Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Abstract

Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

Keywords: DArTseq markers; West Africa; genetic diversity; landraces; maize improvement; population structure.

Figure 1

Graphical representation of the population structure of the 208 maize panel. (a) Plot of mean likelihood of delta K against the number of K groups. The highest peak observed at K = 3 signifies the grouping of accessions into three groups, while the small peak at K = 2 and 4 signifies further grouping of accessions into two and four groups, respectively. (b) Subpopulations at K = 3. The colors represent three subpopulations of 208 accessions. The separation of accessions into subpopulation 1 (red), 2 (green), and 3 (blue) was based on membership coefficient ≥80%.

Figure 2

Population structure of Burkinabe (a), Ghanaian (b), and Togolese (c) landrace gene pools, including a reference population (d) at K = 2, K = 9, and K = 4, respectively.

Figure 3

Discriminant analysis of principal components (DAPC) using 5974 DArTseq markers. The axes represent the first two linear discriminants (LD). Each color represents a cluster, while each dot represents an individual. Numbers represent the different subpopulations identified by DAPC analysis.

Figure 4

Cluster analysis of 208 maize accessions using principal coordinate analysis (PCoA). Accessions are colored according to origin. The orange, ash, and violet circles represent subpopulation 1, 2, and 3, respectively.

Figure 5

Phylogenetic tree estimated through the neighbor-joining method for 208 maize accessions from West Africa. The green, red, blue, and yellow clades and taxa represent Togolese, Burkinabe, Ghanaian, and reference populations, respectively. The orange, violet, and ash highlights represent subpopulations 1, 2, and 3, respectively.

Figure 6

Unrooted neighbor joining tree depicting genetic relationships among Burkinabe (a), Ghanaian (b), and Togolese (c) landrace gene pools, and a reference population (d). Colors of each tree represent genetic groups.