Genomics-assisted selection of Solanum chilense introgression lines for enhancing drought resistance in tomatoes

西红柿是仅次于谷物和马铃薯的最大粮食作物，是人类饮食中营养素、维生素和其他促进健康的代谢物的重要来源：必须增加产量，培育可持续生产是一个高度优先事项。提高水分利用效率的育种和在水分供应不足的情况下获得高产的能力是番茄和其他茄类作物（包括马铃薯和茄子）的重要性状。pennellii Solanum、chilense Solanum和sitiens Solanum是发现于干旱地区、对水限制环境适应性最强的3种番茄野生近缘植物，它们具有独特的形态、分类和生态类型。然而，良好的遗传和基因组资源仅存在于pennellii，其中建立和高度成功的策略已被用于开发等位基因变异。在这个项目中，我们将为剩余的干旱适应物种S. chilense和S. sitiens开发新的遗传和基因组资源。我们将生成bb0 400 x深度的基因组序列数据，并对这两个基因组进行从头组装，以提供一个具有不同尺度结构变异的优秀参考序列；这项工作将与从事其他茄类植物基因组研究的欧洲生物信息学专家（瓦赫宁根大学、亚琛工业大学和马克斯普朗克分子植物生理学研究所）密切合作，并将在生物信息学技能和计算能力方面提供强大的能力建设。基因组序列将用于设计SNP标记和构建番茄葡萄球菌群体的遗传图谱。随着QTL研究向基因水平的发展，基因组序列将成为极为宝贵的资源。我们将利用高通量SNP基因分型平台，从IIVR获得的一种独特杂交开始，快速创建一个智利玉米的渐渗系群体，现在是BC1F1代。完成后的文库将进行水分利用效率、根系性状和抗萎蔫性的筛选，以发现新的QTL。MicroTom中的快速回交程序将用于对含有两个智利葡萄和一个秘鲁葡萄等位基因的复杂杂交产生的渗入进行表型选择。在选择过程结束时出现的基因渗入将通过基因组重新测序来精确定义，为精细定位做准备。

Tomato, the biggest food crop after cereals and potato, is a vital source of nutrients, vitamins and other health promoting metabolites in the human diet: production must increase, and breeding for sustainable production is a high priority. Breeding for improved water use efficiency and ability to give high yields where water availability is poor are important traits for tomato, and other Solanaceous crops, including potato and Brinjal. Solanum pennellii, Solanum chilense and Solanum sitiens are the three tomato wild relatives that are found in arid areas and have the greatest adaptation to water-limited environments, and each has a distinct morphology, classification and ecotype. However, good genetic and genomic resources only exist for S. pennellii, where well-established and highly successful strategies have been employed to exploit allelic variation. In this project we will develop novel genetic and genomic resources for the remaining drought-adapted species, S. chilense and S. sitiens. We will generate >400 x depth genomic sequence data and perform de novo genome assembly for these two genomes to provide an excellent reference sequence complete with structural variants at different scales; this will be done in close collaboration with European bioinformatics experts working with other Solanum genomes (Wageningen UR, RWTH Aachen University and Max Planck Institute of Molecular Plant Physiology), and will provide strong capacity building in bioinformatic skills and computing power. Genome sequences will be used for SNP marker design and a genetic map constructed for an S. chilense x S. lycopersicum population. Genome sequences will become extremely valuable resources as QTL studies progress to the gene level. We will rapidly create, using a high-throughput SNP genotyping platform, a population of introgression lines for S. chilense starting with a unique hybrid obtained by IIVR, now in the BC1F1 generation. The completed library will be screened for water use efficiency, root traits and resistance to wilting to discover new QTL. A rapid backcross program in MicroTom will be used to phenotypically select introgressions arising from a complex hybrid containing alleles from two S. chilense and one S. peruvianum accession. Introgressions present at the end of the selection process will be precisely defined by genome re-sequenced in preparation for fine mapping.