Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize

G3 : Genes - Genomes - Genetics
Heather ManchingRandall J Wisser

Abstract

High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using Zea mays our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high...Continue Reading

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Citations

Nov 2, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Danilo Hottis LyraRoberto Fritsche-Neto
Oct 3, 2020·Genome Génome / Conseil National De Recherches Canada·Davoud TorkamanehFrançois Belzile
Sep 23, 2018·Genome Biology·Mona SchreiberMartin Mascher
Mar 7, 2020·Frontiers in Genetics·Davoud TorkamanehFrançois Belzile
Feb 16, 2021·G3 : Genes - Genomes - Genetics·Kang HuangBaoguo Li
Apr 13, 2019·Evolutionary Applications·Keith R HopperJohn M Heraty
Sep 21, 2021·G3 : Genes - Genomes - Genetics·Randall J WisserNicole M Donofrio
Nov 10, 2021·G3 : Genes - Genomes - Genetics·Kameron T WittmeyerKeith R Hopper

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Datasets Mentioned

BETA
PRJNA385842
PRJNA385849

Methods Mentioned

BETA
genotyping
PCR
MDS

Software Mentioned

CutAdapt
hcf
ade4
FASTX
Windows
vcf
FigTree
generate
BIONJ
GATK Unified Genotyper

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