Table_1_Pre-emptive Breeding Against Karnal Bunt Infection in Common Wheat: Combining Genomic and Agronomic Information to Identify Suitable Parents.XLSX

Wheat (Triticum aestivum L.) is the most widely grown cereal crop in the world and is staple food to half the world’s population. The current world population is expected to reach 9.8 billion people by 2050, but food production is not expected to keep pace with demand in developing countries. Significant opportunities exist for traditional grain exporters to produce and export greater amounts of wheat to fill the gap. Karnal bunt, however, is a major threat, due to its use as a non-tariff trade barrier by several wheat-importing countries. The cultivation of resistant varieties remains the most cost-effective approach to manage the disease, but in countries that are free of the disease, genetic improvement is difficult due to quarantine restrictions. Here we report a study on pre-emptive breeding designed to identify linked molecular markers, evaluate the prospects of genomic selection as a tool, and prioritise wheat genotypes suitable for use as parents. In a genome-wide association (GWAS) study, we identified six DArTseq markers significantly linked to Karnal bunt resistance, which explained between 7.6 and 29.5% of the observed phenotypic variation. The accuracy of genomic prediction was estimated to vary between 0.53 and 0.56, depending on whether it is based solely on the identified Quantitative trait loci (QTL) markers or the use of genome-wide markers. As genotypes used as parents would be required to possess good yield and phenology, further research was conducted to assess the agronomic value of Karnal bunt resistant germplasm from the International Maize and Wheat Improvement Center (CIMMYT). We identified an ideal genotype, ZVS13_385, which possessed similar agronomic attributes to the highly successful Australian wheat variety, Mace. It is phenotypically resistant to Karnal bunt infection (

小麦（Triticum aestivum L.）乃全球种植最广泛的谷物作物，也是全球一半人口的主食。据预测，到2050年，世界人口将增至98亿，但粮食生产预计无法与发展中国家需求同步增长。传统谷物出口国在生产和出口更多小麦以满足需求缺口方面存在着巨大的机遇。然而，由于数个小麦进口国将其作为非关税贸易壁垒， Karnal bunt（小麦腥黑穗病）构成了主要威胁。培育抗病品种是管理该疾病最具成本效益的方法，但在无病国家，由于检疫限制，遗传改良难度较大。在本研究中，我们报告了一项旨在识别连锁分子标记、评估基因组选择作为工具的前景，并优先考虑适合作为亲本的 wheat genotypes（小麦基因型）的预防性育种研究。在基因组关联（GWAS）研究中，我们确定了六个与Karnal bunt抗性显著相关的DArTseq标记，这些标记解释了7.6%至29.5%的观察到的表型变异。基因组预测的准确性估计在0.53至0.56之间变化，这取决于它是否仅基于已确定的数量性状位点（QTL）标记或使用全基因组标记。鉴于作为亲本的基因型需要具备良好的产量和物候特性，我们进一步开展了研究，以评估国际玉米小麦改良中心（CIMMYT）提供的Karnal bunt抗性种质资源的农艺价值。我们鉴定了一个理想的基因型，ZVS13_385，其农艺特性与成功程度极高的澳大利亚小麦品种Mace相似。该基因型在表型上对Karnal bunt感染具有抗性（