Estudo genômico de populações de piquiá (Caryocar villosum (Aubl.) Pers., Caryocaraceae): elucidando o processo de domesticação de populações da espécie

Abstract

The piquiá (Caryocar villosum) is na Amazonian tree with diverse applications, including food, medicinal, and timber uses. The species exhibits incipiently domesticated populations, a co-evolutionary process that likely began between the late Pleistocene and early Holocene. Currently, traditional peoples and communities select and cultivate piquiá trees, 8ncipie to expected genetic 8ncipiente between trees in 8ncipie cultivation systems, such as home gardens, and those in mature forests. Thus, the objective of this study was to analyze the genetic diversity and structure of piquiá trees across four 8ncip, comparing home gardens and mature forests to understand their domestication process. The study 8ncip included the Caxiuanã National Forest (FLONA), Tapajós FLONA, Tefé FLONA, and the Amanã Sustainable Development Reserve (RDS). A total of 207 leaf tissue samples were used, and genotyping by-sequencing was performed using double-digest DNA (ddGBS). For the analyses, 6,900 single nucleotide polymorphisms (SNPs) were considered. To characterize genetic diversity, parameters such as allelic richness (AR) and the number of rarefied private alleles (RPA) were calculated. Genetic structure was evaluated based on two approaches: sNMF and fineRADstructure. The migration rate was calculated using the MIGRATE software. The results showed 8ncipi genomic variation between 8ncip (8.92%) than within 8ncip 8nci comparing home gardens and forests (2.14%), suggesting the existence of four genetic populations. Within each population, the 8ncipien variation between home gardens and forests was found in the Caxiuanã FLONA (6.30%), while the lowest was in the Amanã RDS (-0.4%), indicating no genetic differentiation between cultivated and forest trees in the RDS. Regarding genetic diversity, the Tapajós FLONA showed the highest diversity (AR: 8.117; RPA: 505), followed by the Caxiuanã FLONA (AR: 8.066; RPA: 438), Tefé FLONA (AR: 8.007; RPA: 352), and finally the Amanã RDS (AR: 7.984; RPA: 255). Considering all 8ncip, forests exhibited 8ncipi diversity (AR: 12.333; RPA: 442) than home gardens (AR: 12.310; RPA: 435). However, 8nci analyzed separately, parameters were 8ncipi in the forest 8nci in the Tapajós FLONA, suggesting that selection in home gardens resulted in a reduction of genetic variability. In the genetic structure analyses, sNMF indicated that four is the likely number of genetic clusters. Structure was observed between at least three 8ncip, with the Tefé FLONA and the Amanã RDS being very similar, potentially representing extensions 8ncipi another. The fineRADstructure revealed the existence of two main groups: one formed by the Caxiuanã FLONA and Tapajós FLONA, and the other by the Tefé FLONA and Amanã RDS. The Tapajós FLONA presented the highest average immigration rate (0.98). These results indicate that distinct human-piquiá interactions occurred across the study 8ncip. In this 8ncipien, the Tapajós FLONA stands out by presenting the highest genetic diversity and immigration rate, alongside lower genetic diversity in home gardens, suggesting that this 8nci may have been the center of origin for the domestication of the species, with na ongoing 8ncipiente domestication process.