Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, MN, USA.
Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
Pest Manag Sci. 2021 May;77(5):2477-2484. doi: 10.1002/ps.6278. Epub 2021 Feb 2.
Amaranthus palmeri is an aggressive and prolific weed species with major impact on agricultural yield and is a prohibited noxious weed across the Midwest. Morphological identification of A. palmeri from other Amaranthus species is extremely difficult in seeds, which has led to genetic testing for seed identification in commercial seed lots.
We created an inexpensive and reliable genetic test based on novel, species-specific, single nucleotide polymorphisms (SNPs) from GBS (Genotyping by Sequencing) data. We report three SNP-based genetic tests for identifying A. palmeri alone or in a mixed pool of Amaranthus spp. Sensitivity ranged from 99.8 to 100%, specificity from 99.59 to 100%. Accuracy for all three tests is > 99.7%. All three are capable of reliably detecting one A. palmeri seed in a pool of 200 Amaranthus spp. seeds. The test was validated across 20 populations of A. palmeri, along with eight other Amaranthus species, the largest and most genetically diverse panel of Amaranthus samples to date.
Our work represents a marked improvement over existing commercial assays resulting in an identification assay that is (i) accurate, (ii) robust, (iii) easy to interpret and (iv) applicable to both leaf tissue and pools of up to 200 seeds. Included is a data transformation method for calling of closely grouped competitive fluorescence assays. We also present a comprehensive GBS dataset from the largest geographic panel of Amaranthus populations sequenced. Our approach serves as a model for developing markers for other difficult to identify species. © 2021 Society of Chemical Industry.
野苋菜 Palmer 是一种具有侵略性和繁殖力的杂草物种，对农业产量有重大影响，是中西部地区禁止的有害杂草。在种子中，从其他苋菜物种中识别野苋菜 Palmer 极其困难，这导致了商业种子批中用于种子鉴定的遗传测试。
我们基于 GBS（测序基因分型）数据中的新型、物种特异性单核苷酸多态性 (SNP) 创建了一种廉价且可靠的遗传测试。我们报告了三种基于 SNP 的遗传测试，用于单独鉴定野苋菜 Palmer 或鉴定苋菜属 spp 的混合池。灵敏度范围为 99.8%至 100%，特异性范围为 99.59%至 100%。所有三种测试的准确率均>99.7%。所有三种测试都能够可靠地检测到 200 个苋菜 spp 种子池中的一个野苋菜 Palmer 种子。该测试在 20 个野苋菜 Palmer 种群以及其他八个苋菜属物种中得到验证，这是迄今为止最大和遗传多样性最多的苋菜属样本面板。
我们的工作代表了对现有商业检测方法的显著改进，产生了一种鉴定检测方法，该方法 (i) 准确，(ii) 稳健，(iii) 易于解释，(iv) 适用于叶片组织和多达 200 个种子的混合物。包括一种用于调用紧密聚集的竞争荧光测定法的数据分析转换方法。我们还提供了迄今为止最大地理面板的苋菜属种群测序的综合 GBS 数据集。我们的方法为开发其他难以识别物种的标记提供了模型。 © 2021 化学工业协会。
