SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance

Sukhjiwan Kaur; Rohan B E Kimber; Noel O I Cogan; Michael Materne; John W Forster; Jeffrey G Paull

doi:10.1016/j.plantsci.2013.11.014

SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance

Plant Sci. 2014 Mar:217-218:47-55. doi: 10.1016/j.plantsci.2013.11.014. Epub 2013 Dec 1.

Authors

Sukhjiwan Kaur¹, Rohan B E Kimber², Noel O I Cogan¹, Michael Materne³, John W Forster⁴, Jeffrey G Paull⁵

Affiliations

¹ Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia.
² South Australian Research and Development Institute, GPO Box 397, Adelaide, South Australia 5001, Australia.
³ Department of Environment and Primary Industries, Biosciences Research Division, Grains Innovation Park, PMB 260, Horsham, Victoria 3401, Australia.
⁴ Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia; La Trobe University, Bundoora, Victoria 3086, Australia. Electronic address: john.forster@depi.vic.gov.au.
⁵ School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia.

PMID: 24467895
DOI: 10.1016/j.plantsci.2013.11.014

Abstract

Ascochyta blight, caused by the fungus Ascochyta fabae Speg., is a common and destructive disease of faba bean (Vicia faba L.) on a global basis. Yield losses vary from typical values of 35-40% to 90% under specific environmental conditions. Several sources of resistance have been identified and used in breeding programs. However, introgression of the resistance gene determinants into commercial cultivars as a gene pyramiding approach is reliant on selection of closely linked genetic markers. A total of 14,552 base variants were identified from a faba bean expressed sequence tag (EST) database, and were further quality assessed to obtain a set of 822 high-quality single nucleotide polymorphisms (SNPs). Sub-sets of 336 EST-derived simple sequence repeats (SSRs) and 768 SNPs were further used for high-density genetic mapping of a biparental faba bean mapping population (Icarus×Ascot) that segregates for resistance to ascochyta blight. The linkage map spanned a total length of 1216.8 cM with 12 linkage groups (LGs) and an average marker interval distance of 2.3 cM. Comparison of map structure to the genomes of closely related legume species revealed a high degree of conserved macrosynteny, as well as some rearrangements. Based on glasshouse evaluation of ascochyta blight resistance performed over two years, four genomic regions controlling resistance were identified on Chr-II, Chr-VI and two regions on Chr-I.A. Of these, one (QTL-3) may be identical with quantitative trait loci (QTLs) identified in prior studies, while the others (QTL-1, QTL-2 and QTL-4) may be novel. Markers in close linkage to ascochyta blight resistance genes identified in this study can be further validated and effectively implemented in faba bean breeding programs.

Keywords: Breeding; Comparative genetics; Disease resistance; Fungal disease; Grain legumes; Trait dissection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ascomycota
Disease Resistance / genetics*
Genetic Linkage
Genome, Plant
Phenotype
Plant Diseases
Polymorphism, Single Nucleotide*
Quantitative Trait Loci*
Synteny
Vicia faba / genetics*
Vicia faba / immunology