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Certified organic crop area is continuously increasing in European Union and in Latvia (Eurostat data), despite somewhat lower yield and higher potential for disease damage in organic farming. It is increasingly recognized that breeding varieties for organic farming requires focus on specific traits that may be less important under conventional agriculture. Molecular markers are becoming essential tools for plant breeding allowing reducing time and cost of development of new varieties by early selection of progeny with desired traits. However, there is lack of information on molecular markers for traits that may be important for organic farming, such as plant morphological traits ensuring competitive ability with weeds, yield and yield stability under organic growing conditions, nutrient use efficiency, and resistance to diseases. We have selected 145 Latvian varieties and breeding lines along with 46 foreign accessions for association mapping panel and genotyped those with 1,536 single-nucleotide polymorphism (SNP) markers using Illumina GoldenGate platform and barley oligo pooled array 1. In parallel to genotyping, 154 of the 191 spring barley genotypes contrasting for traits that are important for organic farming are currently in field trials under conventional and organic management. The success of association mapping in structured natural populations depends on the extent of linkage disequilibrium (LD) and ability to control for the population structure during statistical analyses. Preliminary results based on principal component and phylogenetic analyses of 1,003 SNP markers with average polymorphism information content (PIC) of 0.394 suggested that the set of germplasm is relatively uniform with the exception of a few six-row varieties. STRUCTURE analysis based on the ΔK value suggested that the population could be partitioned into two clusters. The mean LD (r 2 > 0.1) extended over 10-cM distance suggesting that the available marker density may be sufficient for association mapping. Plots of pairwise LD along the chromosomes indicated uneven distribution of LD blocks in barley genome. |
