Data from: Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

To selectively capture flowering associated sequences specific to strawberry, genomic DNA subtraction was performed between a pool of five strawberry genotypes and nine non-angiosperm species using Suppression Subtractive Hybridisation (SSH) technique. A total of 287 subtracted fragments were used to construct a strawberry-specific Subtracted Diversity Array (SDA). Validation of the array revealed a high subtraction efficiency (99%), indicating that the subtracted fragments are strawberry-specific. To investigate the ability of SDA for marker-trait association, three segregating populations: (1) DN ‘01-061-311’ x SD ‘Juliette’, (2) DN ‘01-061-311’ x DN ‘05-069-63’ and (3) DN ‘01-061-311’ x DN ‘05-069-194’ were chosen for BSA based on flowering habits of parental genotypes. The DNA of the individuals derived from the F1 populations were pooled into four bulks: strong day-neutral (DN1), intermediate day-neutral (DN2), weak day-neutral (DN3) and short day (SD) according to flowering strength. Each DNA bulk was hybridised separately onto the SDA. All hybridisations were performed with six technical replicates and two biological replicates to ensure microarray reproducibility, resulting in 12 data points per feature.

为选择性捕获草莓特异性开花相关序列，本研究采用抑制性消减杂交（Suppression Subtractive Hybridisation, SSH）技术，以5个草莓基因型混合池与9个非被子植物物种混合池为材料开展基因组DNA消减杂交实验。共计获得287个消减片段，用于构建草莓特异性消减多样性阵列（Subtracted Diversity Array, SDA）。阵列验证结果显示其消减效率达99%，表明所获得的消减片段具有草莓特异性。为探究SDA应用于标记-性状关联分析的能力，本研究依据亲本基因型的开花习性，选取3个分离群体：(1) DN ‘01-061-311’ × SD ‘Juliette’、(2) DN ‘01-061-311’ × DN ‘05-069-63’ 及(3) DN ‘01-061-311’ × DN ‘05-069-194’ 用于集团分离分析（Bulked Segregant Analysis, BSA）。将来自F1群体的单株DNA按开花强度划分为4个混合池：强日中性（DN1）、中等日中性（DN2）、弱日中性（DN3）及短日照（SD）。将每个DNA混合池分别与SDA进行杂交反应，所有杂交实验均设置6次技术重复与2次生物学重复，以保障微阵列实验的可重复性，最终每个特征位点可获得12组有效数据。