Genetic diversity, linkage disequilibrium and population structure in a sunflower association mapping population revealed through double digest RADseq

MERINO GABRIELA A.; MONTECCHIA JUAN; PANIEGO NORMA; FILIPPI CARLA V; RIVAROLA MÁXIMO L; LÍA VERÓNICA V; AGUIRRE NATALIA; HEINZ RUTH A

Workshop; Workshop on Mathematical and Statistical Aspects of Molecular Biology; 2019

European Bioinformatics Institute (EBI-EMBL)

Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity, (ii) detect the patterns of LD, and (iii) to estimate the levels of population structure in the sunflower association mapping population of INTA, a diverse collection of 135 cultivated sunflower inbred lines (ILs) from both local and international origin.Plants were genotyped using double digest RADseq approach combining SphI and EcoRI restriction enzymes. Illumina sequencing data were processed through a bioinformatics workflow and single nucleotide polymorphisms (SNPs) were called using Stacks (Catchen et al 2013). Data was filtered for quality and loci with >30% missing data and minor allele frequency lower than 5% were discarded. The resulting SNP matrix was imputed using a random forest algorithm with predictors, rendering a total of 18161 SNPs. The number of SNPs on each chromosome was consistent with the physical length of the respective chromosomeIn general, the estimates of genetic variability were moderate. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was first detected, with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. Further analyses identified six subgroups using fastSTRUCTURE and Discriminant Analysis of Principal Components (DAPC).Overall, we found variable levels of linkage disequilibrium (LD) across the genome. For example, chromosome 10 exhibits a relatively slow overall decay in LD, whereas chromosome 9 shows a much more rapid decay of LD. We also estimated FST between the two primary breeding pools (i.e. mantainer vs. Restorer lines) for the full set of markers, observing genomic regions exhibiting significantly elevated differentiation on several chromosomes (10, 13, and 16).The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation.