基于高通量测序的棉花InDel标记开发及其应用  

Development and Application of Cotton In Del Markers Based on High Throughput Sequencing

作　　者：陆海燕[1] 陈璐 王显生[1] 赵涵[1] 沈奇[1] Lu Haiyan;Chen Lu;Wang Xiansheng;Zhao Han;Shen Qi(Provincial Key Laboratory of Agrobiology,Jiangsu Academy of Agricultural Sciences,Nanjing 210014,China;Yancheng Teachers University,Yancheng,Jiangsu 224007,China)

机构地区：[1]江苏省农业科学院/江苏省农业生物学重点实验室,南京210014 [2]盐城师范学院,江苏盐城224007

出　　处：《棉花学报》2019年第4期297-306,共10页Cotton Science

基　　金：农业农村部物种品种资源保护费(111821301354051027)

摘　　要：【目的】获得可以用于棉花品种鉴定和纯度检测的二态性InDel标记,提高棉花种子的检验精确度和效率,为棉花的分子育种发挥作用。【方法】基于来源不同的121份棉花全基因组信息,根据高多态性信息含量筛选多态性高的InDel位点,开发二态性InDel标记,并在我国66个棉花品种的遗传距离分析和聚类分析中进行应用。【结果】基于121份棉花的二代测序数据获得10967个InDel位点,合成了85对InDel引物,选择其中有效引物64对,其中At亚组的特异引物35对、Dt亚组特异引物29对,At、Dt亚组染色体的平均最小等位频率分别为0.45、0.32,多态信息含量分别为0.49、0.40;所用的66个棉花品种的遗传距离范围是0.04~0.65cM(厘摩),平均为0.39cM,遗传距离最大的2个品种是泗棉3号和中棉所36,遗传距离最小的是徐棉18和徐杂3号。【结论】开发的64个棉花二态性InDel标记能有效地通过揭示品种间的遗传距离反映品种之间的亲缘关系,区分来源不同的棉花品种,具有一定的理论意义和应用价值。[Objective] Dimorphic InDel markers can be used for cotton variety identification and purity detection, to improve the accuracy and efficiency of cotton seed testing, and to play a role in molecular breeding of cotton.[Method] Based on the whole genome sequencing of 121 cotton varieties from different sources, the InDel markers with high polymorphism were developed according to polymorphism information content(PIC) and were applied in the genetic distance analysis and cluster analysis by using 66 cotton varieties in China.[Result] Totally 10 967 InDel were identified based on the next generation sequencing data of 121 cotton varieties. Among the 85 pairs of InDel primers synthesized, 64 were selected including 35 from At group and 29 from Dt group. The minimum average allelic frequency(MAF) of At and Dt chromosomes were 0.45 and 0.32, respectively, while the PIC were 0.49 and 0.40, respectively. The genetic distances of the 66 cotton varieties ranged from 0.04 to 0.65 centimorgan (cM), with an average of 0.39 cM. The two varieties with the largest genetic distance were Simian 3 and CCRI 36, and the two varieties with the smallest genetic distance were Xumian 18 and Xuza 3.[Conclusion] The 64 cotton dimorphic InDel markers can effectively reveal the relationships among varieties based on the genetic distance, and distinguish cotton varieties from different sources, which has certain theoretical significance and application value.

关 键 词：棉花 重测序 INDEL标记 品种鉴定 

分 类 号：S562[农业科学—作物学]