Passport data and genotyping data related to the WEW-GB collection

Plant material A panel of 283 accessions of wild emmer wheat collected across countries of the Fertile Crescent was organized and is currently maintained at the CREA Research Centre for Genomics and Bioinformatics (WEW-GB: Wild Emmer Wheat at CREA Research Centre for Genomics and Bioinformatics). Accessions were obtained either from genebanks (the United States Department of Agriculture - Agricultural Research Service National Small Grains Collection (USDA-ARS NSGC), the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), the National BioResource Project (NBRP) through KOMUGI) or from partners. The plant materials represent the entire Fertile Crescent region where wild emmer naturally occurs, from the Northern East area, encompassing Turkey, Iraq and Iran to the Southern region (Southern Levant), which includes Israel, Lebanon and Syria. All accessions have been undergone to one cycle of single seed descendance (SSD). Genotyping, filtering and mapping of the polymorphic SNPs on the reference wild emmer genome Young leaves of a single plant from each SSD were collected and genomic DNA was extracted using the CTAB method (Doyle and Doyle, 1987). The 283 accessions were genotyped with the Affymetrix 35K Axiom array at the Genomics Facility of University of Bristol. Allele calling was carried out using the Affymetrix proprietary software package Axiom Analysis Suite®, according to the Axiom Best Practices Genotyping workflow. It includes a Bayesian based clustering that was performed selecting generic priors, as this setting produced less mis-clustering than when bread wheat specific priors had been applied. Only SNPs classified as polymorphic at high resolution and as off-target variants by the Affymetrix software were selected. They were then filtered for missing data (max 10%) and for heterozygosity (max 10%). The probe sequences of the polymorphic SNPs were used as queries in BLASTn similarity searches against the pseudomolecules of the wild emmer v2 reference genome (accession Zavitan, Zhu et al., 2019) to obtain marker physical position. Parameters for BLASTn were as follows: word size 11, gap open 5, gap extend 2, penalty -2, reward 1. Both allele variants were individually considered for BLAST. Analogous parameters were used to BLASTn sequences of SNP markers against the T. aestivum reference genome (IWGSC RefSeqv2.1, Zhu et al. 2021) and the T. durum reference genome (Svevo v1, Maccaferri et al., 2019).

植物材料：本研究整理了一套覆盖新月沃地（Fertile Crescent）各国的283份野生二粒小麦（wild emmer wheat）种质资源，目前保藏于基因组与生物信息学研究中心（CREA Research Centre for Genomics and Bioinformatics），种质资源编号为WEW-GB：CREA基因组与生物信息学研究中心野生二粒小麦资源。
这些种质资源分别来自种质库：美国农业部农业研究服务局国家小谷物种质资源库（USDA-ARS NSGC）、莱布尼茨植物遗传与作物植物研究所（IPK）、通过KOMUGI获取的国家生物资源计划（NBRP），以及合作单位。
该批植物材料覆盖了野生二粒小麦自然分布的全部新月沃地区域，北至包含土耳其、伊拉克与伊朗的东北区域，南至涵盖以色列、黎巴嫩与叙利亚的南部黎凡特（Southern Levant）地区。所有种质资源均经过一轮单粒传代（single seed descendance, SSD）处理。
对参考野生二粒小麦基因组上的多态性单核苷酸多态性（single nucleotide polymorphism, SNP）进行基因分型、过滤与定位：采集每一份单粒传代材料单株的幼叶，采用CTAB法（Doyle与Doyle, 1987）提取基因组DNA。
283份种质资源均在布里斯托大学基因组学平台使用Affymetrix 35K Axiom基因分型芯片完成基因分型。依据Axiom最佳实践基因分型流程，使用Affymetrix专有软件包Axiom Analysis Suite®进行等位基因分型（allele calling）。该流程包含基于贝叶斯的聚类分析，本次分析选择通用先验参数进行聚类，相较于使用普通小麦特异性先验参数的设置，该参数组合的聚类错误率更低。
仅保留Affymetrix软件鉴定为高分辨率多态性且为脱靶变异（off-target variants）的SNP位点，随后对这些位点进行过滤：缺失数据率不超过10%，杂合率不超过10%。
将多态性SNP的探针序列作为查询序列，针对野生二粒小麦v2版参考基因组（材料Zavitan，Zhu等, 2019）的拟分子（pseudomolecules）进行BLASTn相似性搜索，以获取标记的物理位置。BLASTn的参数设置如下：单词长度（word size）为11，空位开放罚分（gap open）为5，空位延伸罚分（gap extend）为2，错配罚分（penalty）为-2，匹配奖励（reward）为1。BLAST分析时分别考虑两种等位基因变异。
使用相同参数将SNP标记序列分别比对至普通小麦（Triticum aestivum, T. aestivum）参考基因组（IWGSC RefSeqv2.1，Zhu等, 2021）以及硬粒小麦（Triticum durum, T. durum）参考基因组（Svevo v1，Maccaferri等, 2019）。