Genetic diversity and environmental adaptation in Ethiopian tef

Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000-1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis (RDA), co..., The Ethiopian Biodiversity Institute provided the genetic materials for this study and granted access to passport information for environmental data curation. Bioclimatic (bio1-bio19) and altitudinal data were obtained using latitude and longitude coordinates from each site, with WorldClim version 2.1 layers at 10-minute resolution based on long-term averages for 1970-2000 (Fick & Hijmans, 2017). Researchers at the Ethiopian Institute of Agricultural Research, including Tadelech Bizuneh, Adanech Teshome, and Doni Hinsene, prepared DNA samples from young leaf samples for each greenhouse-grown tef accession. DNA concentration and quality were determined using a 1.5% agarose gel and a NanoDrop Spectrophotometer. The extracted DNA was sent to the BioFrontiers Sequencing Core at the University of Colorado Boulder for unique dual indexing 10 bp library preparation. Genomic libraries of the Ethiopian tef accessions were then sent to the Genomics and Microarray Core at the University of Col..., , # Data from: Genetic diversity and environmental adaptation in Ethiopian tef [https://doi.org/10.5061/dryad.8kprr4xw3](https://doi.org/10.5061/dryad.8kprr4xw3) ## Description of the data and file structure Additional_Files_SuppInfo.xlxs * S1.1: Detailed information on tef germplasm collection, DNA extraction, and plate coordinates referenced through the Illumina NovaSeq 6000 platform. - S1.2: Geographic and environmental (WorldClim version 2.1) data associated with each sample. - S1.3: Individual population genetic assignments for all samples, including axis loadings from discriminant analysis of principal components (LD1 - LD4), principal components analysis (PC1 and PC2), and K-means cluster assignments. - S1.4: Genetic distances estimated as pairwise FST, alongside geographical and environmental distance matrices, based on 39 individual samples from 16 distinct geographic locations and using 20 WorldClim environmental variables. Only sampling locations with two or more collecte...孤儿作物（orphan crops）是当地社区保障营养供给与获取经济收入的核心资源，同时可为应对粮食安全与气候脆弱性挑战提供潜在解决方案。埃塞俄比亚画眉草（tef，学名Eragrostis tef (Zucc.)）是一种小粒异源四倍体C4谷类作物，主要种植于埃塞俄比亚，因其对边际生境的适应性与极高的营养价值而备受瞩目，兼具本地与全球应用潜力。尽管其重要性不言而喻，但由于遗传改良研究有限、依赖自给自足型农业，加之其营养、经济与文化价值，该作物仍被归类为孤儿作物。尽管埃塞俄比亚前闪米特族群已种植埃塞俄比亚画眉草数千年（公元前4000年至公元前1000年），但其本地适应性的遗传与环境驱动机制仍鲜为人知。为此，我们对一批多样化的传统埃塞俄比亚画眉草种质资源进行了重测序，以解析其遗传结构，并通过冗余分析（redundancy analysis, RDA）等方法识别受环境选择的基因组区域，[原文后续内容截断]。 本研究的遗传材料由埃塞俄比亚生物多样性研究所（Ethiopian Biodiversity Institute）提供，并获准获取用于环境数据整理的种质护照信息。基于各采样点的经纬度坐标，我们获取了生物气候变量（bio1至bio19）与海拔数据，所用的WorldClim 2.1版本图层分辨率为10弧分，数据基于1970-2000年的长期平均值（Fick & Hijmans, 2017）。埃塞俄比亚农业研究所（Ethiopian Institute of Agricultural Research）的研究人员Tadelech Bizuneh、Adanech Teshome与Doni Hinsene，从温室种植的各埃塞俄比亚画眉草种质材料的幼叶中制备了DNA样本。通过1.5%琼脂糖凝胶电泳与NanoDrop分光光度计检测DNA的浓度与质量。提取得到的DNA被送至科罗拉多大学博尔德分校生物前沿测序中心，进行独特双索引10 bp文库构建。随后，埃塞俄比亚画眉草种质材料的基因组文库被送至科罗拉多大学[原文机构名称截断]基因组与微阵列中心进行后续处理。 # 数据来源：埃塞俄比亚画眉草的遗传多样性与环境适应性 https://doi.org/10.5061/dryad.8kprr4xw3 ## 数据与文件结构说明 Additional_Files_SuppInfo.xlxs * S1.1：埃塞俄比亚画眉草种质资源采集、DNA提取以及基于Illumina NovaSeq 6000测序平台的测序板坐标的详细信息。 - S1.2：与各样本相关的地理数据与环境数据（WorldClim 2.1版本）。 - S1.3：所有样本的群体遗传个体归属信息，包括主成分判别分析的轴载荷（LD1至LD4）、主成分分析结果（PC1与PC2）以及K-means聚类归属结果。 - S1.4：基于16个不同地理区域的39个个体样本，以及20个WorldClim环境变量，估算得到的成对FST遗传距离，配套地理距离与环境距离矩阵。仅保留采集样本数≥2的采样地点[原文后续内容截断]。