Genetic diversity, linkage disequilibrium and population structure in a diverse sunflower collection revealed through Genotyping-by-Sequencing (GBS)

FILIPPI, C.V.; AGUIRRE, NATALIA C.; MERINO, GABRIELA A.; RIVAROLA, MÁXIMO; MONTECCHIA, JUAN F.; PUEBLA, A.F.; ALVAREZ, D.; HEINZ R.A.; LIA, V.V.; PANIEGO, N.B.

Simposio; Third International Harlan Symposium; 2019

Argentina has a long tradition of sunflower breeding, and its germplasm is a valuablegenetic resource worldwide. Depiction of the genetic diversity, linkage disequilibrium(LD) and population structure is essential for the efficient organization and exploitationof genetic resources. The objectives of this study were to (i) to evaluate the geneticdiversity, (ii) detect the patterns of LD, and (iii) to estimate the levels of populationstructure in a diverse collection of 135 cultivated sunflower inbred lines from both localand international origin, preserved at the Active Germplasm Bank of the InstitutoNacional de Tecnología Agropecuaria (Argentina).Plants were genotyped using GBS - double digest RADseq approach combining SphI andEcoRI restriction enzymes. Illumina sequencing data were processed through abioinformatics workflow and single nucleotide polymorphisms (SNPs) were called usingStacks. Data was filtered for quality and loci with >30% missing data and minor allelefrequency lower than 5% were discarded, rendering a total of 18161 good quality SNPs.In general, the estimates of genetic variability were moderate. Bayesian andmultivariate methods were used to infer population structure. Evidence for theexistence of three different genetic groups was first detected, with themaintainer/restorer status being the most prevalent characteristic associated withgroup delimitation. Further analyses using fastSTRUCTURE and Discriminant Analysis ofPrincipal Components identified six subgroups.Overall, we found variable levels of LD across the genome. For example, chromosome10 exhibits a relatively slow overall LD decay, whereas chromosome 9 shows a muchmore rapid LD decay. We also estimated FST between the two primary breeding pools(i.e. mantainer vs. restorer lines), observing genomic regions exhibiting significantlyelevated differentiation on several chromosomes (10, 13 and 16).The generated knowledge about the levels of diversity and population structure ofsunflower germplasm is an important contribution to this crop breeding andconservation.