Full-sib Progeny Research Articles

Early selection for rust resistance in eucalypt progenies and implications for other traits of interest in tree breeding

Planting of resistant clones is the main control strategy for rust caused by Austropuccinia psidii on eucalypts in Brazil. Phenotyping for resistance to rust is performed at the last stage of the breeding programme on genetic material preselected for growth and industrial traits, which therefore may include susceptible genotypes. An alternative way to increase the frequency of resistant individuals in the breeding population is to perform resistance phenotyping during the initial stages of the programme. However, the impact of this approach on other characteristics considered as priority in the selection of genetic material should be assessed. In this study, we evaluated whether early selection for resistance to rust influenced total diameter at breast height (DBH), height (TH), average annual increment (IMA) and basic wood density (BWD), which are important selection criteria in eucalypt breeding. For this, a total of 6 703 plants from 70 full-sib progenies of Eucalyptus grandis, E. urophylla and hybrids of these species were phenotyped for rust resistance before transplanting, under controlled conditions, and again at seven months after transplanting, under field conditions and natural infection. Subsequently, the breeding population was evaluated for BWD indirectly through pilodyn penetration at 24 months after planting, and for DBH, TH and MAI at 37 months. Considering the final phenotype, 25.3% individuals were classified as resistant and 74.7% were susceptible to rust. Comparative genetic analyses between resistant and susceptible individuals showed that selection for resistance, performed early, did not influence DBH, TH, MAI or BWD traits. Thus, the early selection of resistant genotypes speeds up the exclusion of susceptible genotypes, saving time and resources in the development of new commercial clones without interfering with other important traits for tree breeding.

Enviromic prediction enables the characterization and mapping of Eucalyptus globulus Labill breeding zones

Genotype-environment interaction is pervasive in forest genetics. Delineation of spatial breeding zones (BZs) is fundamental for accommodating genotype-environment interaction. Here we developed a BZ classification pipeline for the forest tree Eucalyptus globulus in 2 Australian regions based on phenotypic, genomic, and pedigree data, as well on a detailed environmental characterization (“envirotyping”) and spatial mapping of BZs. First, the factor analytic method was used to model additive genetic variance and site–site genetic correlations (rB) in stem volume across 48 trials of 126,467 full-sib progeny from 2 separate breeding programs. Thirty-three trials were envirotyped using 145 environmental variables (EVs), involving soil and landscape (71), climate (73), and management (1) EVs. Next, sparse partial least squares-discriminant analysis was used to identify EVs that were required to predict classification of sites into 5 non-exclusive BZ classes based on rB. Finally, these BZs were spatially mapped across the West Australian and “Green Triangle” commercial estates by enviromic prediction using EVs for 80 locations and 15 sets of observed climate data to represent temporal variation. The factor analytic model explained 85.9% of estimated additive variance. Our environmental classification system produced within-zone mean rB between 0.76 and 0.84, which improves upon the existing values of 0.62 for Western Australia and 0.67 for Green Triangle as regional BZs. The delineation of 5 BZ classes provides a powerful framework for increasing genetic gain by matching genotypes to current and predicted future environments.

Enviromic analysis for prediction of Eucalyptus globulus genotype-environment interaction and mapping of breeding zones

Genotype-environment interaction (GE) is pervasive in forest genetics and is a substantial cause of erosion in genetic gain. Delineation of spatial breeding zones (BZs) is fundamental for controlling GE. We developed a BZ classification pipeline for Eucalyptus globulus in 2 Australian regions based on phenotypic, genomic and pedigree data, as well as on a detailed environmental characterization (‘envirotyping’) and spatial mapping of BZs. First, the factor analytic method was used to model additive genetic variance and site-site correlations (rB) in stem volume across 48 trials of 126,467 full-sib progeny from 2 separate advanced-generation breeding programs. Single-step genomic BLUP (ssGBLUP) was used to create a joint relationship matrix combining both programs for factor analytic analysis. Thirty-three trials were envirotyped using 145 environmental variables (EVs), involving soil and landscape (71), climate (73), and management (1) EVs. Next, sparse partial least squares-discriminant analysis (sPLS-DA) was used to identify EVs that were required to predict classification of sites into 5 non-exclusive BZ classes on the basis of rB. These BZs were then spatially mapped across the West Australian (WA) and ‘Green Triangle’ (GT) commercial estates by enviromic prediction using EVs for 80 locations and 15 sets of observed climate data to represent temporal variation. Finally, stem volume breeding value accuracy and genetic gain from ssGBLUP across 40 trials were compared using the new enviromic BZ classification and the previous regional BZ classification. The FA model explained 85.9% of additive genetic variation. Our environmental classification system produced within-zone mean rB between 0.76 and 0.84, which improves upon the existing values of 0.62 for WA and 0.67 for GT as regional BZs. One to two sPLS-DA components were required for each BZ definition, with 5 to 8 EV’s per BZ. The enviromic BZ classification provided for more accurate breeding values and greater stem volume gain. This work raises highly relevant topics for discussion, including a) the drivers of GE in E. globulus, b) methods of collecting and curating environmental data for envirotyping with eucalypts, c) the advantages and challenges of adopting non-exclusive (i.e. overlapping) BZs, d) the need for developing a phenological system for eucalypts, e) accommodating temporal environmental variation in GE analysis, and f) breeding and improvement strategies for a changing climate.

Genetic control of growth and wood traits in Eucalyptus camaldulensis × E. urophylla and reciprocal hybrids

Eucalyptus camaldulensis (Ec) × E. urophylla (Eu) and reciprocal hybrid crosses were evaluated for growth and wood traits at four years at West Godavari Dt, Andhra Pradesh State located in Southern India, in relation to full and half sib progenies of pure E. camaldulensis maternal parents. Interspecific hybrid progenies had 16.6% higher average growth and 8% lower average wood basic density than pure species progeny. The interspecific hybrid progenies fibre properties viz., fibre length, fibre width, lumen diameter and fibre wall thickness were comparably higher than pure species progeny and check clones. The Ec × Eu crosses had comparable growth and wood basic density as the reciprocal hybrid progeny, but fibre length was 3.4% higher than the Eu × Ec hybrids, the values being statistically significant at p<.001 level. Analysis of variance of data was done using the 20th Edition of Genstat software (VSNi). Growth and fibre traits showed a positive relation but wood basic density showed a negative correlation (r = -0.94). There was a positive correspondence between the General Combining Ability (GCA) of pure E. camaldulensis maternal parents and their General Hybridizing Ability (GHA) for growth. The study showed that parents of Ec and Eu could be used to improve the growth and fibre traits in interspecific hybrids.

Estimation of Genetic Diversity between and within Biparental Clones and Full-Sib Families of the Chinese Pine Using SSR Markers

Quantifying the genetic diversity present in plant populations is crucial for the success of selection of elite plants and breeding programs. The population structure and partition of genetic variance within and between plant populations allows inferences about the distribution and extent of variation available in plant breeding populations. The Chinese pine (Pinus tabuliformis Carriere) is a native species that is ecologically and economically important to Northern China. Studying the genetic variation and partition of P. tabuliformis will be invaluable for its efficient utilization. In this study, we selected 21 pairs of SSR primers to estimate the genetic diversity of 35 clones from four populations and 216 progenies from 22 full-sib families of P. tabuliformis. Our results showed that P. tabuliformis was a typical outcrossing plant (FIS = −0.053/−0.165) containing moderately high genetic diversity (He = 0.542/0.605) both for the clone populations and the progenies produced by the clone crosses via controlled pollination. The genetic differentiation between the clones (FST = 0.076) was lower than that between the full-sib progenies (FST = 0.155). Such diverse FST may be promoted by different gene flows (Nm = 3.881/1.546) due to distinct pollination patterns. The clustering methods showed a lack of significant division of the clone populations, with a similar genetic admixture found for each of the clones. However, two groups were found between the full-sib families with genetic admixture between them. The analysis of molecular variance (AMOVA) showed that the most plentiful genetic variability exists between the cloned individuals (98%) as well as within the full-sib progenies (89%). Such distribution of genetic variation suggests rich internal variance and thus it is feasible to select the elite plants within each population or family. These results provide genetic materials and theoretical guidance for the selection and breeding of the Chinese pine.

Evaluation of Cocoa Full-Sib Progenies in Challenging Conditions in Cameroon

The improved vegetal material cultivated by cocoa farmers in Cameroon consists in full-sib progenies issued from pods harvested in bi-clonal seed gardens set up during the 1970s. Interviews of cocoa farmers revealed their general satisfaction with the yield level obtained from these progenies but also their disappointment with the high level of susceptibility to black pod disease, a disease caused by Phytophthora megakarya, which is a serious challenge for cocoa production in this country. In order to select new future varieties that would combine high yield and resistance to black pod disease, new progeny trial plots were set up from 2005, in research stations and on farm.
 23 cocoa full-sib progenies were assessed and compared to 3 control progenies. in a trial plot set up in 2005 in a research station located in the south western region of Cameroon. The cocoa trees were assessed during eight consecutive years of cocoa production. A large level of variation was observed among the progenies for mortality rate (ranging between 6 and 52%), annual potential yield (ranging between 151 and 1,808 kg/ha), annual actual yield (ranging between 114 and 1,159 kg/ha) and black pod disease incidence (ranging between 19 and 39,8%) caused by Phytophthora megakarya. Nine of the assessed full-sib progenies were identified as promising and the authors suggest how to confirm their performances before their release to farmers.

Cadmium Accumulation in Cacao Plants (Theobroma cacao L.) under Drought Stress

The objective of this study was to determine Cd accumulation under water-deficit conditions by young cacao plants. The study was conducted under greenhouse conditions. Two full-sib families (IMC67 × PA121 and SCA6 × PA121), obtained through controlled crosses, and an open pollinated half-sib seedling family of IMC67, widely used as rootstock in Colombia, were employed. Plants were grown in Cd-contaminated soil (0.356 mg kg−1) without external sources of the metal. They were subjected to water deficit by suspending irrigation for consecutive periods of 19 and 27 days (D19 and D27), followed by rehydration. Water stress reduced leaf water potential (Ψleaf) with values from −1.51 to −2.09 MPa, with full-sib family SCA6 × PA121 being the most tolerant to water deficit. Cd concentration was influenced by biomass reduction (observed in IMC67 × PA121 and SCA6 × PA121) and transpiration rate (evident in IMC67) caused by water deficit. Full-sib progenies IMC67 × PA121 and SCA6 × PA121 accumulated more Cd in the plants than open pollinated IMC67, with higher Cd accumulation in leaves. The translocation factor (TF) revealed that the aboveground organs of the progenies were enriched with Cd (TF > 4). Water deficit increased Cd translocation from roots to leaves in IMC67 × PA121 and IMC 67, while there were no significant changes in SCA6 × PA121. Full-sib family SCA6 × PA121 stood out as the most promising progenies due to their water-stress tolerance and Cd accumulation stability. This study introduces a discussion about the influence of water stress on Cd accumulation in Theobroma cacao.

Using Transferable Eucalypt Microsatellite Markers to Identify QTL for Resistance to Ceratocystis Wilt Disease in Eucalyptus pellita F. Muel. (Myrtales, Myrtaceae)

The deployment of Eucalyptus pellita trees that are resistant to Ceratocystis manginecans is essential for the commercial plantations and therefore the sustainability of forest industries in Southeast Asia that utilize this resource. Current screening procedures are time-consuming and expensive but could be expedited with the aid of marker-assisted selection and breeding. The identification of genotypes with resistance to the disease may be facilitated if microsatellite markers developed in other Eucalyptus species are transferable and can be linked to quantitative trait loci (QTL) for disease resistance. This possibility was tested in 111 full-sib progenies and their parents by genotyping with 49 microsatellite markers developed in other Eucalyptus species. Disease development was assessed after stem inoculation with C. manginecans isolate Am60C. The disease index (DI) varied from 0 to 20% of stem length. There was a continuous distribution of resistant and susceptible seedlings with 60% in the resistant category. Of the 30 acceptable markers, 17 (56%) defined two linkage groups (LG). In each LG, one QTL with a significant logarithm of odds (LODs > 13) was identified. The transferability of microsatellite markers developed in other Eucalyptus species facilitated the rapid identification of LGs and QTLs in E. pellita. To further refine the linkage map, the testing of more microsatellite markers and a larger population of progenies are required.

An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions.

Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non-inbred and unrelated individuals (F = 0) and inbred individuals (full-sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness-related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non-inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.

Optimising selection in full-sib progeny of the cashew

In Brazil, the productivity and quality of the peduncle and nut of the cashew have increased significantly due to the use of binomial hybridisation-cloning. In the present research, genetic parameters (variance components – individual REML) and genetic values (mean components – individual BLUP) were estimated in a test of full-sib segregating progenies, aiming at the selection of superior cashew progenies and individuals. A controlled-pollination, segregating population from the cashew genetic breeding program of Embrapa Agroindústria Tropical, comprising four different progenies, each represented by 48 full-sib (FS) individuals, were evaluated over six consecutive crops. The following traits were evaluated: nut yield, mean nut weight, reaction to Anacampsis phytomiella, and reaction to oidium (powdery mildew). The experimental design was of randomised blocks, with four replications and 12 plants per plot. The REML/BLUP geneticstatistical procedure was used to optimise the selection process. It seems reasonable to opt for a selection limit of 14 individuals with superior behaviour to comprise the recombination unit of the next cycle of recurrent selection using the remaining seeds from this breeding population. Plants 25 and 27 from the progeny identified as having the best performance (FS 13/3) for direct cloning were selected to comprise the local trial of the cashew genetic breeding program.

Full-sib progenies show greater genetic diversity than half-sib progenies in sour passion fruit: an approach by ssr markers.

Genetic variability is the most important parameter in plant breeding based on selection. There is a need for morpho-agronomic and molecular characterization of Passiflora species, to exploit their genetic resources more efficiently. No study has yet been carried out to compare half-sib and full-sib families in relation to the magnitude of the genetic variability obtained in them, and then to elucidate the advantages or disadvantages of each one. In the present study, SSR markers were used to evaluate the genetic structure and diversity of half-sib and full-sib progenies of sour passion fruit. Two full-sib progenies (PSA and PSB), and a half-sib progeny (PHS), together with their parents, were genotyped with a set of eight pairs of SSR markers. Discriminant Analysis of Principal Components (DAPC) and Structure software were used to study the genetic structure of the progenies. The results indicate that the half-sib progeny has lower genetic variability, although it has higher allele richness. By the AMOVA most of the genetic variability was found within the progenies. Three groups were clearly observed in the DAPC analysis, while two hypothetical groups (k = 2) were observed in the Bayesian approach. The PSB progeny showed a high genetic mixture between the PSA and PHS progenies. Lower genetic variability is found in half-sib progenies. The results obtained here allow us to suppose that the selection within full-sib progenies will possibly provide better estimates of genetic variance in sour passion fruit breeding programs, since they provide greater genetic diversity.

Cytogenetic Characterization and Metabolomic Differences of Full-Sib Progenies of Saccharum spp.

Sugarcane smut is a worldwide fungal disease. Disease resistance breeding is the most economical and effective measure to prevent and control sugarcane smut. The cytogenetic characteristics and metabolomic differences of sugarcane F1s are closely related to disease resistance. Zhongzhe 1 and G160 sugarcane from the same parents (ROC25 and Yunzhe89-7) were used; the plants were grown in accordance with the barrel method. When the seedlings had 4-5 leaves, genomic in situ hybridization (GISH) was performed; digoxigenin (DIG)-labeled female parental (ROC25)DNA and biotin-labeled male parental (Yunzhe89-7) DNA were used as probes, and the karyotypes of two hybrids were analyzed. The new sugarcane smut-resistant variety (Zhongzhe 1) and the susceptible variety (G160) derived from the same parent were analyzed via gas chromatography-mass spectrometry technology (GC-MS) to compare the metabolomic differences between them. GISH analysis revealed that the chromosome ploidy number of Zhongzhe 1 sugarcane and G160 sugarcane were 114 and 110, respectively. However, the two contain different numbers of chromosomes from the female (ROC25) and male (Yunzhe89-7) parents. Moreover, 258 significantly changed metabolites were identified in smut-resistant Zhongzhe 1, as compared with the smut-susceptible G160 sugarcane: 56 flavonoids, 52 phenolic acids, 30 lipids, 26 organic acids, 26 amino acids and derivatives, 19 nucleotides and derivatives, 5 alkaloids, 9 terpenoids, and 35 others. Multivariate statistical analysis revealed a distinct difference in metabolic pathways between Zhongzhe 1 sugarcane and G160, and both of these varieties had unique functional metabolites. Differences in chromosome composition may constitute the genetic basis for the difference in resistance to smut disease between Zhongzhe 1 sugarcane and G160 sugarcane, and a high accumulation of flavonoids, lipids, terpenoids and tannins may constitute the basis of resistance to smut disease for the Zhongzhe 1 variety.

Female flowers first: QTL mapping in eastern black walnut (Juglans nigra L.) identifies a dominant locus for heterodichogamy syntenic with that in Persian walnut (J. regia L.)

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia “Chandler” V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

Bias in sex ratios and polyandry rate in reproduction of Leptinotarsa decemlineata

The Colorado potato beetle (CPB, Leptinotarsa decemlineata Slechtd.) is an invasive pest with economic importance worldwide. Sex ratios during egg-hatching and a frequency of polyandry in single-female families were analysed to clarify the reproduction strategy of CPB, which was still known only in fragments. 1296 just hatching 1st instar CPB larvae were collected from 19 single-female families, of which 13 were random families collected from potato fields and 6 were families produced by laboratory farming of naturally fertilised females. All larvae were analysed to detect a sex using a qPCR-based method and to detect polymorphisms in genotypes of 9 microsatellite (SSR) markers. The bias in sex ratio in favour of females was confirmed using linear mixed-effects model in both experimental groups of families: field collections (F = 36.39; P = 0.0001) and laboratory farming (F = 13.74; P = 0.0139). The analysis of diversity in microsatellites proved the polyandry in all progenies as 73% of analysed segregation patterns did not match with the patterns expected for full-sib progenies; on average per locus, 46% of allelic and 49.7% of genotype ratios showed irregular segregation. Both findings contribute toward understanding CPB success rate as an invasive species, as the preferential bearing of females with polyandry has a great potential to keep fitness of progenies, to maintain and operate population diversity, and to accelerate the reproduction of the pest.

Variation of Chromosome Composition in a Full-Sib Population Derived From 2x × 3x Interploidy Cross of Populus.

Interploidy cross commonly results in complex chromosome number and structural variations. In our previous study, a progeny with segregated ploidy levels was produced by an interploidy cross between diploid female parent Populus tomentosa × Populus bolleana clone TB03 and triploid male parent Populus alba × Populus berolinensis ‘Yinzhong’. However, the chromosome compositions of aneuploid genotypes in the progeny were still unclear. In the present study, a microsatellite DNA allele counting–peak ratios (MAC-PR) method was employed to analyze allelic configurations of each genotype to clarify their chromosome compositions, while 45S rDNA fluorescence in situ hybridization (FISH) analysis was used to reveal the mechanism of chromosome number variation. Based on the MAC-PR analysis of 47 polymorphic simple sequence repeat (SSR) markers distributed across all 19 chromosomes of Populus, both chromosomal number and structural variations were detected for the progeny. In the progeny, 26 hypo-triploids, 1 hyper-triploid, 16 hypo-tetraploids, 10 tetraploids, and 5 hyper-tetraploids were found. A total of 13 putative structural variation events (duplications and/or deletions) were detected in 12 genotypes, involved in chromosomes 3, 6, 7, 14, 15, 16, and 18. The 46.2% (six events) structural variation events occurred on chromosome 6, suggesting that there probably is a chromosome breakpoint near the SSR loci of chromosome 6. Based on calculation of the allelic information, the transmission of paternal heterozygosity in the hypo-triploids, hyper-triploid, hypo-tetraploids, tetraploids, and hyper-tetraploids were 0.748, 0.887, 0.830, 0.833, and 0.836, respectively, indicating that the viable pollen gains of the male parent ‘Yinzhong’ were able to transmit high heterozygosity to progeny. Furthermore, 45S rDNA–FISH analysis showed that specific-chromosome segregation feature during meiosis and chromosome appointment in normal and fused daughter nuclei of telophase II of ‘Yinzhong,’ which explained that the formation of aneuploids and tetraploids in the progeny could be attributed to imbalanced meiotic chromosomal segregation and division restitution of ‘Yinzhong,’ The data of chromosomal composition and structural variation of each aneuploid in the full-sib progeny of TB03 × ‘Yinzhong’ lays a foundation for analyzing mechanisms of trait variation relying on chromosome or gene dosages in Populus.

Genetic-molecular characterization in guava full-sib progeny

Brazil is one of the world’s largest producers of guava (Psidium guajava L.), a very promising fruit in the northern region of the state of Rio de Janeiro. Despite this, no guava cultivar has been developed for the region. Thus, this study proposed to examine a population of guava full sibs using microsatellite markers and to identify which genotypes are the most divergent for future crosses, to select cultivars better adapted to the soil and climatic conditions of northern Rio Janeiro. Ninety-six superior genotypes were selected according to their agronomic traits, which were characterized using 45 microsatellite markers. The genetic distance between the analyzed genotypes, their clustering pattern and the genetic structure of the population were estimated. Hierarchical cluster analysis by the neighbor joining method indicated the formation of three distinct groups. The use of molecular information revealed the existence of moderate genetic variability between the genotypes of the full-sib families. Bayesian analysis separated the genotypes into only two groups, as the individuals shared most of the analyzed genomic regions. The most genetically divergent guava genotypes, that is, those allocated to different groups, such as genotypes 5 and 85, should be recommended for future crosses to obtain segregating populations, thus giving continuity to the guava breeding program.

Estimating of Additive, Dominance, and Epistatic Genetic Variance in Eucalypt Hybrid Population

Abstract Additive, dominance and epistasis genetic variances were estimated from analysis of a clonally replicated full-sib progeny test grown in the Republic of Congo. Phenotypic variance components were estimated for ages 4 through 25 months for growth and at ages 8 and 18 months for ecophysiological traits. The estimation of genetics effects was derived from the individual mixed model. Genetic structure was incorporated into variances and covariance’s effects based on markers information. The detected genetic effects of epistasis are significant in some traits. This study shows that epistasis variance can be non-zero and contribute significantly to the genetic variability of growth and ecophysiological traits. We conclude that the epistatic effect for quantitative traits may exist, but estimates may not be obtained, either because the models used are inappropriate or because the epistasis variance is too small relative to other components of the genetic variance to be estimated.

Rootstock-Mediated Genetic Variance in Cadmium Uptake by Juvenile Cacao (Theobroma cacao L.) Genotypes, and Its Effect on Growth and Physiology.

Grafting typically offers a shortcut to breed tree orchards throughout a multidimensional space of traits. Despite an overwhelming spectrum of rootstock-mediated effects on scion traits observed across several species, the exact nature and mechanisms underlying the rootstock-mediated effects on scion traits in cacao (Theobroma cacao L.) plants often remain overlooked. Therefore, we aimed to explicitly quantify rootstock-mediated genetic contributions in recombinant juvenile cacao plants across target traits, specifically cadmium (Cd) uptake, and its correlation with growth and physiological traits. Content of chloroplast pigments, fluorescence of chlorophyll a, leaf gas exchange, nutrient uptake, and plant biomass were examined across ungrafted saplings and target rootstock × scion combinations in soils with contrasting levels of Cd. This panel considered a total of 320 progenies from open-pollinated half-sib families and reciprocal full-sib progenies (derived from controlled crosses between the reference genotypes IMC67 and PA121). Both family types were used as rootstocks in grafts with two commercial clones (ICS95 and CCN51) commonly grown in Colombia. A pedigree-based best linear unbiased prediction (A-BLUP) mixed model was implemented to quantify rootstock-mediated narrow-sense heritability (h2) for target traits. A Cd effect measured on rootstocks before grafting was observed in plant biomass, nutrient uptake, and content of chloroplast pigments. After grafting, damage to the Photosystem II (PSII) was also evident in some rootstock × scion combinations. Differences in the specific combining ability for Cd uptake were mostly detected in ungrafted rootstocks, or 2 months after grafting with the clonal CCN51 scion. Moderate rootstock effects (h2> 0.1) were detected before grafting for five growth traits, four nutrient uptake properties, and chlorophylls and carotenoids content (h2 = 0.19, 95% CI 0.05–0.61, r = 0.7). Such rootstock effects faded (h2< 0.1) when rootstock genotypes were examined in soils without Cd, or 4 months after grafting. These results suggest a pervasive genetic conflict between the rootstock and the scion genotypes, involving the triple rootstock × scion × soil interaction when it refers to Cd and nutrient uptake, early growth, and photosynthetic process in juvenile cacao plants. Overall, deepening on these findings will harness early breeding schemes of cacao rootstock genotypes compatible with commercial clonal scions and adapted to soils enriched with toxic levels of Cd.

Theobroma grandiflorum breeding optimization based on repeatability, stability and adaptability information

The cultivation of Theobroma grandiflorum in the Brazilian Amazon is mainly conducted by family farmers who use a range of different management strategies. Thus, breeding programs of the species must address the challenge of developing cultivars that are adapted and stable in a variety of cultivation environments. In this context, this study aimed to estimate the optimum number of harvests for genetic selection of T. grandiflorum progenies and identify the most promising ones in terms of productivity, stability, and adaptability. The trials were implemented in three environments, using a randomized complete block design, with 25 full-sib progenies, five replications, and three plants per plot. The traits mean number of fruits/plant, mean fruit production/plant, and rate of infection with witches’ broom (Moniliophthora perniciosa) were evaluated over 11 harvests. The Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) procedure was used to estimate genetic parameters and predict genetic values, which were then applied to assess stability and adaptability. The results show that there is genetic variability among the studied T. grandiflorum progenies and that accurate genetic selection aiming at recombination and recommendation is effective after three and eleven harvests, respectively. Six progenies were selected that met the requirements for productivity, stability, and adaptability to different cultivation environments. These results can be used to optimize and advance T. grandiflorum breeding programs.

Heterosis for Biomass-Related Traits in Interspecific Triploid Hybrids of Willow (Salix spp.)

Species hybridization is key for the improvement of shrub willow (Salix spp.) bioenergy crops because hybrids often display heterosis for yield. The development of high-yielding genotypes requires numerous broad attempts at hybridization followed by field evaluation and selection for stable performance. Selection of improved shrub willow varieties for use as a bioenergy crop involves evaluation of full-sib progeny in family-based selection trials. Improving the accuracy of evaluation through the use of components of yield would greatly improve the efficiency of selection. Heterosis for biomass yield in intra- and interspecific F1 and F2 shrub willow crosses, made between Salix sections and ploidy, was examined by utilizing a suite of morphological, physiological, and chemical composition traits collected over the course of 12 weeks in the greenhouse and over 3 years in the field. Triploid families generated from diploid S. viminalis and tetraploid S. miyabeana displayed the greatest levels of heterosis for harvestable biomass and biomass-related growth traits in the greenhouse and in the field. While intraspecific S. purpurea diploids exhibited low levels of heterosis for these traits, interspecific diploids produced moderate levels of heterosis in greenhouse experiments. Differences between greenhouse and field trial results can largely be explained by pest damage, which negatively impacted interspecific diploids. Heterosis for the traits that form the basis for biomass yield, including stem growth, foliar, and physiological traits, was quantified, and family-level differences are discussed.