The groundnut improvement network for Africa (GINA) germplasm collection: a unique genetic resource for breeding and gene discovery

Abstract

Cultivated peanut or groundnut (Arachis hypogaea L.) is a grain legume grown in many developing countries by smallholder farmers for food, feed, and/or income. The speciation of the cultivated species, that involved polyploidization followed by domestication, greatly reduced its variability at the DNA level. Mobilizing peanut diversity is a prerequisite for any breeding program for overcoming the main constraints that plague production and for increasing yield in farmer fields. In this study, the Groundnut Improvement Network for Africa assembled a collection of 1,049 peanut breeding lines, varieties, and landraces from 9 countries in Africa. The collection was genotyped with the Axiom_Arachis2 48K SNP array and 8,229 polymorphic single nucleotide polymorphism (SNP) markers were used to analyze the genetic structure of this collection and quantify the level of genetic diversity in each breeding program. A supervised model was developed using dapc to unambiguously assign 542, 35, and 172 genotypes to the Spanish, Valencia, and Virginia market types, respectively. Distance-based clustering of the collection showed a clear grouping structure according to subspecies and market types, with 73% of the genotypes classified as fastigiata and 27% as hypogaea subspecies. Using STRUCTURE, the global structuration was confirmed and showed that, at a minimum membership of 0.8, 76% of the varieties that were not assigned by dapc were actually admixed. This was particularly the case of most of the genotype of the Valencia subgroup that exhibited admixed genetic heritage. The results also showed that the geographic origin (i.e. East, Southern, and West Africa) did not strongly explain the genetic structure. The gene diversity managed by each breeding program, measured by the expected heterozygosity, ranged from 0.25 to 0.39, with the Niger breeding program having the lowest diversity mainly because only lines that belong to the fastigiata subspecies are used in this program. Finally, we developed a core collection composed of 300 accessions based on breeding traits and genetic diversity. This collection, which is composed of 205 genotypes of fastigiata subspecies (158 Spanish and 47 Valencia) and 95 genotypes of hypogaea subspecies (all Virginia), improves the genetic diversity of each individual breeding program and is, therefore, a unique resource for allele mining and breeding.

Keywords: breeding; core collection; genotyping; germplasm diversity; groundnut improvement; network.

Fig. 1.

Map of origin of the African germplasm collection. Numbers in brackets are the number of varieties contributed by each country.

Fig. 2.

Dapc analysis of the 625 USDA accessions based on market type grouping factor. The market type groups were further divided into 3 subgroups by k-means clustering of the PCA space.

Fig. 3.

Ward hierarchical clustering tree of the African breeders’ germplasm collection. Six layers of information are depicted as concentric circles: (1) the region (East Africa (E) or West Africa (W) of provenance of the varieties, (2) the/breeding program (Country) that nominated the variety, (3) the market type group assigned by the dapc model, (4) the structure barplot of individual ancestry proportions for the genetic clusters inferred at K = 5, (5) the structure group assigned At a minimum membership of 0.8, and vi- the inclusion of each variety in the core collection following a selection by breeders (Yes Breeder choice) or diversity sampling (Yes Diversity). The pale-yellow highlighted varieties are those that are part of clusters of closely related material. The pale-green highlighted varieties are part of the same interspecific population. Other colors represent varieties that are duplicated 3 or more times.

Fig. 4.

Barplot of expected heterozygosity (he) in different programs. He-all: He computed with all genotypes; He-no-related: He computed with all genotypes except the closely related ones; He-no-related-fastigiata: He computed with genotypes from fastigiata subspecies except the closely related ones; He-no-related-hypogaea: He computed with genotypes from hypogaea subspecies except the closely related ones. The horizontal line represents the He value in the subset of germplasm that belongs to the core collection.