GWAS Studies

Genotyping by Sequencing

Genotyping by sequencing, or next-generation genotyping, is a genetic screening method for discovering novel plant and animal SNPs and performing genotyping studies. For some applications, such as genotype screening and genetic mapping, sequence-based genotyping provides a lower-cost alternative to arrays for studying genetic variation. Sequences predetermined areas of genetic variation over many samples.

  • Provides a low cost per sample for certain applications
  • Reduces ascertainment bias compared to arrays
  • Identifies variants other than SNPs, including small insertions, deletions, and microsatellites
  • Enables comparative analyses across samples in the absence of a reference genome
  • Informs genetic mapping, screening backcross lines, purity testing, constructing haplotype maps, association mapping, and genomic selection for plant studies

ddRAD Sequencing

Double digest restriction-site associated DNA (ddRADseq), also called ddRAD, is a variation on the RAD sequencing protocol, which is used for SNP discovery and genotyping. In this variation, the fragment shearing is replaced with a second restriction digestion to improve the tunability and accuracy of the size-selection step. The protocol also includes a second index to allow combinatorial indexing. Several RAD variations 2b-RAD, SLAF-seq, and hyRAD have been developed to address specific applications and there are multiple software packages available to analyze RAD data. No reference genome is required.

  1. Relatively inexpensive, compared to whole-genome sequencing
  2. The degree of genome coverage can be adjusted by selecting various restriction enzymes

QTL Sequencing

Quantitative trait locus (QTL)-Seq is a method that combines bulked segregate analysis (BSA) and high-throughput whole-genome re-sequencing to detect the major locus of a certain quantitative trait in a segregating population. A quantitative trait locus (QTL) is a region of DNA associated with a specific phenotype or trait that varies within a population. Typically, QTLs are associated with traits with continuous variance, such as height or skin color, rather than traits with discrete variance, such as hair or eye color. QTL mapping is a statistical analysis to identify which molecular markers lead to a quantitative change of a particular trait. Since a single loci may include many variants, imputation or whole genome sequencing is a key prerequisite for QTL mapping to enable precise identification of the contributing molecular marker. QTLs have been expanded to include variants that act at different levels throughout the genotype-to-phenotype continuum.

DArT Seq

Array-based approaches to SNP screening have been the method of choice in analyzing and associating traits with regions of the genome for many plants and animals. As sequencing costs continue to decline, new approaches that leverage next-generation sequencing (NGS) technology are being developed to perform genotyping studies. The term next-generation sequencing–based genotyping (NGG), or sequence-based genotyping, encompasses genotyping methods that leverage NGS technology. NGG includes targeted, reduced representation, and hybridization-based approaches to discover and genotype SNPs, often simultaneously in many individuals or specimens.