Genotyping By Sequencing (GBS) Based Approach in Ultra-Density Genetic Mapping, SNP Discovery and Population Evolution

Genotyping by Sequencing (GBS) based approach in ultra-density genetic mapping, SNP discovery and population evolution

Noel Chen, Ph. D.

Nana Zhang, Ph. D.

Joyce Peng, Ph. D.

Novogene Corporation

NGS based genotyping by sequencing (GBS) is a unique, rapid and cost-effective approach for large scale breeding program and population genetics study. It is a restriction enzyme based sequencing method that generates large numbers of SNPs. GBS is especially useful in species with complex genomes with no reference genome available. Applications of GBS include tracking plant and animal genotypes in breeding programs and conservation projects, examining the diversity of natural populations, discovery of new genetic markers, and screening variants prior to whole genome resequencing. This talk uses published examples to show how GBS has been applied in genetic mapping, population evolution and GWAS in crop and animal species. In the maize study, GBS was used to analyze the genetic basis of variation in plant architecture. An ultra-high density bin map was constructed with 4183 bin markers and 35 QTL affecting plant 35 QTL affecting plant architecture were detected across three environments, facilitating identification of genes and exploration of QTL for plant architecture in maize. In the chickpea example, GBS was used to explore genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. In the switchgrass study, new insights on genomic diversity, ploidy and population evolution was explored from the network-based SNP discovery protocol. GBS will play an increasingly important role in facilitating genetic mapping, traits screening and complex genetic diversity among populations in many more species, with new applications remained to be explored.