Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet.
Abdoul-Aziz Saidou,Cédric Mariac,Vivianne Luong,Jean-Louis Pham,Gilles Bezançon,Yves Vigouroux +5 more
TLDR
An association framework to identify genetic variations associated with the phenotype in pearl millet was developed and a significant association between genetic variation in this gene and these characters was confirmed.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.read more
Citations
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References
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Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
Journal ArticleDOI
AFLP: a new technique for DNA fingerprinting.
Pieter Vos,René Cornelis Josephus Hogers,Marjo Bleeker,Martin Reijans,Theo van de Lee,Miranda Hornes,Adrie Friters,Jerina Pot,Johan Paleman,Martin Kuiper,Marc Zabeau +10 more
TL;DR: The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity that allows the specific co-amplification of high numbers of restriction fragments.
Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
Journal ArticleDOI
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated in this article.