Narrow genetic diversity in germplasm from the Guinean and Sudano-Guinean zones in Benin indicates the need to broaden the genetic base of sweet fig banana (Musa acuminata cv Sotoumon)

Abstract

Sweet fig (M. acuminata cv. Sotoumon) is an economically important dessert banana in Benin, with high nutritional, medicinal, and cultural values. Nevertheless, its productivity and yield are threatened by biotic and abiotic stresses. Relevant knowledge of the genetic diversity of this economically important crop is essential for germplasm conservation and the development of breeding programs. However, very little is known about the genetic makeup of this cultivar in Benin. To advance the understanding of genetic diversity in sweet fig banana germplasm, a Genotype-By-Sequencing (GBS) was performed on a panel of 273 accessions collected in different phytogeographical zones of Benin. GBS generated 8,457 quality SNPs, of which 1992 were used for analysis after filtering. The results revealed a low diversity in the studied germplasm (He = 0.0162). Genetic differentiation was overall very low in the collection as suggested by the negative differentiation index (Fstg = -0.003). The Analysis of Molecular Variance (AMOVA) indicated that the variation between accessions within populations accounted for 83.8% of the total variation observed (P < 0.001). The analysis of population structure and neighbor-joining tree partitioned the germplasm into three clusters out of which a predominant major one contained 98.1% of all accessions. These findings demonstrate that current sweet fig banana genotypes shared a common genetic background, which made them vulnerable to biotic and abiotic stress. Therefore, broadening the genetic base of the crop while maintaining its quality attributes and improving yield performance is of paramount importance. Moreover, the large genetic group constitutes an asset for future genomic selection studies in the crop and can guide the profiling of its conservation strategies.

Fig 1. Map illustrating sweet fig banana accessions sampling points in Benin.

Population codes and associated Districts: GPO: 1. Grand-Popo; LOA: 2. Lokossa, 3. Athiémè; DOL: 4. Dogbo, 5. Lalo; ZTA: 6. Zè, 7. Tori-Bossito, 8. Allada; SAD: 9. Adjohoun, 10. Sakété; ZOO: 11. Zogbodomey, 12. Ouinhi; BBG: 13. Bantè; 14. Bassila, 15. Glazoué; PST: 16. Parakou; 17. Savè, 18. Tchaourou. The base map was obtained from the National Geographic Institute of Benin. The current version of the map was generated using ArcGIS (Version 10.4) [43].

Fig 2. Morphology of the two phenotypes of sweet fig banana.

(a) Clone set of the major phenotype. (b) Clone set of the minor phenotype.

Fig 3. Morphology of the male bud in the two phenotypes of sweet fig banana.

(a) Major phenotype. (b) Minor phenotype.

Fig 4. Morphological aspect of the male flower of the two phenotypes of sweet fig banana.

(a) Major phenotype. (b) Minor phenotype.

Fig 5. Population structure using 1992 SNPs in STRUCTURE software.

(a) DeltaK for different number of sub-populations or genetic groups. (b) Plot for different genetic groups at K = 3, each color representing one genetic group. Red color for the first genetic group (G1), blue color for the second genetic group (G2) and green color for the third genetic group (G3).

Fig 6. Phylogenetic tree constructed with neighbor-joining (NJ) for 273 sweet fig banana accessions from Benin.

The topology revealed three genetic groups (C1: red; C2: blue and C3: green). The dendrogram was drawn using MEGA 7.