Microhaplotypes Improve Kinship Estimation in Heterozygous, Mixed-Ploidy Populations of Actinidia
Millar, T. R.; Koot, E. M.; Heywood, A.; Grande, A.; Thomson, S. J.; McCallum, J. A.; Wilcox, P. L.; Black, M. A.
Show abstract
Over the past decade there has been increasing interest in the use of microhaplotype markers in autopolyploid taxa. This has been driven by theoretical and observed improvements in signals of allelic dosage, linkage, and heritability. Yet, to date there has been little investigation into the suitability of microhaplotype markers for estimating kinship. Here, we develop the theory of kinship estimation from microhaplotypes, introduce the MCHap microhaplotype caller for autopolyploid populations, and apply these methods to a highly diverse germplasm population of mixed-ploidy Actinidia (kiwifruit and relatives). We find that microhaplotype-based kinship estimates are generally superior to equivalent single nucleotide variant based estimates. This is because microhaplotypes minimize the coalescent signal among alleles which may bias estimates within the context of a recent reference population. Hence, kinship estimates from microhaplotypes more accurately capture the recent demographic history of a population. These findings are supported by both coalescent simulations and the analysis of real data. Our findings are relevant to organisms of any ploidy, but most actionable in highly heterozygous taxa such as Actinidia.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Nearly unbiased estimator of contemporary effective population size using within-cohort sibling pairs incorporating parental and non-parental reproductive variations 93%
- Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations. 92%
- Predicting recombination frequency from map distance 91%
Similar papers in this journal
Similar papers in this journal
- Inferring the distributions of fitness effects and proportions of strongly deleterious mutations 92%
- Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias 92%
- QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae) 91%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.