Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay

• Published in: Molecular breeding 2013-03, Vol.31 (3), p.631-654
• Main Authors: Locatelli, Andrés, Cuesta-Marcos, Alfonso, Gutiérrez, Lucía, Hayes, Patrick M, Smith, Kevin P, Castro, Ariel J
• Format: Article
• Language: English
• Subjects: Adaptation; agronomic traits; Agronomy; alleles; ancestry; Barley; Biomedical and Life Sciences; Biotechnology; Chromosomes; crops; field experimentation; Field tests; Gene mapping; Genetics; Genomes; Genomics; Genotypes; Germplasm; Haplotypes; Hordeum vulgare; Life Sciences; Linkage disequilibrium; malting barley; Mapping; Molecular biology; Nucleotides; phenotype; Phenotypes; Plant biology; Plant breeding; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; planting; Quantitative trait loci; Single-nucleotide polymorphism
• ISSN: 1380-3743; 1572-9788
• DOI: 10.1007/s11032-012-9820-x

The genetic basis of agronomic traits determining adaptation to specific production conditions is a key factor for the improvement of crops, including malting barley (Hordeum vulgare L.). The aim of this study was to determine the genome-wide genetic components associated with agronomic phenotypes of local and global significance in a population of 76 barley genotypes that have been introduced into Uruguay in different chronological periods. The phenotypic database was obtained from five field experiments, planted in 2 years and in two locations, where a total of 13 agronomic traits were determined. The population was genotyped with 1,033 single nucleotide polymorphisms. We found a total of 41 quantitative trait loci (QTL) in a combined analysis using all datasets and 79 QTL if we considered all the trait/experiment combinations analyzed. The highest concentration of QTL was detected on chromosomes 2H and 4H. Most QTL were detected for grain plumpness and weight. Two linkage disequilibrium (LD) blocks associated with a large number of traits were detected on 2HS. The largest LD block was composed of three haplotypes, possibly derived from three ancestors of different geographical origin. We also detected three genomic regions in different chromosomes (2H, 5H and 7H) in LD between them, associated with agronomic traits. This study provides a contribution to the understanding of the genetics of barley adaptation in the southern cone of South America. Our results showed that elite varieties have favorable alleles at different QTL, indicating that gains can be made through plant breeding.