qPCR data of ALS gene copies expression in Echinochloa spp.

The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid Echinochloa spp. resistant to ALS inhibitors, in particular E. crus-galli and E. oryzicola. Molecular characterization led to identification three ALS genes in E. crus-galli and two in E. oryzicola. The two species also carried different point mutations conferring resistance: Ala122Asn in E. crus-galli and Trp574Leu in E. oryzicola. Mutations involved in ALS-inhibitor resistance in the different species were associated to the same gene copy (ALS1), which resulted to be significantly more expressed than the other copies (ALS2 and ALS3) in both species. These results explain the high resistance level of these populations and why mutations in the other ALS copies are not involved with herbicide resistance. This study was used to analyze the relative expression of the ALS gene copies: ALS1 carrying the mutations responsible for target-site resistance to the ALS inhibitor penoxsulam with respect to the expression of the other ALS gene copies (ALS2-3). Comparisons also were made among populations belonging to different Echinochloa species, having different resistance pattern and collected in sites far from each other. Two susceptible populations (16S and 161S) and four resistant populations (42R, 44R, 45R and 46R=102R) were included in the analyses. Among these populations, one belonged E. crus-galli species (16S) and the others belonged E. oryzicola species. They were collected in different rice areas of Italy: 16S, 161S, 42R and 44R were collected in the main Italian rice area, i.e. Lombardy and Piedmont, whereas 45R was collected in Sardinia and 46R in Emilia Romagna. Among the eight reference genes analyzed, the two with expression, on average, higher and with more primer specificity were chosen as reference genes for the gene expression study, Rubisco and 18S. Specific primers for the different ALS gene copies were designed based on an ALS gene part including two allele-specific SNPs: F1_590Tm 5’-GAGCACACACATACTTGGGGCAT-3’, F2_590Cm 5’-AGCACACACATACTTGGGGCAC-3’, R1_621 5’-GAGCATCTTCTTAATTGCTGCACGG-3’, R2_621 5’-GAGCATCTTCTTGATTGCTGCACGT-3’. cDNA diluted at 1:25 of three herbicide-treated (T) and three non-treated (NT) plants per population (in three technical replicates) were tested in the qPCR analyses to determine the relative expression of the different ALS gene copies using two reference genes. In this repository, we reported the amplification plots and dissociation curves obtained from: - the analyses of the two reference genes, Rubisco and 18S, in all populations included in the experiment; - the analyses of ALS genes with the specific primers for all populations included in the experiment.水稻种植系统的可持续性正受到大量多倍体稗属（Echinochloa spp.）种群的威胁，这类种群对乙酰乳酸合酶（ALS）抑制剂具有抗性，其中尤以光头稗（E. crus-galli）和稻稗（E. oryzicola）最为典型。通过分子表征分析，研究人员在光头稗中鉴定出3个ALS基因拷贝，在稻稗中则鉴定出2个。两个物种的抗性均由不同的点突变介导：光头稗为Ala122Asn突变，稻稗为Trp574Leu突变。两类物种中介导ALS抑制剂抗性的突变均靶向同一基因拷贝（ALS1），且在两个物种中，ALS1的表达量均显著高于另外两个拷贝（ALS2与ALS3）。上述结果阐明了此类种群具备高抗性水平的原因，同时解释了为何其余ALS基因拷贝的突变不会介导除草剂抗性。 本研究旨在分析ALS基因拷贝的相对表达水平：对比携带介导ALS抑制剂五氟磺草胺（penoxsulam）靶标抗性突变的ALS1，与其余ALS基因拷贝（ALS2、ALS3）的表达量。同时，研究还对隶属于不同稗属物种、具备不同抗性类型且采自异地的种群进行了比较分析。 本分析共纳入2个敏感种群（16S与161S）以及4个抗性种群（42R、44R、45R与46R=102R）。其中仅16S属于光头稗（E. crus-galli），其余种群均为稻稗（E. oryzicola）。所有种群均采自意大利不同水稻产区：16S、161S、42R与44R采自意大利核心水稻产区伦巴第（Lombardy）与皮埃蒙特（Piedmont）；45R采自撒丁岛（Sardinia），46R采自艾米利亚-罗马涅（Emilia Romagna）。 在分析的8个内参基因中，筛选出平均表达量更高、引物特异性更强的两个作为本基因表达研究的内参基因：核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco）与18S核糖体RNA（18S）。 针对不同ALS基因拷贝的特异性引物，基于包含两个等位基因特异性单核苷酸多态性（SNP）的ALS基因片段设计，引物序列如下： F1_590Tm 5'-GAGCACACACATACTTGGGGCAT-3' F2_590Cm 5'-AGCACACACATACTTGGGGCAC-3' R1_621 5'-GAGCATCTTCTTAATTGCTGCACGG-3' R2_621 5'-GAGCATCTTCTTGATTGCTGCACGT-3' 将每个种群的3株除草剂处理组（T）与3株未处理组（NT）的cDNA按1:25比例稀释，设置3次技术重复，采用两个内参基因通过实时荧光定量PCR（qPCR）分析不同ALS基因拷贝的相对表达量。 本数据集仓库中收录了以下实验获得的扩增曲线与熔解曲线： - 实验中所有种群的两个内参基因（Rubisco与18S）扩增分析结果； - 实验中所有种群采用特异性引物开展的ALS基因扩增分析结果。