This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

All nineteen Colletotrichum isolates causing anthracnose in lupin plants growing in southern Chile belong to Colletotrichum lupini, confirming an absence of interspecific variation in the causal agent of anthracnose. Nevertheless, intraspecific genetic diversity was detected with random amplified polymorphic DNA (RAPD) markers. Based on a multiloci analysis, 14 molecular phenotypes were described among the local C. lupini isolates. The largest genetic distance between two isolates was 0.57. The analyzed isolates showed clear differences in virulence on susceptible cultivar 'Kiev Mutant' with disease severity ranging from 15 to 75% of seedlings. The high degree of DNA polymorphism, the large number of different molecular phenotypes, and the variation in virulence suggest the existence of different strains. Study of strain virulence and diversity may aid in the development of more efficient genetic improvement programs for anthracnose tolerance.

ABSTRACT. 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°58' S, 72°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. Keywords:Hordeum vulgare, mixed model, recombinant chromosome substitution lines, segregation distortion.Identificação de QTL associados a características agronômicas, morfológicas e fisiológicas em cevada sob condições de sequeiro, usando marcadores SNP RESUMO. Cevada (Hordeum vulgare L.) é uma cultura modelo para a avaliação genética dos mecanismos de tolerância à seca; a ameaça mais importante para a produção agrícola a nível mundial. Objetivou-se identificar polimorfismos de nucleotídeo único (SNP) associados a características agronômicas, morfológicas e fisiológicas numa população de 137 linhas recombinantes com substituição cromossômica (RCSL) de cevada, avaliadas sob condições de sequeiro, em Cauquenes, sul do Chile (35°58' S, 72°17' O). A precipitação anual foi de 299 mm durante o período vegetativo. Cinquenta e dois QTLs foram encontrados para as características estudadas, explicando entre 5% e 13.8% da variação fenotípica. A região genômica no cromossomo 1H (que compreende os SNPs 2711-234 e 1923-265) foi responsável de ~13% da variação no rendimento de grãos. Além disso, os SNPs 8388-578 e 7639-122 no cromossomo 5H teve um efeito moderado, explicando 12,8% da variação para altura da planta. Além disso, alguns SNPs foram associados com mais de uma característica, e grupos de QTLs para rendimento de grãos e características relacionadas também foram encontrados. Finalmente, os QTLs identificados no presente estudo podem ser de particular interesse para fins de melhoramento de cevada em ambiente de sequeiro.Palavras-chave: Hordeum vulgare, modelo misto, linhas recombinantes com substituição cromossômica, distorção de segregação.