棉花是我国主要的天然纤维作物，而随着耕地面积的不断减少，为了保障国家粮食及棉花安全，发展盐碱地植棉是一个重要策略。新疆是我国最主要的植棉区，但土地次生盐碱化严重。陆地棉是最主要的栽培种，但现有品种的遗传背景狭窄，其野生类型即半野生棉的遗传多样性丰富，有耐盐碱等优异基因源。本研究以前期新疆次生盐碱地鉴定出来的耐、感半野生棉材料为基础，通过构建遗传分离群体及各种组学分析，利用QTL定位和次生盐胁迫下耐、感材料间的转录组、小RNA组及蛋白组差异，发掘出半野生棉中与次生盐碱应答相关遗传位点并进行精细定位、候选基因的筛选及功能标记的开发，为将来棉花耐盐分子标记辅助育种提供参考；结合棉花现有基因组测序结果以及模式生物中相对明确的抗逆应答与信号转导途径，构建棉花次生盐碱胁迫的应答途径，并筛选出该途径中耐、感材料间差异显著的基因，通过遗传转化对这些基因进行功能验证，为将来转基因抗逆育种提供基因资源。

Cotton is the main natural fiber crop in China, but the cotton plantation areas have been reduced seriously with the decreasing of arable land. And thus cultivating saline lands is a alternative strategy. Xinjiang is the most important province for cotton production in China, though, that had faced the serious problem of soil secondary salinization. Upland cotton is the main cultivated cotton variety, characterised with limited genetic diversity. Semi-wild cotton, the wild-type upland cotton, is in the advantage of abundant genetic diversity, salt-tolerance, drought-tolerance and so on. This project is carried out to unravel and exploit the mechanism of response to soil secondary salinization stress in Xinjiang for semi-wild cotton. Quantitative trait loci (QTL) and omics analyses, combined with the elucidated aboitic response and regulation pathways in model organisms, were used to identify the genetic loci and candidate genes associated with abiotic-stress response. And then fine mapping and functional markers development were carried out for marker-assisted selection (MAS) breeding. Moreover, the soil secondary salinization stress response pathway were constructed based on the data of omics analysis and differentially expressed genes in this pathway were selected for functional analysis. And thus these may provide useful gene resource for improving soil secondary salinization stress tolerance in transgenic breeding.