metabolic rates were measured at 5, 16, 29, and 47 days posteclosion, while life spans were measured in the same genotypes in mixed-sex population cages and in single-sex vials. We observed much heritable variation between lines in age-specific metabolic rates, evidence for genotype x age interaction, and moderate to large heritabilities at all ages except the youngest. Four traits exhibit evidence of coordinate genetic control: day 16 and day 29 metabolic rates, life span in population cages, and life span in vials. Quantitative trait loci (QTL) for those traits map to the same locations on three major chromosomes, and additive genetic effects are all positively correlated. In contrast, metabolic rates at the youngest and oldest ages are unrelated to metabolic rates at other ages and to survival. We suggest that artificial selection for long life via delayed reproduction also selects for increased metabolism at intermediate ages. Contrary to predictions of the "rate of living" theory, we find no evidence that metabolic rate varies inversely with survival, at the level of either line means or additive effects of QTL.     

Molecular prevalence of different genotypes of Theileria orientalis detected from cattle and water buffaloes in Thailand

Here we report on an epidemiological study regarding the molecular prevalence of different genotypes of Theileria orientalis present among domestic cattle and water buffalo populations bred in Thailand. A phylogenetic analysis based on the parasitic gene encoding a major piroplasm surface protein revealed the presence of 5 genotypes (Types 1, 3, 5, 7, and N-3) in cattle and 7 genotypes (Types 1, 3, 4, 5, 7, N-2, and N-3) in water buffaloes. Types 4, 7, and N-3 of T. orientalis were reported for the first time in water buffaloes. The previously reported C and Thai types from Thailand clustered as types 7 and 6, respectively, in the present analysis. Great similarities were observed among nucleotide sequences of isolates of the same genotype from cattle and water buffaloes, and, therefore, water buffaloes were considered to serve as a reservoir for these genotypes of T. orientalis in Thailand. In conclusion, T. orientalis parasites circulating in Thailand are more diverse in their genetic characters than previously anticipated.