Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections.

Genes
Carla V FilippiNorma B Paniego

Abstract

Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America-Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linka...Continue Reading

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Citations

Jul 10, 2020·BMC Plant Biology·C V FilippiV V Lia
Nov 11, 2020·Nucleic Acids Research·Marcela K Tello-RuizDoreen Ware

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Datasets Mentioned

BETA
SRP092899

Methods Mentioned

BETA
genotyping
chip
PCA

Software Mentioned

Ensembl
Stacks
GATK UnifiedGenotyper
R package “ Synbreed ”
custom
ddRADseq
Adegenet
Circa
Bowtie2 aligner
GATK

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