Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping

Abstract

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype-phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS-box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty-one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non-model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation.

Evolutionary dynamics of cycle length in pearl millet: the role of farmer’s practices and gene flow

“…This phenomenon should be more pronounced in type I villages than in type II villages. Identification of genes involved in the control of earliness in pearl millet (Saïdou et al 2009;Mariac et al 2011) open promising investigation of the diversity of pearl millet landraces at the gene level .…”

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

“…Genome scans and genetic association mapping have identified several genes tightly linked to adaptive traits of pearl millet in semi-arids areas. A SNP in the Phytochrome C locus ( PgPHYC ) and an indel variation in PgMADS11 gene were associated with flowering time variation, annual rainfall and spike length of pearl millet (Saïdou et al, 2009; Mariac et al, 2011; Vigouroux et al, 2011). From framers point of view, distinction between early- and late-flowering landraces is very clear but it is not always associated with clear genetic differentiation (Dussert et al, 2015).…”

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

“…Secondly, various demographic events and aspects of population structure can elevate F ST and increase the frequency of false positives [24,25,27,28]. This makes it vital to couple genome scans with other methods [24], such as identifying outliers at which allelic differences correlate with environmental variables [29,30], combining genome scans with ecological genetic manipulations [31], or choosing markers in genes with functional effects that are relevant to the particular situation [30][31][32]. Performing a genome scan with markers chosen from a quantitative trait locus (QTL) map (see glossary) reveals F ST outliers linked to bona fide candidate genes by their proximity to QTLs that affect phenotypic traits involved in population divergence [12,26,28,[33][34][35].…”