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Genotyping by Sequencing (GBS)

How Genotyping-by-sequencing (GBS) Works

GBS is a marker-assisted selection (MAS) technology to accelerate plant breeding. This technology consists of the sequencing of a reduced representation of an entire genome. The sequencing is performed on samples from a population of interest, and this population is selected based on its variability for a certain set of yield traits or disease responses.

A reduced representation of the genome is obtained through digesting DNA samples with some restriction enzymes. Adapters are then ligated and library size is selected and sequenced. The focus is on the part of the genome around the restriction enzyme, simplifying analysis complexity without sacrificing genotyping capabilities.

After samples are sequenced, they go through a comprehensive pipeline that can associate markers (or mutations) from different samples with phenotypic data, leading to identification of high-resolution molecular markers related to yield traits or disease responses.

Figure #1: Genetic Distance Matrix
Demultiplexing & Quality Control
  • Deconvolute sequencing library data into multiple samples
  • Insert length determination
  • Contamination removal
  • Low quality sequence trimming
  • Sequence quality report
Map reads to the reference
  • Alignment of short-reads
  • BAM manipulation
  • Quality and coverage mapping report
Marker Detection
  • Multi sample variant detection
  • Variant filtering
  • Genotype imputation
  • Functional annotation of genomic variants
  • Summary variants report
Diversity Analysis
  • Genetic distance matrix calculation
  • Population structure analysis
  • PCA, K-Means, hierarchical clustering
  • Phylogeny
  • Population diversity report
Genotype-phenotype Associations (Optional)
  • Variants filtering
  • Genome wide association studies
  • Filtering of variants associated with phenotype
  • Statistical analysis of markers associated with traits
  • Final report

GBS is an ultimate marker-assisted selection (MAS) technology to accelerate plant breeding.Some more details.....