Genome scan of landrace populations of the self-fertilizing crop species
rice, collected across time, revealed climate changes' selective
footprints in the genes network regulating flowering time.
Abstract
Analysis of the genetic bases of adaptation to climate changes are often
conducted on natural populations. We report here on a study based on
diachronic sampling (1980 & 2010) of the self-fertilising crop species,
Oryza sativa (Asian rice) and Oryza glaberrima (African rice), in the
tropical forest and the Sudanian savannah of West Africa. First, using
historical meteorological data we confirmed changes in temperatures
(+1°C on average) and rainfall regime (less predictable and reduced
amount) in the target area. Second, phenotyping the populations for
phenology, we observed significantly earlier heading time (up to 10
days) in the 2010 samples. Third, we implemented two genome-scan
methods, one of which specially developed for selfing species, and
detected 31 independent selection footprints. These loci showed
significant enrichment in genes involved in reproductive processes and
bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB.
This rapid adaptive evolution, originated from subtle changes in the
standing variation in genetic network regulating heading time, did not
translate into predominance of multilocus genotypes, as it is often the
case in selfing plants, and into notable selective sweeps. We argue that
this high adaptive potential results from the multiline genetic
structure of the rice landraces, and the rather large and imbricated
genetic diversity of the rice meta-population at the farm, the village
and the region levels, that hosted the adaptive variants in multiple
genetic backgrounds well before the advent of the environmental
selective pressure. The complex selection footprints observed in this
empirical study calls for further model development on genetic bases of
plant adaptation to environmental changes.