Genotyping‐by‐Sequencing for Plant Breeding and Genetics

Abstract

Rapid advances in "next-generation" DNA sequencing technology have brought the US$1000 human (Homo sapiens) genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotypingby-sequencing (GBS) has been developed as a rapid and robust approach for reduced-representation sequencing of multiplexed samples that combines genome-wide molecular marker discovery and genotyping. The fl exibility and low cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Furthermore, we highlight areas in which GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improvement of bioinformatics. The ultimate goal of plant biology scientists is to connect phenotype to genotype. In plant breeding, the genotype can then be used to predict phenotypes and select improved cultivars. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics-assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.

Forest genomics research and development in Canada: Priorities for developing an economic framework

“…In summary, the introduction of genomic selection with emphases on large selection intensity, coupled with SE is expected to produce gains far exceeding those obtained through traditional breeding (El-Kassaby; unpublished). Costs for whole-genome sequencing and genotyping have dropped almost exponentially over the past 10 years (Poland and Rife 2012), yet phenotyping for important wood characteristics is still tedious and costly (Porth et al 2013b). With traditional tree breeding, every single tested tree requires phenotyping, with genomic selection, only a fraction needs to be phenotyped for the proper development of accurate genomic-based prediction models as progeny testing can be omitted.…”

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

“…Recently the high-throughput SNP genotyping techniques based on NGS method are used to analyze the genetic diversity (Kumar et al 2012;Shirasawa et al 2016). The NGS based advanced techniques such as genotyping-by-sequencing (GBS) (Elshire et al 2011;Poland and Rife 2012) and restriction site-associated DNA sequencing (RAD-Seq) have become popular choice for genetic analysis because they are low cost and flexible (Davey et al 2011) in experiment design.…”

Perceived Acceptability of Implementing Marker-Assisted Selection in the Forests of British Columbia

“…Prices have dropped from over $5000 per sequenced Mb in 2001 to just over $0.10 per sequenced Mb in 2011 [11]. In a study that examined genomic selection in Eucalyptus, it was estimated that progeny tests performed on 20,000 individuals would cost $51 USD per seedling [12].…”