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.

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

“…Our data therefore indicate that in parallel with an overall reduction in diversity, domestication increased the functional diversity at target loci. This can be imputed to novel mutations (or those that exist at low frequencies) that were selected because of the crop expansion into new environments with unexpected biotic and abiotic stress or because of selection for traits that improved the use of the plant organs by humans (de Alencar Figueiredo et al, 2008). As such, the data contribute to resolving the Darwin paradox (Darwin, 1878;Glémin and Bataillon, 2009): Domestication is associated with an increased phenotypic diversity at target traits and a reduction of nucleotide variation.…”

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

“…Sampling haplotypes from a core collection Instead of taking each cultivar, a diploid genotype, as the unit of the work, a haplotype-based approach was conducted as performed successfully in human (Tishkoff et al, 2007) and plant evolutionary studies (de Alencar Figueiredo et al, 2008). This was done to overcome the difficulty of interpreting migration and hybridization phenomena linked to an ancient and widespread diffusion of grapevines.…”

Diverse Roles of Strigolactone Signaling in Maize Architecture and the Uncoupling of a Branching-Specific Subnetwork

“…This contrast may have implications for the genetics of domestication in grasses. Selection for a strong central stem through increased apical dominance has occurred multiple times during the domestications of foxtail millet, sorghum, and maize from highly branched, wild ancestors (Doust et al, 2004;Doust, 2007;de Alencar Figueiredo et al, 2008, Remigereau et al, 2011. In maize, increased apical dominance is attributed principally to selection at the Tb1 locus.…”