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Genomic Selection (GS) in tree breeding optimizes genetic gains by leveraging genomic data to enable early selection of seedlings without phenotypic data reducing breeding cycle and increasing selection intensity. Traditional assessments of the potential of GS in forest trees have typically focused on model performance using cross-validation within the same generation but evaluating effectively realized predictive ability (RPA) across generations is crucial. This study estimated RPAs for volume growth (VOL), wood density (WD), and pulp yield (PY) across four generations breeding of Eucalyptus grandis. The training set spanned three generations, including 34,461 trees with three-year growth data, 6,014 trees with wood quality trait data, and 1,918 trees with 12,695 SNPs (single nucleotide polymorphisms) data. Employing single-step genomic BLUP, we compared the genomic predictions of breeding values (GEBVs) for 1,153 fourth-generation full-sib seedlings in the greenhouse with their later-collected phenotypic estimated breeding values (EBVs) at age three years. RPAs were estimated using three GS targets (individual trees, trees within families, and families), two selection criteria (single- and multiple-trait), and training populations of either all 1,918 genotyped trees or the 67 direct ancestors of the selection candidates. RPAs were higher for wood quality traits (0.33 to 0.59) compared to VOL (0.14 to 0.19) and improved for wood traits (0.42 to 0.75) but not for VOL when trained only with direct ancestors, highlighting the challenges in accurately predicting growth traits. GS was more effective at excluding bottom-ranked candidates than selecting top-ranked ones. The between-family GS approach outperformed individual-tree selection for VOL (0.11 to 0.16) and PY (0.72 to 0.75), but not for WD (0.43 vs. 0.42). Furthermore, higher levels of relatedness and lower genotype by environment (G × E) interaction between training and testing populations enhanced RPAs for VOL (0.39). In summary, despite limited effectiveness in ranking top VOL individuals, GS effectively identified low-performing individuals and families. These multi-generational findings underscore GS's potential in tree breeding, stressing the importance of considering relatedness and G × E interaction for optimal performance. [ABSTRACT FROM AUTHOR]

Introduction: The coconut tree crop (Cocos nucifera L.) provides vital resources for millions of people worldwide. Coconut germplasm is largely classified into 'Tall' (Typica) and 'Dwarf' (Nana) types. While Tall coconuts are outcrossing, stress tolerant, and late flowering, Dwarf coconuts are inbred and flower early with a high rate of bunch emission. Precocity determines the earlier production of a plantation and facilitates management and harvest. Methods: A unique outbred F2 population was used, generated by intercrossing F1 hybrids between Brazilian Green Dwarf from Jiqui (BGDJ) and West African Tall (WAT) cultivars. Single-nucleotide polymorphism (SNP) markers fixed for alternative alleles in the two varieties, segregating in an F2 configuration, were used to build a high-density linkage map with ~3,000 SNPs, anchored to the existing chromosome-level genome assemblies, and a quantitative trait locus (QTL) mapping analysis was carried out. Results: The linkage map established the chromosome numbering correspondence between the two reference genome versions and the relationship between recombination rate, physical distance, and gene density in the coconut genomes. Leveraging the strong segregation for precocity inherited from the Dwarf cultivar in the F2, a major effect QTL with incomplete dominance was mapped for flowering time. FLOWERING LOCUS T (FT) gene homologs of coconut previously described as putatively involved in flowering time by alternative splice variant analysis were colocalized within a ~200-kb window of the major effect QTL [logarithm of the odds (LOD) = 11.86]. Discussion: Our work provides strong phenotype-based evidence for the role of the FT locus as the putative underlying functional variant for the flowering time difference between Dwarf and Tall coconuts. Major effect QTLs were also detected for developmental traits of the palm, plausibly suggesting pleiotropism of the FT locus for other precocity traits. Haplotypes of the two SNPs flanking the flowering time QTL inherited from the Dwarf parent BGDJ caused a reduction in the time to flower of approximately 400 days. These SNPs could be used for high-throughput marker-assisted selection of early-flowering and higher-productivity recombinant lines, providing innovative genetic material to the coconut industry. [ABSTRACT FROM AUTHOR]

Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenanceprogeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positivelywith narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed. [ABSTRACT FROM AUTHOR]

To identify stable and productive Eucalyptus urophylla S.T. Blake families across diverse climate zones in Brazil, we evaluated growth and survival of 322 open-pollinated families derived from 13 genetically improved seed sources in 10 trials across the country. Survival and growth data were analyzed using linear mixed models and REML/BLUP. Survival ranged from 51% to 92%, and the mean annual increment varied from 19 to 46 [m.sup.3] x [ha.sup-1] x [year.sup.-1]. Although planted in suitable climatic zones, some trials had low survival and (or) productivity. Conversely, the highest productivity was recorded in a zone considered to be of low suitability. These results show the importance of assessing the climatic requirements of eucalypts beyond those determined from analyses of their natural distribution, especially when testing already improved seed sources. A number of productive and stable families were identified based on analysis of the interaction between genotype and environment, and from these, 144 individuals were selected and had their genetic diversity estimated using 19 microsatellite DNA markers. The genetic diversity of these selected trees was equivalent to that observed in previous studies of natural populations of E. urophylla, indicating that breeding programs of E. urophylla in Brazil still retain high levels of diversity for sustainable genetic gains.Key words: genotype-environment interaction, productivity and stability, family selection, genetic diversity, abiotic and biotic stress.De facon a identifier des familles d'Eucalyptus urophylla S.T. Blake stables et productives pour diverses zones climatiques du Bresil, nous avons evalue la croissance et la survie de 322 familles a pollinisation libre provenant de 13 sources de semences genetiquement ameliorees deployees dans 10 stations reparties dans tout le pays. Les donnees de survie et de croissance ont ete analysees a l'aide de modeles lineaires mixtes et d'approches par le maximum de vraisemblance restreinte et par le meilleur predicteur lineaire non biaise. La survie variait de 51 a 92 % et l'accroissement annuel moyen de 19 a 46 [m.sup.3]x[ha.sup.-1]x[an.sup.-1]. Bien que les familles aient ete plantees dans des zones climatiques favorables, la survie ou la productivite etaient faibles dans certaines stations. A l'inverse, la plus forte productivite a ete observee dans une zone consideree comme etant peu favorable. Ces resultats montrent l'importance d'evaluer les exigences climatiques des eucalyptus au-dela de celles qui sont determinees par l'analyse de leur repartition naturelle, surtout lorsqu'on teste des sources de semences deja ameliorees. Un certain nombre de familles productives et stables ont ete identifiees sur la base de l'analyse de l'interaction entre le genotype et l'environnement. Parmi celles-ci, 144 individus ont ete selectionnes pour estimer leur diversite genetique a l'aide de 19 marqueurs d'ADN microsatellites. La diversite genetique de ces arbres selectionnes etait equivalente a celle observee lors d'etudes precedentes portant sur les populations naturelles d'E. urophylla, ce qui indique que les programmes de selection d'E. urophylla au Bresil conservent toujours des niveaux eleves de diversite pour des gains genetiques durables. [Traduit par la Redaction]Mots-cles : interaction entre la genetique et l'environnement, productivite et stabilite, selection de familles, diversite genetique, stress biotiques et abiotiques., IntroductionEucalyptus urophylla S.T. Blake (Timor mountain gum) is one of the most economically important forest trees in the world, planted both as a pure species and in hybrid combinations (Denison [...]

Introduction: Genomic selection (GS) experiments in forest trees have largely reported estimates of predictive abilities from cross-validation among individuals in the same breeding generation. In such conditions, no effects of recombination, selection, drift, and environmental changes are accounted for. Here, we assessed the effectively realized predictive ability (RPA) for volume growth at harvest age by GS across generations in an operational reciprocal recurrent selection (RRS) program of hybrid Eucalyptus. Methods: Genomic best linear unbiased prediction with additive (GBLUP_G), additive plus dominance (GBLUP_G+D), and additive single-step (HBLUP) models were trained with different combinations of growth data of hybrids and pure species individuals (N = 17,462) of the G1 generation, 1,944 of which were genotyped with ~16,000 SNPs from SNP arrays. The hybrid G2 progeny trial (HPT267) was the GS target, with 1,400 selection candidates, 197 of which were genotyped still at the seedling stage, and genomically predicted for their breeding and genotypic values at the operational harvest age (6 years). Seedlings were then grown to harvest and measured, and their pedigree-based breeding and genotypic values were compared to their originally predicted genomic counterparts. Results: Genomic RPAs ≥0.80 were obtained as the genetic relatedness between G1 and G2 increased, especially when the direct parents of selection candidates were used in training. GBLUP_G+D reached RPAs ≥0.70 only when hybrid or pure species data of G1 were included in training. HBLUP was only marginally better than GBLUP. Correlations ≥0.80 were obtained between pedigree and genomic individual ranks. Rank coincidence of the top 2.5% selections was the highest for GBLUP_G (45% to 60%) compared to GBLUP_G+D. To advance the pure species RRS populations, GS models were best when trained on pure species than hybrid data, and HBLUP yielded ~20% higher predictive abilities than GBLUP, but was not better than ABLUP for ungenotyped trees. Discussion: We demonstrate that genomic data effectively enable accurate ranking of eucalypt hybrid seedlings for their yet-to-be observed volume growth at harvest age. Our results support a two-stage GS approach involving family selection by average genomic breeding value, followed by within-top-families individual GS, significantly increasing selection intensity, optimizing genotyping costs, and accelerating RRS breeding. [ABSTRACT FROM AUTHOR]

Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world's planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complementarity are planted worldwide, but little is known about their actual genomic ancestry. In this study we examined a set of 440 trees of 16 different Eucalyptus species and 44 interspecific hybrids of multi-species origin conserved in germplasm banks in Brazil. We used genome-wide SNP data to evaluate the agreement between the alleged phylogenetic classification of species and provenances as registered in their historical records, and their observed genetic clustering derived from SNP data. Genetic structure analyses correctly assigned each of the 16 species to a different cluster although the PCA positioning of E. longirostrata was inconsistent with its current taxonomy. Admixture was present for closely related species' materials derived from local germplasm banks, indicating unintended hybridization following germplasm introduction. Provenances could be discriminated for some species, indicating that SNP-based discrimination was directly proportional to geographical distance, consistent with an isolation-by-distance model. SNP-based genomic ancestry analysis showed that the majority of the hybrids displayed realized genomic composition deviating from the expected ones based on their pedigree records, consistent with admixture in their parents and pervasive genome-wide directional selection toward the fast-growing E. grandis genome. SNP data in support of tree breeding provide precise germplasm identity verification, and allow breeders to objectively recognize the actual ancestral origin of superior hybrids to more realistically guide the program toward the development of the desired genetic combinations. [ABSTRACT FROM AUTHOR]

Tropical fruit tree species constitute a yet untapped supply of outstanding diversity of taste and nutritional value, barely developed from the genetics standpoint, with scarce or no genomic resources to tackle the challenges arising in modern breeding practice. We generated a de novo genome assembly of the Psidium guajava, the super fruit "apple of the tropics", and successfully transferred 14,268 SNP probesets from Eucalyptus to Psidium at the nucleotide level, to detect genomic loci linked to resistance to the root knot nematode (RKN) Meloidogyne enterolobii derived from the wild relative P. guineense. Significantly associated loci with resistance across alternative analytical frameworks, were detected at two SNPs on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome to determine the order and orientation of the contigs. The P. guineense-derived resistance response to RKN and disease onset is conceivably triggered by mineral nutrients and phytohormone homeostasis or signaling with the involvement of the miRNA pathway. Hotspots of mapped resistance quantitative trait loci and functional annotation in the same genomic region of Eucalyptus provide further indirect support to our results, highlighting the evolutionary conservation of genomes across genera of Myrtaceae in the adaptation to pathogens. Marker assisted introgression of the resistance loci mapped should accelerate the development of improved guava cultivars and hybrid rootstocks. [ABSTRACT FROM AUTHOR]

Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S1 or S2 cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S1 and S2 families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees. [ABSTRACT FROM AUTHOR]

Twelve years have passed since the early outlooks of applying genomic selection (GS) to forest tree breeding, initially based on deterministic simulations, soon followed by empirical reports. Given its solid projections for causing a paradigm shift in tree breeding practice in the years to come, GS went from a hot, somewhat hyped, topic to a fast-moving area of applied research and operational implementation worldwide. The hype cycle curve of emerging technologies introduced by Gartner Inc. in 1995, models the path a technology takes in terms of expectations of its value through time. Starting with a sudden and excessively positive "peak of inflated expectations" at its introduction, a technology that survives the "valley of disappointment" moves into maturity to climb the "slope of enlightenment", to eventually reach the "plateau of productivity". Following the pioneering steps of GS in animal breeding, we have surpassed the initial phases of the Gartner hype cycle and we are now climbing the slope of enlightenment towards a wide application of GS in forest tree breeding. By merging modern high-throughput DNA typing, time-proven quantitative genetics and mixed-model analysis, GS moved the focus away from the questionable concept of dissecting a complex, polygenic trait in its individual components for breeding advancement. Instead of trying to find the needle in a haystack, i.e., the "magic" gene in the complex and fluid genome, GS more efficiently and humbly "buys the whole haystack" of genomic effects to predict complex phenotypes, similarly to an exchange-traded fund that more efficiently "buys the whole market". Tens of studies have now been published in forest trees showing that GS matches or surpasses the performance of phenotypic selection for growth and wood properties traits, enhancing the rate of genetic gain per unit time by increasing selection intensity, radically reducing generation interval and improving the accuracy of breeding values. Breeder-friendly and cost-effective SNP (single nucleotide polymorphism) genotyping platforms are now available for all mainstream plantation forest trees, but methods based on low-pass whole genome sequencing with imputation might further reduce genotyping costs. In this perspective, I provide answers to why GS will soon become the most efficient and effective way to carry out advanced tree breeding, and outline a simple pilot demonstration project that tree breeders can propose in their organization. While the fundamental properties of GS in tree breeding are now solidly established, strategic, logistics and financial aspects for the optimized adoption of GS are now the focus of attentions towards the plateau of productivity in the cycle, when this new breeding method will become fully established into routine tree improvement. [ABSTRACT FROM AUTHOR]

The genetic diversity of a comprehensive germplasm collection involving 192 Jatropha curcas L. accessions collected throughout Brazil, spanning a wide latitudinal range from the states of Maranhao (1[degrees]49' S, 44[degrees]52' W) to Rio Grande do Sul (29[degrees]33' S, 55[degrees]07' W), was studied with 96 random amplified polymorphic DNA (RAPD) primers and six selected microsatellite markers. Only 23 of the 381 replicated RAPD markers and one microsatellite were polymorphic. Surprisingly, all accessions were homozygous at all but one microsatellite, in contrast with the outcrossing mating system reported for the species, suggesting that J. curcas not only supports selfing but possibly breeds by geitonogamy. Similarity based clustering revealed only 43 unique multilocus profiles in the 192 accessions. The probabilities of accessions with indistinguishable multilocus profiles being true duplicates varied between 83 and 99%. No relationship between clustering of accessions and geographic origin was observed, suggesting that J. curcas has experienced a widespread dispersion across regions by seeds and possibly vegetative propagules. The narrow genetic base and extent of potentially duplicated accessions likely reflects a recent common ancestry, drift, and intensive selection of the currently cultivated materials since the time of introduction. This result highlights an urgent need for the introduction of new and diverse accessions to this germplasm collection if Brazil is to drive and sustain successful breeding programs. doi: 10.2135/cropsci2010.02.0112

The relationship between vitamin D receptor (VDR) ApaI, CDX2, BsmI, FokI, and TaqI polymorphisms and fat-free mass (FFM) were examined in 191 postmenopausal Brazilian women (mean age 67.87 [+ or -] 5.22 years). Participants underwent FFM measurements by dualenergy x-ray absorptiometry (DEXA). Whole-blood-extracted genomic DNA was genotyped to the aforementioned polymorphisms and to ancestry-informative markers through minisequencing, using the SNaPshot Multiplex System. Association between VDR polymorphisms and FFM variables was assessed by analysis of covariance. Haplotypes were estimated, and regression-based, haplotype-specific association tests were carried out with the studied phenotypes. No departure from Hardy--Weinberg equilibrium was detected for any polymorphism. None of the investigated VDR allelic variations, individually or analyzed as haplotypes, was associated with FFM phenotypes. The inclusion of individual African genomic ancestry was used as an attempt to correct for population stratification. Further studies in larger sample population are required to confirm these findings.