Search Results (95)

Nonlinear mixed-effects models (NLMMs) provide a flexible framework for modeling repeated-measures trajectories. However, how best to forecast future observations, especially at ages well beyond those represented in the data, remains relatively underexamined. In this study, we develop a Chapman–Richards NLMM with a spatial-power autocorrelation structure for irregularly spaced repeated measures and compare three forecasting strategies: (i) population-averaged forecasts based on the fixed-effects component only; (ii) subject-specific forecasts in which empirical best linear unbiased predictors (EBLUPs) of the random effects are obtained via a first-order Taylor series expansion with an iterative Newton–Raphson update, including the case of new progenies not used in model fitting; and (iii) forecasts that combine the population-averaged prediction with prior repeated measures through the fitted autocorrelation matrix. Forecast accuracy was assessed with progeny-level validation under fully held-out and partially observed scenarios, using root mean square prediction error (RMSPE) and mean absolute error (MAE), and was examined as a function of: (i) the number of available prior measures and (ii) the accuracy of the fixed-effects component of the NLMM. The methods were illustrated with repeated-measures data from hybrid spruce (Picea engelmannii Parry ex Engelmann × Picea glauca (Moench) Voss) progeny trials at three planting sites in British Columbia, Canada, with measurement ages from 2 to 42 years. Subject-specific forecasts had the lowest prediction errors when sufficient prior measures were available and were also the least affected by misspecification of the fixed-effects component. With only two prior measurements, autocorrelation-based forecasts had the lowest or tied-lowest observed errors, although differences among the three approaches were small. Using all measurements taken before age 42, subject-specific forecasts of height at age 42 achieved an RMSPE of 0.50 m. With only two prior measurements, the corresponding RMSPEs were approximately 1.31–1.33 m across the forecasting approaches. Although demonstrated with a single hybrid spruce dataset from three planting sites, the comparison is, in principle, applicable to other repeated-measures settings in which long-horizon predictions are required from short observation histories; broader applicability remains to be confirmed. Full article

The increasing stresses imposed on forests by climatic changes require agile and adaptive management, in which tree breeding plays a crucial role. Assessment of G×E interactions has been highlighted as an explicit source of information for targeted breeding for resilience and productivity via better coupling of the demands of genotypes and locally anticipated climatic changes. Commonly, the genetic effects are evaluated for morphometric traits, which are a cumulative representation of the past conditions. In this study, the variability of increment and its relation to weather fluctuations were addressed as a climate-sensitive functional trait. Parallel Scots pine (Pinus sylvestris) progeny trials representing hemiboreal conditions and a local productivity (edaphic) gradient in Lithuania were studied to evaluate G×E effects on increment, combining tree-ring analysis and quantitative genetics. Scots pine progenies showed low environmental sensitivity of radial increment, which, however, showed complex region-specific relationships with winter temperature and summer moisture regimes. Negligible genetic controls were estimated for the weather sensitivity of increment, yet the genetic controls manifested in response to the co-occurrence of meteorological extremes. The genetic control over increment showed nonlinear relationships with site productivity, being strongest under oligotrophic and eutrophic rather than extremely poor or mesotrophic site conditions. Site productivity showed marginal effects on climatic controls over heritability estimates, indicating weak environmental interactions. Hence, the observed relationships suggest some limited potential for targeted pine breeding based on local populations. Full article

Pinus kesiya var. langbianensis is a major commercial conifer in subtropical Yunnan, China, yet systematic genetic evaluation of its breeding populations remains scarce. We estimated genetic parameters for growth and stem form (SF) traits to support advanced-generation selection. In a progeny trial of 113 open-pollinated half-sib families established in 2013 at Pu’er, 2201 surviving trees were assessed at age 11 for height, diameter at breast height (DBH), stem volume, height to crown base (HCB), crown width, and an ordinal SF score. Variance components and breeding values (BVs) were estimated using linear mixed models, with a Bayesian threshold model as a sensitivity analysis for ordinal data. Family-mean heritabilities showed a gradient across growth traits (height 0.14, DBH 0.29, and volume 0.24). Stem volume had the highest genetic coefficient of variation (18.85%), the optimal selection target, whereas HCB lacked detectable genetic variance and SF was weakly controlled (0.09). Phenotypic and BV rankings diverged: although Yunjing Seed Orchard showed the highest phenotypic means, best linear unbiased prediction identified Jinggu Seed Orchard as contributing nine of the top ten families and 26 of the 35 elite individuals. A combined backward–forward strategy, ranking materials by volume BVs under a phenotypic threshold (SF ≥ 7), yielded predicted volume gains of 14.35% (family) and 15.01% (individual), providing a basis for second-cycle breeding pending multi-environment validation. Full article

The genetic parameters at 6, 9 and 12 years were studied in two progeny trials (one half-sib and one full-sib) of silver fir (Abies alba Mill.) in Romania, in order to establish an appropriate breeding strategy for advancing second-generation seed orchards. The half-sib trial (HS) consists of 60 open-pollinated families of plus trees from four first-generation seed orchards, while the full-sib trial (FS) consists of 51 half-diallel crosses of 11 plus trees from one seed orchard. Tree height and diameter were found to be under moderate to strong genetic control at both the family and individual levels. Total height showed a higher percentage of additive genetic variance than diameter in both types of progenies. Additive genetic variances increased with age for the diameter (from 12% to 36%), while for the total height, it decreased (from 76% to 35%). In the HS trial, family heritability was higher than individual heritability for both traits. The highest values of heritability were obtained for total height, both at the individual (0.76–0.35) and family levels (0.88–0.63). In FS progenies, the estimates of the narrow-sense individual heritability were lower than those at the family level and remained almost constant over time. The additive age-age genetic correlations and genetic correlations among growth traits were more stable and stronger in FS progeny than in HS progenies. Expected genetic gains were calculated at individual and family levels for different breeding strategies. The highest genetic gain will be obtained through selection of the best parents. Genetic gain slightly varied over age and for progeny tests. The level of genetic diversity, calculated for selected parents based on the breeding values, was high, while the inbreeding coefficient reduced. Combining the backward selection strategy with SSR analyses allows optimization for seed orchard design in order to mitigate inbreeding depression risks and enhance genetic diversity in the next breeding generation. Full article

Sitka spruce (Picea sitchensis (Bong.) Carr.) is among the most commercially important tree species in European and North American forestry, and genetic improvement programmes are therefore essential for promoting its productivity and sustainability. This research emphasises the significance of the breeding programmes. The primary objective of this study was to provide more reliable information on family selection for the improvement programme of Sitka spruce by accounting for competition and environmental heterogeneity effects. Analyses in the present study were carried out on historical inventory data of height (HT) and diameter at breast height (DBH) from a half-sib progeny trial of Sitka spruce in Ireland. Tree measurement data were collected at ages 6, 12, 15 and 20 years. A mixed linear model incorporating spatial and competition terms was applied to estimate genetic parameters of the Sitka spruce population. The direct genetic effects of each family on its own phenotypes and the competition effect on its neighbour’s phenotype were examined over time. The study demonstrated an analytical approach for assessing both genetic as well as environmental aspects of competition in a Sitka spruce progeny trial. The combined model integrating competition and spatial terms (model CS) improved model fit compared with the basic model, which only included the random effects of genetic and experimental design factors (model B), with an AIC difference of up to 3609 between them. Residual error obtained from model CS was usually smaller than from model B, with the greatest reduction of 85%. Furthermore, model CS generally improved the estimation of heritability for growth traits, by up to 241, when compared with model B. In addition, genetic differences in competitive ability among families were also observed. Families with favourable combinations of direct genetic and competitive breeding values were suggested for selection in subsequent cycles of the breeding programme, i.e., families with relatively high direct genetic breeding value but low and consistent competitive breeding value over time. This work develops a practical framework to inform future family selection for Sitka spruce improvement programmes. Full article

The bollworm/corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), is one of the most economically damaging crop pests in North America. Colonies of H. zea are notoriously difficult to maintain and frequently collapse in laboratory rearing. The persistent difficulty in maintaining healthy H. zea colonies has become a major obstacle to performing many research activities on the insect. To optimize colony maintenance, six populations were evaluated across three trials and six tests examining pupal maturity at diet removal, adult emergence synchrony, and cohort size at mating and reproduction. Females emerging from mature pupae produced more eggs than those from mid-aged (5–7 d) or young pupae (0–2 d). Synchronizing male and female emergence within one day yielded higher mating frequency, spermatophore transfer, and progeny, whereas a two-day difference reduced these metrics by 45–67%. Adult cohort size also influenced the outcomes, with ≥10 males and ≥10 females per cage enhancing reproductive success. Most matings occurred on nights 2–3, peaking within 2.5 h after lights off. Positive correlations were observed among mating frequency, spermatophore transfer, and progeny production. Overall, optimal performance was achieved by removing pupae only at maturity, synchronizing adult emergence within one day, and maintaining larger adult cohorts. These findings should establish key conditions to improve the mating success, reproduction, and laboratory rearing of H. zea. Full article

The conservation and genetic improvement of rare and endangered tree species are crucial for sustainable forest management. Liriodendron chinense, a relict species with limited distribution in China, exhibits high cross-compatibility with Liriodendron tulipifera, providing opportunities for interspecific hybrid breeding. In this study, 29 Liriodendron hybrids were established in a progeny trial plantation in Fujian Province, China, and subjected to multi-year evaluation of tree height, diameter at breast height (DBH), and individual stem volume. Significant differences (p < 0.01) among hybrids and hybrid × replicate interactions were detected for all traits across all assessment years, with individual stem volume showing the highest phenotypic coefficient of variation (35.30–40.56%). The mean annual increment in tree height increased during the early years, peaking at 1.50 m in the fourth year. Broad-sense and narrow-sense heritabilities for growth traits were consistently high (0.4073–0.7253 and 0.3410–0.6501, respectively), and the ratio of narrow-sense to broad-sense heritability ranged from 0.64 to 0.99, supporting the feasibility of early hybrid and individual selection. At a 10% selection intensity, hybrids No. 39, No. 59, and No. 74 were identified as elite, with selection based on individual stem volume providing the highest predictive accuracy and genetic gain (26.54–34.69%). Individual selection at a 1% intensity yielded genetic gains of 95.55–107.12% for stem volume. These results demonstrate substantial potential for early and efficient genetic improvement in Liriodendron hybrids, providing a theoretical foundation for the selection and deployment of elite hybrids and individuals in subtropical forest plantations. Full article

Wheat is among the most important staple crops worldwide; however, its yield and quality are severely threatened by stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). CH806 is a Thinopyrum intermedium-derived resistant breeding line developed in our laboratory that is highly resistant to the prevalent Chinese Pst races CYR32, CYR33, and CYR34 in field trials. A genetic population was developed by crossing CH806 with the susceptible cultivar Chuanmai 24. Phenotypic evaluation of the progeny under field conditions revealed segregation for stripe rust resistance in the F₂ generation. On the basis of the resistance phenotypes of the F₂ and F_2:3 populations, homozygous resistant and homozygous susceptible F₂ individuals were selected to construct resistant and susceptible DNA bulks, respectively, for genotyping using the Wheat 120K SNP array. Bulked segregant analysis indicated that the most significant SNPs were predominantly clustered on chromosome 4A. Subsequently, publicly available simple sequence repeat (SSR) markers on chromosome 4A and newly developed SSR markers within the candidate region that were enriched for polymorphic SNPs were used for linkage analysis. The resistance locus, temporarily designated YrCH806, was mapped to an interval flanked by markers Xwmc48/Xwmc89 and SSR4A-60, with genetic distances of 4.4 cM and 2.5 cM, respectively, corresponding to a physical position of 515.8–574.7 Mb on the wheat reference genome. The closest flanking marker, SSR4A-60, was successfully converted into a Kompetitive Allele-Specific PCR (KASP) marker. This high-throughput marker was subsequently utilized to screen a panel of wheat germplasms for the distribution of YrCH806. This study provides a novel resistance source and associated molecular markers for improving stripe rust resistance in wheat breeding programs. Full article

Sapium discolor is a valuable native species in southern China, valued for its rapid growth and vibrant foliage, and widely used in ecological restoration and landscaping. To identify superior propagation materials with fast growth and red leaves, regional open-pollinated progeny trials of 10 elite trees were established in Nanping, Sanming, and Zhangzhou (Fujian Province) in 2015. Growth (tree height and diameter) was monitored from 2015 to 2023, and leaf color (the proportion of red in leaf color) was assessed in 2024. The species showed early fast growth, with mean tree height and diameter at breast height (DBH) reaching 7.98 m and 9.99 cm at six years, then slowing. Family-level phenotypic variation was limited. ANOVA revealed highly significant differences among families for growth traits from 2016 onward and for leaf color in 2024. Broad-sense heritability was moderate for 2023 tree height (0.3839), DBH (0.1879), and 2024 leaf color (0.2102), with low narrow-sense heritability, indicating non-additive genetic effects. Clonal selection based on genotypic values achieved notable genetic gains, especially for growth. One superior clone combined improvements in height (13.1%), diameter (10.1%), and red coloration (8.3%). These results highlight the value of clonal selection and the need to consider genotype × environment interactions in breeding programs. Full article

Bread wheat variety development suited to organic farming conditions remains a major challenge mainly because of the high breeding costs involved and the few cultivars adapted to low-input systems. The present work explores whether early generation selection needs to take place under organic conditions for subsequent adaptation or whether conventional testing at an early stage could be adequate. A diverse set of crosses involving Greek landraces and commercial cultivars were developed and advanced by honeycomb pedigree selection under both organic and conventional environments. Subsequently, F₄ progenies and an upgraded landrace were evaluated over two years in neighboring organic and conventional trials. Both statistical and GGE biplot analyses revealed significant genotype × environment interactions. The results clearly indicate that early selection under organic conditions did not provide a consistent advantage for subsequent performance under organic management compared with conventional early selection. Genotypes derived from the Africa × Atheras cross consistently showed the highest and most stable yields across the two environments, irrespective of the early selection environment. These results indicate that genetic background and landrace-derived diversity are more important than the early selection environment for the expression of performance. A staged breeding strategy involving initial selection in conventional management followed by multi-environment testing in organic conditions can provide a cost-effective approach to developing resilient, high-yielding wheat cultivars suitable for organic farming systems, which are typically characterized by low-input management practices, and in tune with the EU targets for expanded organic farming. Full article

(1) Background: In the Sudano-Sahelian zone of Cameroon, which is affected by drought and forest decline, Vachellia nilotica leaves and seeds are fodder for livestock. (2) Methods: A provenance and progeny study on growth performance and heritability of V. nilotica was carried out to provide a reliable database for tree selection, improvement programs, and the creation of future forested areas in this region. Open-pollinated seeds from 120 mother trees (10 half-sib families per provenance) representing twelve provenances, 50–100 km apart, were used for a progeny trial near Maroua, the Far North region of Cameroon. The experimental design was a Fisher block. (3) Results: The results reveal significant differences among provenances only for the number of leaves, and the variability was marked by coefficients of variation ranging from 0.24−0.63. Narrow-sense heritability was measured, varying from 0.01 ± 0.009 to 0.74 ± 0.02, and genetic gain reached 21.83 at the selection intensity of 5% for the number of leaves per plant. The phenotypic coefficient of variation varied between 14% and 90%. Half-sib families were classified into three subgroups using hierarchical ascending classification, and provenances were grouped into five groups using principal component analysis. (4) Conclusions: These results could contribute to initiating tree selection, but more provenances, longer-term experiments, and molecular genetic testing are needed to complement these nursery-level observations. Full article

Scots pine (Pinus sylvestris L.) is a key species in boreal forests, valued both economically and ecologically, in part due to its associations with foliar fungi. These fungi influence plant health, nutrient cycling, and resistance induction. To investigate these interactions, we collected 1367 needle and shoot samples across 12 plus tree genotypes grown in 4 progeny trials in Estonia. Amplifying the ITS1-5.8S-ITS2 gene region, we obtained over 1.3 million high-quality sequences and identified 1261 fungal OTUs at the 98% species hypothesis level. Among the identified OTUs, 24.6% were classified as saprotrophic and 18.2% as pathogenic fungi. Fungal diversity varied significantly between tree tissue types, progeny trial locations, and plus tree origins. Fungal community composition varied across tissue types, with older needles tending to harbor more complex communities. Plus trees 593 and 267-1 progenies stood out for their high phyllosphere fungal richness, and genotype-specific correlations indicated associations between fungal diversity and tree height or needle retention, suggesting potential genotype-dependent effects on tree performance. Heritability of fungal diversity between ramets in seed orchard and progeny trees was found for saprotrophic fungi but was negligible for total fungi and pathogens, indicating strong influence of microclimate conditions. These findings underscore the potential value of integrating fungal community traits into Scots pine breeding programs. Considering microbial associations alongside traditional growth traits may help identify genotypes better suited for future forestry needs under changing environmental conditions. Additionally, Setomelanomma holmii is reported here as a new fungal pathogen on Scots pine shoots in Estonia. Full article

Soybeans are a primary source of plant-based protein, with seeds containing approximately 40% protein—a key quality trait. Selecting superior hybrid combinations and managing progeny effectively are crucial for developing high-protein soybean varieties. Using a recombinant inbred line population (RIL3613) derived from Dongnong L13 × Heihe 36 and its previously constructed high-density genetic linkage map, QTLs and QTL × environment interactions (QEIs) associated with seed protein content (SPC) were identified through the bi-parental population (BIP) model and multi-environment trials (MET) model in QTL IciMapping v4.2. Candidate genes were then predicted via sequence alignment and haplotype analysis between the parents. Finally, simulated breeding was conducted using the B4L function in the In Silico Breeding (ISB) module of the Blib platform to determine optimal breeding strategies across diverse environments. The analysis identified 19 QTLs associated with SPC and 97 QEIs linked to SPC. These QTLs collectively explained 84.442% of the phenotypic variance, with four QTLs exhibiting significant contributions. A key candidate gene, Glyma.12G231400, associated with soybean SPC, was predicted within the 38,995,090–39,293,825 bp interval on chromosome 12. Across 11 environments, three to six optimal breeding schemes were selected, all employing modified pedigree selection. These findings enhance our understanding of the genetic basis of soybean protein formation and provide technological support for molecular breeding for seed quality improvement. Full article

With over 1000 species of pests causing losses in both the quantity and quality of stored food, insect contamination poses significant challenges. The present study assesses the efficacy of the combination of λ-cyhalothrin and chlorantraniliprole against four key storage pests—Trogoderma granarium, Sitophilus oryzae, Rhyzopertha dominica, and Tribolium castaneum. Laboratory bioassays demonstrated species-dependent mortality, with S. oryzae and R. dominica suffering 100% mortality in several tested scenarios. A 90-day persistence trial revealed decreased efficacy over time, especially for T. granarium (32.0–71.4% at 0 days and 0.0–7.5% at 90 days) and T. castaneum (38.8–82.7% at 0 days and 0.0–12.7% at 90 days) vs. S. oryzae and R. dominica. Progeny production of S. oryzae and R. dominica was almost suppressed in persistence trials (0.4 individuals per vial and 1 individual per vial, respectively) after 30 days of storage at the dose of 5 mg/kg wheat. The results highlight the variability in insecticidal performance based on species, dose, exposure, and commodity type, emphasizing the need for tailored pest management strategies in the storage environment. Full article

Cassava brown streak disease (CBSD) remains the most severe threat to cassava production in the Great Lakes region and Southern Africa. Screening for virus resistance by subjecting cassava to high virus pressure in the epidemic zone (hotspots) is a common but lengthy process because of unpredictable and erratic virus infections requiring multiple seasons for disease evaluation. This study investigated the feasibility of graft-infections to provide a highly controlled infection process that is robust and reproducible to select and eliminate susceptible cassava at the early stages and to predict the resistance of adapted and economically valuable varieties. To achieve this, a collection of cassava germplasm from the Democratic Republic of Congo and a different set of breeding trials comprising two seed nurseries and one preliminary yield trial were established. The cassava varieties OBAMA and NAROCASS 1 infected with CBSD were planted one month after establishment of the main trials in a 50 m² plot to serve as the source of the infection and to provide scions to graft approximately 1 ha. Grafted plants were inspected for virus symptoms and additionally tested by RT-qPCR for sensitive detection of the viruses. The incidence and severity of CBSD and cassava mosaic disease (CMD) symptoms were scored at different stages of plant growth and fresh root yield determined at harvesting. The results from the field experiments proved that graft-infection with infected plants showed rapid symptom development in susceptible cassava plants allowing instant exclusion of those lines from the next breeding cycle. High heritability, with values ranging from 0.63 to 0.97, was further recorded for leaf and root symptoms, respectively. Indeed, only a few cassava progenies were selected while clones DSC260 and two species of M. glaziovii (Glaziovii20210005 and Glaziovii20210006) showed resistance to CBSD. Taken together, grafting scions from infected cassava is a highly efficient and cost-effective method to infect cassava with CBSD even under rugged field conditions. It replaces an erratic infection process with a controlled method to ensure precise screening and selection for virus resistance. The clones identified as resistant could serve as elite donors for introgression, facilitating the transfer of resistance to CBSD. Full article