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玉米低密度育种芯片开发及在种质资源评价中的应用
郭子锋1, 王山荭1, 刘 蓓2, 李文学1, 王红武1
0
(1.中国农业科学院作物科学研究所;2.中玉金标记生物(北京)技术股份有限公司)
摘要:
SNP基因分型芯片是分子育种的重要工具,高密度SNP芯片往往存在标记冗余、价格高、目标性不强等问题,是分子育种走向常规化、规模化的主要限制因素之一。在此,我们开发了一款低密度育种芯片,并就芯片在种质资源评价中的价值进行了分析。首先,我们对37份玉米自交系进行10X重测序,获得了18.2Mb的SNP标记,从中挑选2,080个SNPs;再从已开发55K芯片中挑选3,390个缺失率低、多态性高、Conversion Type为Poly High Resolution的标记;最后从HapMap3中挑选586个标记,设计的育种芯片共包含6,056个SNPs,采用靶向测序基因型检测(Genotyping by target sequencing, GBTS)技术对标记进行检测。通过自然群体、双亲群体和多亲本重组自交系(Multiparent advanced generation inter-cross, MAGIC)群体验证表明,设计的育种芯片平均捕获率为70.6%,检测到的原始设计位点数为4,773~5,963个,MAF>0.4和PIC>0.4的标记比例分别为57.6%和88.6%。用该芯片对226份玉米种质资源进行评价,主成分分析可以将其划分为温带和热带两大类群,UPGMA聚类分析进一步将其划分为6个已知类群,分别是瑞德、兰卡斯特、PB、旅大红骨、四平头和热带类群,Structure群体结构分析没有出现最佳K值,但热带材料都独立成群;类群内和类群间的遗传距离平均值分别为0.394和0.472,其中PB群内的遗传距离最小(0.316),热带类群内的遗传距离最大(0.424);类群间,瑞德与热带之间的遗传距离最大(0.493);类群间的遗传分化系数(FST)表明,PB类群与其他类群间的FST均较大。
关键词:  玉米  SNP  育种芯片  种质资源
DOI:10.13430/j.cnki.jpgr.20210712001
投稿时间:2021-07-12修订日期:2021-08-24
基金项目:国家重点研发计划课题(2017YFD0101201);中央级公益性科研院所基本科研业务费专项(Y2020PT20)
Development of Maize Low Density Breeding Chip and Its Application in Germplasm Resources Evaluation
GUO Zi-feng1, WANG Shan-hong1, LIU Bei2, LI Wen-xue1, WANG Hong-wu1
(1.Institute of Crop Science, Chinese Academy of Agricultural Sciences;2.China Golden Marker Biotechnology Co, Ltd)
Abstract:
SNP genotyping chip is an important tool for molecular breeding. High density SNP chip often has some problems such as marker redundancy, high price, and poor target, limiting its use in the normalization and scale of molecular breeding. Here we developed a low density breeding chip. The panel of 6,056 markers were assembled using three resources, consisting of: (1) 2,080 key SNPs of 18.2Mb SNPs which were identified from 10X sequencing of 37 maize inbred lines; (2) 3,390 qualified markers with low missing rate, high polymorphism and Conversion Type being as Poly High Resolution within 55K SNP array; (3) 586 markers that were selected from HapMap3. Genotyping by target sequencing (GBTS) technology was used to detect the markers. Through the verification of natural population, bi-parent population and multiparent advanced generation inter-cross (MAGIC) population, the average capture rate of the breeding chip was 70.6%. The original design markers were detected ranged from 4,773-5,963, and 57.6% and 88.6% markers were found by applying minor allele frequency (MAF) > 0.4 and polymorphic information content (PIC) > 0.4, respectively. We evaluated 226 inbred lines with this breeding chip. Within this collection two groups (temperate vs. tropical) had been classified by principal component analysis (PCA), and six known groups (Reid, Lancaster, PB, LRC, SPT and tropical) were proposed using cluster analysis. Structure analysis has not revealed the best K value. The mean genetic distance within and among groups were 0.394 and 0.472, respectively. The genetic distance within PB group was the smallest (0.316), and the genetic distance within tropical group was the largest (0.424). The largest genetic distance (0.493) was observed between group Reid and tropical. The genetic differentiation coefficient (FST) among the groups indicated that the FST of PB group was larger than that of other groups.
Key words:  maize  SNP  breeding chip  germplasm resource