新疆是我国最大的棉花生产基地，干旱已成为制约新疆棉花生产持续发展的关键因子，造成新疆棉花减产、品质下降。如何提高新疆棉花耐旱性一直是育种家的研究重点。全集因组关联分析（GWAS）是一种基于群体结构、全基因组连锁不平衡队数量性状位点及表型性状进行高精度定位的方法，现已成为已成为基因挖掘和群体研究的重要手段之一。转录组测序技术（RNA-seq）作为一种新的转录组研究手段,利用新一代测序技术能够更为快速、准确地为人们提供更多的生物体转录信息。本研究旨在利用SLAF简化基因组测序技术对280份陆地棉种质材料开展GWAS研究，结合已定位的抗旱性状QTL定位结果以及抗旱种质材料RNA-seq的数据进行联合分析，解析新疆陆地棉抗旱机制，挖掘陆地棉种质材料抗旱性状有利等位基因，开发与抗旱及产量性状紧密相关 SNP 标记，为深入研究棉花抗旱分子机理和抗旱分子设计育种等打下坚实基础。

Xinjiang is the most important cotton-growing areas in China. Drought is one of the most principal factors that restrict cotton production in Xinjiang. How to improve future drought resistance of cotton in Xinjiang has been the focus of cotton breeders. Genome-wide association studies (GWAS) which is based on theory of linkage disequilibrium is one of the most important tools to excavate excellent genes and carry out population genetics research. RNA-seq as a new research method, it can be more quickly and afford more accurate transcriptome’s information while using the Next-generation Sequencing (NGS) technology. In this research, drought resistance traits will be investigated and analyzed utilizing 280 upland cotton germplasm accessions natural population. Association analysis of drought tolerance related traits and phenotype effect analysis will be completed via the technology of Specific-Locus Amplified Fragment sequencing (SLAF-seq) and RNA-sequencing combining QTLs of drought tolerance related traits. QTLs of cotton drought tolerance related traits will be accurate located furthermore, excellent alleles will be dig out for molecular marker-assisted selection and ultimately achieve cotton genetic improvement and breeding application.