Markers are an important tool in plant breeding, which can improve conventional phenotypic breeding, generating more accurate information outcoming better decision making. This study aimed to apply and compare the fit of different Bayesian models BRR, BayesA, BayesB, BayesB (setting the value from very low to $$\pi$$π = $${10}^{-5}$$10 - 5 ), BayesC and Bayesian Lasso (LASSO) for predictions of the genomic genetic values of productivity and quality traits of a guava population. The models were fitted for traits fruit mass, pulp mass, soluble solids content, fruit number, and production per plant in the genomic prediction with SSR markers, obtained through the CTAB extraction method with 200 primers. The Bayesian ridge regression model showed the best results for all traits and was chosen to predict the individual’s genomic values according to the cross-validation data. A good stabilization of the Markov and Monte Carlo chains was observed with the mean values close to the observed phenotypic means. Heritabilities showed good predictive accuracy. The model showed strong correlations between some traits, allowing indirect selection.

Theobroma cacao is well known for its role in producing cacao. Many different cacao varieties are cultivated in equatorial regions, each distinguished by unique phenotypic traits. An instance of this is the pod color variation, which has been linked to differences in anthocyanin content. Anthocyanins are produced by one branch of the flavonoid biosynthesis. The highly continuous genome sequence and comprehensive gene set generated in this study enabled an investigation of the genetic basis of the flavonoid biosynthesis. Expression differences between paralogs in the proanthocyanidin biosynthesis suggest subfunctionalization. In pod husks, one copy of the leucoanthocyanidin reductase gene ( LAR ) displayed substantially higher expression than the other copy.

Aquilegia vulgaris is a widespread ornamental plant. The species is well known for its extensive variation of different flower colors and can even be considered as a model species for the evolution of flower morphology. Anthocyanins are a major pigment group responsible for pigmentation of flowers in A. vulgaris and many plant species. Here, we report a highly continuous genome sequence of an European Aquilegia vulgaris plant displaying purple flowers and a genome sequence of a plant displaying white flowers. The corresponding annotation facilitates research on flower color and morphology evolution. Long-read alignments revealed different structural variants in an anthocyanidin synthase ( ANS ) gene, crucial for pigment biosynthesis, that could explain the white flower phenotype. Candidate genes for all steps in the core anthocyanidin biosynthesis were identified. The identification of a flavonoid 3’,5’ hydroxylase ( F3’5’H ), a gene essential for the biosynthesis of bluish delphinidin derivatives, corroborates previous reports about metabolites and transcripts in A. vulgaris .

Tacca chantrieri , black bat flower, has showy flowers often appearing almost black. Here, we present the genome sequence and corresponding annotation to identify the genetic basis of the pigmentation. Candidate genes associated with the anthocyanin biosynthesis were identified based on this genome sequence and investigated with respect to their properties. The best dihydroflavonol 4-reductase (DFR) candidate, which harbours all amino acid residues believed to be required for DFR activity, shows a threonine in the substrate preference determining position where most characterized DFRs display asparagine or aspartate. This amino acid residue appears to be frequent in the Dioscoreaceae family as a comprehensive investigation revealed.