Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation

Abstract

SUMMARYGenome-wide association studies rely upon segregating natural genetic variation, particularly the patterns of polymorphism and correlation between adjacent markers. To facilitate association studies in the model legume Medicago truncatula, we present a genome-scale polymorphism scan using existing Affymetrix microarrays. We develop and validate a method that uses a simple information-criteria algorithm to call polymorphism from microarray data without reliance on a reference genotype. We genotype 12 inbred M. truncatula lines sampled from four wild Tunisian populations and find polymorphisms at approximately 7% of features, comprising 31 419 probes. Only approximately 3% of these markers assort by population, and of these only 10% differentiate between populations from saline and non-saline sites. Fifty-two differentiated probes with unique genome locations correspond to 18 distinct genome regions. Sanger resequencing was used to characterize a subset of maker loci and develop a single nucleotide polymorphism (SNP)-typing assay that confirmed marker assortment by habitat in an independent sample of 33 individuals from the four populations. Genome-wide linkage disequilibrium (LD) extends on average for approximately 10 kb, falling to background levels by approximately 500 kb. A similar range of LD decay was observed in the 18 genome regions that assort by habitat; these LD blocks delimit candidate genes for local adaptation, many of which encode proteins with predicted functions in abiotic stress tolerance and are targets for functional genomic studies. Tunisian M. truncatula populations contain substantial amounts of genetic variation that is structured in relatively small LD blocks, suggesting a history of migration and recombination. These populations provide a strong resource for genome-wide association studies.

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

“…However, one of seven windows that fell into the lowest 1% of the distribution of both D T and θ W contains an early nodulin gene (ENOD93) (5), suggesting that this episode of selection may have been associated with host-rhizobia interactions. Genes previously identified as targets of selection in M. truncatula, including DMI1, a nodulation-related gene (3), as well as genes identified as possible targets of adaptation to saline environments in Tunisian populations of M. truncatula (35) were not located in chromosomal regions harboring unusual levels of diversity or skewed frequency distributions (i.e., D T ) in our sample. The lack of correspondence between this study and previous studies may not be surprising-the studies by De Mita et al (3) and Friesen et al (35) both sampled from geographically restricted locations, whereas our range-wide sample may be powerful for detecting species-wide sweeps but poorly suited for identifying genes involved in local adaptation to biotic or abiotic conditions.…”

Parental environments and interactions with conspecifics alter salinity tolerance of offspring in the annual Medicago truncatula

“…Previous research has demonstrated that three of the four populations (i.e. TN 1, 8 and 9) used in this study are genetically differentiated and linked by moderate levels of gene flow, but are locally adapted to soil salinity levels (Friesen et al 2010). Saline populations' environments have 14 times greater soil sodium and 4.6 times greater magnesium levels than non-saline populations' environments (Table S1 in Supporting Information).…”

“…Medicago truncatula Gaertn (Fabaceae) is a self-compatible annual plant from the Mediterranean region found in a range of environments including saline and non-saline soils in Tunisia (Lazrek et al 2009;Friesen et al 2010). The genotypes used in this study are part of a larger collection of 39 genotypes from two populations of saline origin [i.e.…”

The integration of activity in saline environments: problems and perspectives

“…In the more closely related barley and wheat, only about one-third of the salinity-related expression responses were overlapping. Intraspecific variation in gene expression is also manifested in locally adapted populations of model plants (Baxter et al 2010;Friesen et al 2010).…”