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

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.

Genetics, genomics and breeding of groundnut (Arachis hypogaea L.).

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers.

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.