Phylogeographic evidence of crop neodiversity in sorghum

Abstract

Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

Figure 1.—

Geographical distribution of RFLP-based clusters (1–10) of sorghum varieties in relation to the different regions of Africa (as in Table 1). The black area is a schematic of the area of initial sorghum domestication and the arrows show the main migrations according to Harlan (1995). The global pattern opposes primary units (clusters 3, 5, 6, and 10) to three secondary units (clusters 1 and 2, clusters 7 and 8, and clusters 4 and 9).

Figure 2.—

Gene representation showing exons (shaded) and sequenced segments (solid). Sh2, Shrunken2 (sorghum sequence); Bt2, Brittle2 (maize sequence); SssI, Soluble starch synthaseI (rice sequence); Ae1, Amylose extender1 (maize sequence); Wx, Waxy (sorghum sequence); O2, Opaque2 (sorghum sequence). The positions of the beginning and the end of the sequenced segments are in base pairs and the number of the fragment are given at the bottom of the representation.

Figure 3.—

Haplotype network for each of the six genes under study, showing the distribution of the various sorghum accessions classified according to their origin, as described in Figure 1. Circled areas are proportional to haplotype frequencies. White is used for accessions belonging to clusters 3, 5, 6, and 10. Red is used for accessions belonging to clusters 1 and 2, all from western Africa. Yellow is used for accessions belonging to clusters 7 and 8, all but one from southern Africa. Blue is used for accessions belonging to clusters 9 and 4, all from Asia. Gray is used for accessions that are unclustered and/or from other regions of the world.