Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato.

ABSTRACT:

Key message

The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays. To study LD and LD decay in tetraploid potato, we simulated autotetraploid genotypes and used it to explore the dependence on: (1) the number of haplotypes in the population (the amount of genetic variation) and (2) the percentage of haplotype specific SNPs (hs-SNPs). Several estimators for short-range LD were explored, such as the average r ², median r ²

SUBMITTER: Vos PG 

PROVIDER: S-EPMC5214954 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature