Abstract
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.
Highlights
Abiotic stresses can significantly reduce crop yields and restrict the latitudes and soils on which commercially important species can be cultivated (Lobell and Field, 2007; Jacobsen et al, 2012)
This study identifies single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population consisting of 137 recombinant chromosome substitution lines (RCSL) of barley (Matus et al, 2003), evaluated under contrasting water availability
The average grain yield (GY) under rain-fed was reduced by 81% in relation to fully irrigated condition, indicating that the barley RCSL lines were exposed to a severe water stress
Summary
Abiotic stresses can significantly reduce crop yields and restrict the latitudes and soils on which commercially important species can be cultivated (Lobell and Field, 2007; Jacobsen et al, 2012). To determine the genetic basis of complex traits, important genetic, and genomic resources have been developed in a wide range of species (Kota et al, 2003; Mora et al, 2015), including barley (Kota et al, 2003; Close et al, 2009; Zhou et al, 2015). Single nucleotide polymorphism (SNP) markers are the most abundant sequence variations encountered in eukaryotic genomes (Griffin and Smith, 2000), and in barley offer the potential for generating very high-density genetic maps (Close et al, 2009), providing a useful tool for quantitative trait locus/loci (QTL) mapping for marker-assisted selection (MAS; Sato and Takeda, 2009; Szucs et al, 2009)
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