Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

By Jesse Poland, P. Brown, M. Sorrells, Jean-Luc Jannink. PLoS ONE, 2012

1,623 citations recorded by the source corpus.

Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 34,000 SNPs and 240,000 tags onto the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W9784×Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/57b8f5810ea62eee4a520fc1e3a4b1cb587bcbd5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Plant Science

Citations in the corpus

Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, methodology): “[14], and 200 ng of DNA were digested using Cut Smart Buffer for 3 h at 37 °C.”
Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton (2014, methodology): “…L.), the employed two-enzyme GBS approach is expected to identify and score SNPs evenly among chromosomes with respect to chromosome length, as well as at a fairly uniform density along chromosomes with the exception of recombinationally suppressed centromeric regions (Poland et al., 2012).”
SNP Discovery through Next-Generation Sequencing and Its Applications (2012, background): “Poland et al. [120] recently demonstrated the use of two restriction enzymes to perform GBS in bread wheat, a hexaploid genome.”
Genomic Selection for Quantitative Adult Plant Stem Rust Resistance in Wheat (2014, methodology): “, 2011) was used to generate genomewide markers according to the protocol described in Poland et al. (2012a). A total of 27,434 polymorphisms were detected.”
Genomic Selection in Wheat Breeding using Genotyping‐by‐Sequencing (2012, methodology): “h e GBS libraries were constructed in 95-plex using the P384A adaptor set (Poland et al., 2012).”
Genetic and Genomic Resources of Small Millets (2016, background): “…which have potentially led to discovery of SNP markers and genetic analysis even in non-model crop plants (Wenzl et al., 2004; Davey et al., 2011; Etter et al., 2011; Elshire et al., 2011; Poland et al., 2012; Kilian et al., 2012; Petroli et al., 2012), may be adopted as alternative approaches.”
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array (2014, background): “, 2013) or reduced-representation sequencing in diverse populations of individuals (Elshire et al., 2011; Poland et al., 2012; Saintenac et al., 2011, 2013; Van Poecke et al., 2013).”
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, positive): “Genotyping by sequencing (GBS) is a related, highly costeffective, genotyping procedure (Elshire et al., 2011; Poland et al., 2012; Peterson et al., 2014).”
Overview and Application of QTL for Adult Plant Resistance to Leaf Rust and Powdery Mildew in Wheat (2014, methodology): “The GBS approach was recently applied to construct genetic maps of crops with large genomes (Elshire et al., 2011; Poland et al., 2012), allowing direct analysis of genetic variation and reducing the effect of ascertainment bias caused by the SNP discovery process.”