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. 2024 Dec 2;47(4):e20240030.
doi: 10.1590/1678-4685-GMB-2024-0030. eCollection 2024.

High genetic structure of Spondias mombin in Brazil revealed with SNP markers

Allison Vieira da Silva  1 , Caroline Bertocco Garcia  1 , Igor Araújo Santos de Carvalho  1 , Wellington Ferreira do Nascimento  2 , Santiago Linorio Ferreyra Ramos  3 , Doriane Picanço Rodrigues  4 , Maria Imaculada Zucchi  5 , Flaviane Malaquias Costa  1 , Alessandro Alves-Pereira  4 , Carlos Eduardo Batista  1 , Edson Ferreira da Silva  6 , Elizabeth Ann Veasey  1
Affiliations

High genetic structure of Spondias mombin in Brazil revealed with SNP markers

Allison Vieira da Silva et al. Genet Mol Biol. .

Abstract

Spondias mombin L. (Anacardiaceae) is an arboreal and allogamous fruit tree native from southern Mexico to southeastern Brazil, with great potential for economic exploitation. This study aimed to evaluate the structure and genomic diversity of yellow mombin accessions collected in nine locations in Brazil using Single Nucleotide Polymorphisms (SNP) markers. Significant genetic structure was observed in the discriminant analysis of principal components (DAPC) and dendrogram construction, in accordance with our hypotheses. The Mantel test identified a highly positive and significant correlation between geographic and genetic distances. The locations from the Amazon biome presented higher genetic diversity values when compared to those from the Atlantic Forest and Cerrado, which is expected considering the higher vulnerability of these biomes. However, although presenting greater genetic diversity, the Amazon biome showed positive inbreeding coefficients (F IS ) in three of the four locations, ranging from 0.0855 to 0.2421, indicating a potential risk of genetic erosion, possibly related to the increased degradation of this biome in recent decades. The results obtained contribute to the understanding of the distribution of genetic variation and conservation status of yellow mombin in Brazil. They could also be used as a subsidy for developing conservation strategies and the genetic improvement of this species.

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Conflict of interest statement

Conflict of Interest: The authors declare that there is no conflict of interest that could be perceived as prejudicial to the impartiality of the reported research.

Figures

Figure 1 -
Figure 1 -. Map of Brazil with the sampling locations of Spondias mombin accessions in the States of Amazonas (AM), Maranhão (MA), Pernambuco (PE), Paraíba (PB), and Bahia (BA). The sampling location codes are described in Table 1.
Figure 2 -
Figure 2 -. Discriminant Analysis of Principal Component (DAPC) performed with 41 yellow mombin (Spondias mombin) individuals and 2,003 SNP markers. A) A scatter plot based on two discriminant functions, with the three groups identified by the k-means method. B) Clustering probability analysis according to the results generated in the DAPC. Each delimited bar represents an individual, while the locations are represented by the interval formed between the dotted lines: PD (Paudalho - Pernambuco), SM (São Lourenço da Mata - Pernambuco), MS (Mata de São João - Bahia), AR (Areia - Paraíba) [Atlantic Forest biome]; CP (Chapadinha - Maranhão) [Cerrado biome]; and NV (Novo Airão -Amazonas), IR (Iranduba - Amazonas), PF (Presidente Figueiredo - Amazonas), and SV (Silves - Amazonas) [Amazon biome].
Figure 3 -
Figure 3 -. Cluster analysis using the neighbor-joining method and Nei’s distance (Nei, 1972) for the yellow mombin (Spondias mombin) accessions collected in the States of Amazonas (AM) (green, Amazon biome), Maranhão (MA) (blue, Cerrado biome), Bahia (BA), Pernambuco (PE) and Paraíba (PB) (red, Atlantic Forest biome). The colors green, blue and red are based on the DAPC groups.
Figure 4 -
Figure 4 -. Results obtained from the pairwise analysis of F ST between yellow mombin (Spondias mombin) locations: PD (Paudalho-Pernambuco), SM (São Lourenço da Mata-Pernambuco), MS (Mata de São João-Bahia), AR (Areia-Paraíba), CP (Chapadinha-Maranhão), NV (Novo Airão-Amazonas), IR (Iranduba-Amazonas), PF (Presidente Figueiredo-Amazonas), and SV (Silves-Amazonas). All values are significant at p-value < 0.05.
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