高粱自交系获得与缺失变异的挖掘及其对重要农艺性状影响的研究

sorghum (Sorghum bicolor) is a C4 annual crop with a high photosynthetic rate, high biomass production, and high tolerance to adverse conditions such as drought, salinity, poor nutrient supplies. In China, sorghum has a long history of cultivation and has been used as an important source of folder, feed, fibre and food. Currently, sorghum is amongst the priority list of biofuel crops and considered the crop of choice for the first and second generation biofuels. However, sorghum has a relative short history of breeding and many bottlenecks still need to be overcome before it is transformed into a dedicated biofuel crop..PAV (Presence and absence variation) is an important type of genome structural variations, which has much larger effects on the size and the number of functional genes in a genome than SNPs and InDels. Recent results obtained through the next-generation sequencing technologies have demonstrated the wide existence of PAV in plant genomes. However, their origins, genome diversity and evolution, molecular functions and potential use for crop genetic improvement are rarely thoroughly examined. In this project, we will take advantage of the next-generation sequencing technology to identify PAVs in representative sorghum inbred lines and examine their frequencies and distribution in a panel of diverse sorghum lines. The associations of important PAVs with agronomic traits will be analysed using the association mapping approach, and subsequently the functions of the candidate genes will be studied using a diverse molecular genetics toolkits to establish the PAV-gene-trait relationship. The research is expected to shed new lights on the origins, diversity and functions of PAV in sorghum genomes and provide novel insights in the use of genome structural variations for genetic improvement of sorghum and related crops.

为满足国家能源和粮食安全需求，急需发展适宜边际土壤种植、多用途的高粱。发掘新的基因资源和拓展育种思路有利于加快高粱分子育种进程。获得与缺失变异（PAV，presence/absence variation）是一种重要的基因组结构变异，直接影响基因数目和基因组大小，影响基因组的尺度远远大于SNP或InDels。PAV广泛存在于作物中，但其对重要农艺性状的影响和分子育种应用的研究稀缺。我们利用遗传多样性丰富的高粱自交系，分析高粱基因组中PAV的类别、数目、分布和进化历史；并对关键的PAV做群体重要农艺性状的关联分析，对其影响的重要基因进行功能分析，建立PAV-基因-性状关系，解决高粱分子遗传育种基因（重要功能变异位点）资源缺乏的问题，为高粱及相关作物分子育种提供新思路。

获得与缺失变异(Presence/absence variants，PAVs)是一类由DNA片段的缺失和插入引起的基因组结构变异。根据缺失或插入的DNA片段的大小，PAV分为小片段PAV(small-size PAV) (40 bp-10 kb)和大片段PAV (large-size PAV) (>10 kb)。PAVs在基因组中发生的频率较低，但PAVs所影响到的基因组大小和基因数目却远高于它们，是生物基因组结构变异和表型变异的重要来源。.高粱（Sorghum bicolour）是一种重要的粮食、经济、能源等多功能C4作物。为满足国家能源和粮食安全需求，发掘新的基因资源和育种思路加速高粱分子育种进程势在必行。本研究利用遗传多样性丰富的高粱自交系，及甜高粱与籽实高粱的重组自交系，分析了高粱基因组中PAVs的数目、分布和遗传多样性；对关键的lsPAVs进行重要农艺性状的关联分析。利用gss PAVs构建遗传图谱，并对它们在不同种植环境下测定的重要农艺学性状进行了QTL定位。.基于3个高粱品种（Keller，E-tian和Ji2731）的重测序数据，比较基因组学分析，挖掘96个大于30kb的PAVs和5511个小片段PAVs。利用分子生物学及遗传学方法进行验证。基因组间lsPAVs在自然选择压力下存在着遗传多样性，发现分布频率与lsPAV影响的基因功能相关，与其序列特征关系不大。关联分析发现21个lsPAVs与15个重要农艺性状相关，共挖掘出41个位点。选取了360个PAVs发展为分子标记，构建了总长为1430.2 cM的遗传图谱。该图谱由325个PAV分子标记和49个SSR分子标记组成。标记间的平均距离为3.83 cM，覆盖了640.4 Mb的物理距离。基于此图谱，对在中国和丹麦条件下种植的3个群体的23个性状进行了QTL定位。结果共获得了64个QTLs，这些QTLs分布在10条连锁群上，LOD值的范围为3.0-20.5，解释率为5.1-37.5%。.综上所述，本研究首次对高粱基因组内的PAVs完成了分布、序列特征及遗传多样性及功能的研究，构建了首张高粱的PAV标记遗传图谱，完成了不同地区种植的高粱群体的重要农艺学性状的QTLs定位，对lsPAVs进行重要农艺性状的关联分析。为高粱的分子育种和遗传改良提供了新的思路和手段。