Abstract
Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public–Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.
Highlights
Barley (Hordeum vulgare L.) is the most widely grown cereal in the Nordic countries, and with 159 million tonnes produced from 51 million hectares globally, it is the fourth most widely produced cereal in the world
We report of three putatively new Quantitative Trait Loci (QTL) located on chromosomes 1HS and 3HS and 5HL and allele combinations associated with scald resistance in Nordic spring barley, detected from Multi-parent Advanced Generation Inter-Cross (MAGIC) populations by using a multi-locus genome-wide association approach in Genomic Association and Prediction Integrated Tool (GAPIT)
MAGIC 1 + 2 had six distinct QTL, MAGIC 3 with LOD values between 4.60 (MAGIC 3) had three, MAGIC 4 had four, and the three significant markers associated in MAGIC 1 to 4 co-localised with three separate QTL detected in the individual populations
Summary
Barley (Hordeum vulgare L.) is the most widely grown cereal in the Nordic countries, and with 159 million tonnes produced from 51 million hectares globally, it is the fourth most widely produced cereal in the world. Most of the barley harvest is used as feed and food, and approximately 20% of worldwide barley production is used by the malting industry (FAOSTAT 2020). Fungal pathogens cause significant yield losses in barley production and Rhynchosporium commune Zaffarano, McDonald and Linde sp. (formerly: R. secalis (Oudem.) J.J. Davis) (Zaffarano et al 2011) is one of the most important diseases worldwide (Avrova and Knogge 2012; Zhang et al 2020). The name R. graminicola Heinsen 1897 is suggested to be used as a replacing synonym for R. commune due to its longer history (Crous et al 2021). R. commune is the causal agent of barley scald, known as leaf scald, leaf blotch or Rhynchosporium
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