Lex Jeannette, Ahlemeyer Jutta, Friedt Wolfgang, Ordon Frank
Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany,
J Appl Genet. 2014 Aug;55(3):295-305. doi: 10.1007/s13353-014-0214-0. Epub 2014 May 1.
A set of about 100 winter barley (Hordeum vulgare L.) cultivars, comprising diverse and economically important German barley elite germplasm released during the last six decades, was previously genotypically characterized by single nucleotide polymorphism (SNP) markers using the Illumina GoldenGate BeadArray Technology to detect associations with phenotypic data estimated in three-year field trials at 12 locations. In order to identify further associations and to obtain information on whether the marker type influences the outcome of association genetics studies, the set of winter barley cultivars was re-analyzed using Diversity Arrays Technology (DArT) markers. As with the analysis of the SNPs, only polymorphic markers present at an allele frequency >5% were included to detect associations in a mixed linear model (MLM) approach using the TASSEL software (P ≤ 0.001). The population structure and kinship matrix were estimated on 72 simple sequence repeats (SSRs) covering the whole barley genome. The respective average linkage disequilibrium (LD) analyzed with DArT markers was estimated at 5.73 cM. A total of 52 markers gave significant associations with at least one of the traits estimated which, therefore, may be suitable for marker-assisted breeding. In addition, by comparing the results to those generated using the Illumina GoldenGate BeadArray Technology, it turned out that a different number of associations for respective traits is detected, depending on the marker system. However, as only a few of the respective DArT and Illumina markers are present in a common map, no comprehensive comparison of the detected associations was feasible, but some were probably detected in the same chromosomal regions. Because of the identification of additional marker-trait associations, it may be recommended to use both marker techniques in genome-wide association studies.
一组约100个冬大麦（Hordeum vulgare L.）品种，包括过去六十年来发布的多样且具有经济重要性的德国大麦优良种质，此前已使用Illumina GoldenGate BeadArray技术通过单核苷酸多态性（SNP）标记进行了基因型特征分析，以检测与在12个地点进行的为期三年的田间试验中估计的表型数据之间的关联。为了识别更多关联，并获取有关标记类型是否会影响关联遗传学研究结果的信息，使用多样性阵列技术（DArT）标记对该组冬大麦品种进行了重新分析。与SNP分析一样，仅纳入等位基因频率>5%的多态性标记，以使用TASSEL软件在混合线性模型（MLM）方法中检测关联（P≤0.001）。基于覆盖整个大麦基因组的72个简单序列重复（SSR）估计群体结构和亲缘关系矩阵。用DArT标记分析的各自平均连锁不平衡（LD）估计为5.73 cM。共有52个标记与至少一个估计性状有显著关联，因此可能适用于标记辅助育种。此外，通过将结果与使用Illumina GoldenGate BeadArray技术生成的结果进行比较，发现根据标记系统的不同，各个性状检测到的关联数量也不同。然而，由于在共同图谱中仅存在少数各自的DArT和Illumina标记，因此无法对检测到的关联进行全面比较，但有些可能在相同的染色体区域被检测到。由于识别出了额外的标记-性状关联，可能建议在全基因组关联研究中同时使用这两种标记技术。
