Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

Barley (Hordeum vulgare L.) is considered a good genetic model for evaluating mechanisms of drought tolerance, and it is the most important threat to crop production worldwide. This study aimed to identify single-nucleotide polymorphisms (SNPs) associated with agronomic, morphological and physiological traits in a population of 137 recombinant chromosome substitution lines (RCSL) of barley, which were evaluated under rainfed conditions, in Cauquenes, southern Chile (35 degrees 58' S, 72 degrees 17' W). The annual precipitation was 299 mm during the growing season. Fifty-two significant QTLs were detected for the studied traits, which explained between 5% and 13.8% of the phenotypic variation. A genomic region on chromosome 1H (that comprises SNPs 2711-234 and 1923-265) accounted for 13.4% and 13.8%, respectively, of the grain yield variation. In addition, SNPs 8388-578 and 7639-122 on the chromosome 5H had a moderate effect, explaining 12.8% of the plant height variation. Moreover, some SNPs were associated with more than one trait, and clusters of QTLs for yield and related traits were also found. Finally, the QTLs identified in the present study are of particular interest for barley-breeding purposes under rainfed conditions.