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Open Access Highly Accessed Research article

An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley

Hui Liu14, Micha Bayer1, Arnis Druka1, Joanne R Russell1, Christine A Hackett2, Jesse Poland3, Luke Ramsay1, Pete E Hedley1 and Robbie Waugh15*

Author Affiliations

1 Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK

2 Biomathematics and Statistics Scotland (BioSS), Invergowrie, Dundee, Scotland DD2 5DA, UK

3 Hard Winter Wheat Genetics Research Unit, USDA-ARS and Department of Agronomy, Kansas State University, 4011 Throckmorton, Manhattan, KS 66506, USA

4 Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Scotland KY16 9ST, UK

5 Division of Plant Sciences, James Hutton Institute, Invergowrie, The University of Dundee. College of Life Sciences, Dundee, Scotland DD2 5DA, UK

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BMC Genomics 2014, 15:104  doi:10.1186/1471-2164-15-104

Published: 6 February 2014

Abstract

Abstract

We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e).

Background

Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today.

Results

Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification.

Conclusions

GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis.

Keywords:
Barley; Dwarfing gene; Genotyping by sequencing; Physical map