10.3389/fpls.2018.00564.s003 Josh P. Clevenger Josh P. Clevenger Walid Korani Walid Korani Peggy Ozias-Akins Peggy Ozias-Akins Scott Jackson Scott Jackson Table_2_Haplotype-Based Genotyping in Polyploids.CSV Frontiers 2018 polyploid SNPs SNP array Arachis haplotype markers sequence-based genotyping 2018-04-26 04:27:03 Dataset https://frontiersin.figshare.com/articles/dataset/Table_2_Haplotype-Based_Genotyping_in_Polyploids_CSV/6187730 <p>Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs) are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2) was developed for Arachis hypogaea (peanut), an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.</p>