Genomic studies of the additive and dominant genetic control on production traits of Euterpe edulis fruits.

In forest genetic improvement programs for non-domesticated species, limited knowledge of kinship can compromise or make the estimation of variance components and genetic parameters of traits of interest unfeasible. We used mixed models and genomics (in the latter, considering additive and non-additive effects) to evaluate the genetic architecture of 12 traits in juçaizeiro for fruit production. A population of 275 genotypes without genetic relationship knowledge was phenotyped over three years and genotyped by whole genome SNP markers. We have verified superiority in the quality of the fits, the prediction accuracy for unbalanced data, and the possibility of unfolding the genetic effects into their additive and non-additive terms in the genomic models. Estimates of the variance components and genetic parameters obtained by the additive models may be overestimated since, when considering the dominance effect in the model, there are substantial reductions in them. The number of bunches, fresh fruit mass of bunch, rachis length, fresh mass of 25 fruits, and amount of pulp were strongly influenced by the dominance effect, showing that genomic models with such effect should be considered for these traits, which may result in selective improvements by being able to return more accurate genomic breeding values. The present study reveals the additive and non-additive genetic control of the evaluated traits and highlights the importance of genomic information-based approaches for populations without knowledge of kinship and experimental design. Our findings underscore the critical role of genomic data in elucidating the genetic control architecture of quantitative traits, thereby providing crucial insights for driving species' genetic improvement.

Single and multi-trait genomic prediction for agronomic traits in Euterpe edulis.

Popularly known as juçaizeiro, Euterpe edulis has been gaining prominence in the fruit growing sector and has demanded the development of superior genetic materials. Since it is a native species and still little studied, the application of more sophisticated techniques can result in higher gains with less time. Until now, there are no studies that apply genomic prediction for this crop, especially in multi-trait analysis. In this sense, this study aimed to apply new methods and breeding techniques for the juçaizeiro, to optimize this breeding program through the application of genomic prediction. This data consisted of 275 juçaizeiro genotypes from a population of Rio Novo do Sul-ES, Brazil. The genomic prediction was performed using the multi-trait (G-BLUP MT) and single-trait (G-BLUP ST) models and the selection of superior genotypes was based on a selection index. Similar results for predictive ability were observed for both models. However, the G-BLUP ST model provided greater selection gains when compared to the G-BLUP MT. For this reason, the genomic estimated breeding values (GEBVs) from the G-BLUP ST, were used to select the six superior genotypes (UFES.A.RN.390, UFES.A.RN.386, UFES.A.RN.080, UFES.A.RN.383, UFES.S.RN.098, and UFES.S.RN.093). This was intended to provide superior genetic materials for the development of seedlings and implantation of productive orchards, which will meet the demands of the productive, industrial and consumer market.

Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest.

The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.

Autotetraploid Coffea canephora and Auto-Alloctaploid Coffea arabica From In Vitro Chromosome Set Doubling: New Germplasms for Coffea.

Polyploidy is more than two chromosomal sets per nucleus, as the allotetraploid Coffea arabica. Due to allotetraploidy, C. arabica shows different phenotypes compare to diploid Coffea species, highlighting by beverage quality produced from its grains. Looking for the possibility of new phenotypes coupled with economic feature, considerable progress since 60's was reached for synthetic chromosome set doubling (CSD) in vitro, involving especially the antitubulin compounds, biological material, and used tissue culture pathway as the indirect somatic embryogenesis (ISE). Here, we aimed to regenerate autotetraploid and auto-alloctaploid plantlets of Coffea canephora and C. arabica, respectively, from a novel in vitro CSD procedure for Coffea. Exploring the ISE pathway, we treated the cellular aggregate suspensions (CAS) with 0.0 (control), 0.5, 1.5, or 2.5 mM of colchicine solution for 48, 72, or 96 h and maintained in liquid medium under constant orbital shaking. After transferring the CAS to semisolid media for somatic embryo regeneration, we considered it as cellular mass. Mature cotyledonary somatic embryos were only regenerated from cellular masses treated with 2.5 mM/48 h and 2.5 mM/72 h for C. canephora and with 0.5 mM/48 h for C. arabica. Evaluating the DNA ploidy level and the chromosome counting revealed that 36 (34.9%) plantlets of C. canephora were autotetraploids (4C = 2.86 pg, 2n = 4x = 44) and 61 (21.1%) of C. arabica were auto-alloctaploids (4C = 5.24 pg, 2n = 8x = 88). The CSD procedure, exploring the CAS proliferation and ISE pathway, promoted whole-genome duplication and resulted in a relatively high number of solid polyploids of both Coffea species. Due to distinct responses, DNA sequence fidelity (genetic) and global level of 5-methylcytosine (epigenetic) were evaluated. We observed that the increase of 5-methylcytosine levels was associated with somatic embryo regeneration from cells showing DNA sequence fidelity for the tested SSR primers. In conclusion, the adopted procedure for in vitro CSD is reproducible for induction, regeneration and propagation of Coffea polyploids and potentially other shrubbery and woody species. In view of the novelty of this procedure to generate new germplasm, we show the key issues and the steps of the CSD procedure.