Haplotype-Based Genotyping in Polyploids

Frontiers in Plant Science
Josh ClevengerScott A Jackson

Abstract

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 ...Continue Reading

References

Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Apr 16, 2011·Bioinformatics·Derek W BarnettGabor T Marth
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Jun 30, 2011·Bioinformatics·Eva-Maria WillingChristine Dreyer
Nov 11, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hongde QinBaozhu Guo
Jul 10, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Joseph Lachance, Sarah A Tishkoff
Jul 15, 2015·G3 : Genes - Genomes - Genetics·Josh P Clevenger, Peggy Ozias-Akins

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Citations

Jun 9, 2020·Critical Reviews in Biotechnology·Ramaswamy ManimekalaiMallikarjuna Kandalam
May 14, 2020·G3 : Genes - Genomes - Genetics·Carolina ChavarroPeggy Ozias-Akins
Mar 8, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hui ZhangCharles Chen
Aug 9, 2020·Frontiers in Plant Science·Natascha D WagnerElvira Hörandl
Jul 1, 2019·Planta·Jean-Marcel Ribaut, Michel Ragot
Sep 6, 2020·G3 : Genes - Genomes - Genetics·Paul I OtyamaEthalinda K S Cannon

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Methods Mentioned

BETA
genotyping
sequence-based prediction

Software Mentioned

samtools mpileup
Samtools
HAPLOSWEEP
ML
Axiom Analysis Suite
bamtools
Axiom Arachis
SWEEP

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