Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet
Saïdou, Abdoul-Aziz, Mariac, Cédric, Luong, Vivianne, Pham, Jean-Louis, Bezançon, Gilles, Vigouroux, Yves, Genetics
The identification of genes selected during and after plant domestication is an important research topic to enhance knowledge on adaptative evolution. Adaptation to different climates was a key factor in the spread of domesticated crops. We conducted a study to identify genes responsible for these adaptations in pearl millet and developed an association framework to identify genetic variations associated with the phenotype in this species. A set of 90 inbred lines genotyped using microsatellite loci and AFLP markers was used. The population structure was assessed using two different Bayesian approaches that allow inbreeding or not. Association studies were performed using a linear mixed model considering both the population structure and familial relationships between inbred lines. We assessed the ability of the method to limit the number of false positive associations on the basis of the two different Bayesian methods, the number of populations considered and different morphological traits while also assessing the power of the methodology to detect given additive effects. Finally, we applied this methodology to a set of eight pearl millet genes homologous to cereal flowering pathway genes. We found significant associations between several polymorphisms of the pearl millet PHYC gene and flowering time, spike length, and stem diameter in the inbred line panel. To validate this association, we performed a second association analysis in a different set of pearl millet individuals from Niger. We confirmed a significant association between genetic variation in this gene and these characters.
DOMESTICATION and dispersion of cultivated plants were associated with their adaptation to the agricultural environment. These adaptations led to genetic changes shared by all individuals of a cultivated species (domestication genes) or to variations between varieties within a cultivated species (genes controlling varietal differences). Domestication genes like tb1 (Doebley et al. 1997; Wang et al. 1999) in maize (Zea mays) were selected very early by human populations ( Jaenicke-Després et al. 2003). After the first early selection, adaptation of the flowering phenotype to different climatic conditions was certainly a key innovation that enabled colonization of new environments. One of the most well-known examples was the adaptation of maize-a tropical plant-to northern climates. Maize cultivation spread late to northeastern America. By 1000 YBP, only maize was an established staple crop (Fritz 1995). A genetic variant of the Dwarf8 gene led to an earlier flowering phenotype (Thornsberry et al. 2001). This early allele was present at a high frequency in North America and was certainly selected after the domestication of maize under northern climatic conditions (Camus-Kulandaivelu et al. 2006).
Pearl millet (Pennisetum glaucum [(L.) R. Br.]), one of the most importantWest African cereals, was most likely domesticated once in the Sahelian zone of West Africa (Oumar et al. 2008). By 3500 YBP, it was already being cultivated throughout Sahelian and tropical West African countries (D'Andrea et al. 2001; D'Andrea and Casey 2002). The adaptation of pearl millet in West Africa was also associated with an environmental gradient (Haussmann et al. 2006). Pearl millet varieties from tropical coastal West Africa flower very late (up to 160 days from planting to female flowering) as compared to varieties from Sahelian West Africa, which may have a flowering time as short as 45 days (Haussmann et al. 2006). The genetic factors underlying the differences between these varieties are still unknown.
Association studies offer new opportunities for assessing the role of a particular gene on a phenotype. Contrary to QTL analysis, association studies have the challenging task of taking an unknown evolutionary history of studied individuals into account. For example, population structure is a common confounding effect in association studies (Pritchard et al. …