Here, we present the Reads2Map workflows to build linkage maps from sequencing data of experimental F1 outcrossing populations testing combinations of upstream tools.
#Genodive for polyploids software#
Thus, good-quality genetic maps validate all upstream procedures and help to identify the best combinations of software and parameters. Genotyping errors lead to an overestimation of recombination events amount, inflated linkage map distances, and issues while grouping and ordering markers. Because the genetic properties of meiotic events are well-known, it is possible to identify low-quality markers using linkage analysis. Changes in a single parameter in the pipeline can cause downstream consequences in the analysis quality. For each step of the procedure, such as alignment of reads, SNPs identification, and genotype calling, several tools are available, all with different methods and parameters to be selected by users. High-throughput sequencing methods produce millions of sequence reads that need to be processed by bioinformatic tools before being applied in genetics research. 3University of Sao Paulo, Sao Paulo, Brazil. 2North Carolina State University, Raleigh, NC. 1 Texas A&M University, College Station, TX. Pereira 2, Marcelo Mollinari 2, and Augusto F. Amadeu 3, David Byrne 1, Oscar Riera-Lizarazu 1, Guilherme S. Reads2Map: Practical and reproducible workflows to build linkage maps from sequencing data - presented by Cris Taniguti et al.Ĭristiane H.Introduction to fitPoly - presented by Roeland Voorrips.Introduction to polyRAD - presented by Lindsey Clark.Introduction to SuperMASSA - presented by Marcelo Mollinari.Overview of genotype calling - presented by Roeland Voorrips.The development version of polyRAD 2.0 can be installed from GitHub. We will also present Miscanthus sacchariflorus as a use case, in which introgression has occurred among diploid, triploid, and tetraploid populations.
#Genodive for polyploids how to#
Examples of how to code this information in various crops will be presented in the digital poster. A new slot called “taxaPloidy” contains one integer for each individual to indicate its ploidy, and acts as a multiplier for the values stored in “possiblePloidies”. The “possiblePloidies” slot will still be used to indicate potential inheritance modes for loci. polyRAD 2.0 will support multiploidy, allowing simultaneous genotyping of individuals of different ploidies. Although the original version of polyRAD allowed inheritance model to vary across the genome, it still required all individuals to be the same ploidy, limiting its use in staple crops such as banana and yam in which breeding populations typically consist of a mixture of ploidies. It can use population structure or mapping population design to inform genotype calls and can export discrete or continuous genotypes. PolyRAD is an R package for Bayesian genotype calling from sequence read depth in diploid and polyploid organisms. Sacks. Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL.
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