Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

Abstract

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.

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

“…We used this method to analyze our real data set. However, as highlighted by Saïdou et al (2009), this projection method does not necessarily lead to a valid kinship matrix (that is, a matrix with elements 40 and o1). Which is the best method when computing the r V 2 measure, either to use a valid kinship matrix or simply a valid variancecovariance matrix, remains an open question.…”

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…Natural variation in phytochrome responses has been detected in other species, including barley (Hordeum vulgare; Biyashev et al, 1997), oat (Avena sativa; Hou and Simpson, 1993), and Plantago lanceolata (Van Hinsberg, 1998), and single nucleotide polymorphisms at PHYB are candidates for causal linkage with clinal variation in bud set in Populus tremula (Ingvarsson et al, 2006). Several recent studies of candidate genes from multiple accessions have linked PHYC or PHYD variation to flowering time and/or morphological variation in Arabidopsis and millet Pennistum glaucum (Balasubramanian et al, 2006;Samis et al, 2008;Ehrenreich et al, 2009;Saïdou et al, 2009) and have identified geographic structuring at PHYA and PHYE in Cardamine nipponica (Ikeda et al, 2008(Ikeda et al, , 2009). The ultimate goal of most of these studies is to link traits to genes, and they provide insight into how light signaling works in natural environments (Maloof et al, 2000).…”

“…These data suggest that phyD and phyE contribute to the precision of responses to variable environments. Additionally, studies of variation in populations across a large spatial scale have linked clinal variation at PHYC with variation in flowering time (Balasubramanian et al, 2006;Saïdou et al, 2009), suggesting its role in photoperiod perception is relevant in natural environments.…”

Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in Cardamine nipponica (Brassicaceae)

“…Indeed, previous studies have reported that distinct photoreceptors are involved in local adaptation across several species (PHYC in A. thaliana, Balasubramanian et al 2006;Samis et al 2008; PHYB2 in Populus tremula, Ingvarsson et al 2006Ingvarsson et al , 2008 CRY1a in Glycine max, Zhang et al 2008; PHYE in C. nipponica, Ikeda et al 2009a; PHYC in Pennisetum glaucum, Saïdou et al 2009). Therefore, local adaptation implemented by photoreceptors cannot be attributed to a single type of photoreceptor across various species, but rather the photoreceptor that plays important roles in local adaptation would be dependent on the species, which might be determined by life cycle, distribution range, and/or demographic history.…”