Blischak, P. | bioRxiv Science

bioRxiv2019

Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

O_LIMany crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. C_LIO_LITo test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all "diploid" flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. C_LIO_LIUsing a combination of approaches, we identified more than 3,000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. C_LIO_LIOur analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture. C_LI

plant biology↗

bioRxiv2017

SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

MotivationGenotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single lineage (auto polyploids), inbreeding can result from mixed mating and/or double reduction. For WGDs that involve hybridization (allopolyploids), alleles are typically inherited through independently segregating subgenomes.\n\nResultsWe present two new models for estimating genotypes and population genetic parameters from genotype likelihoods for auto- and allopolyploids. We then use simulations to compare these models to existing approaches at varying depths of sequencing coverage and ploidy levels. These simulations show that our models typically have lower levels of estimation error for genotype and parameter estimates, especially when sequencing coverage is low. Finally, we also apply these models to two empirical data sets from the literature. Overall, we show that the use of genotype likelihoods to model non-standard inheritance patterns is a promising approach for conducting population genomic inferences in polyploids.\n\nAvailabilityA C++ program, EBG, is provided to perform inference using the models we describe. It is available under the GNU GPLv3 on GitHub:\n\nhttps://github.com/pblischak/polyploid-genotyping.\n\nContact: blischak.4@osu.edu.

bioinformatics↗