玉米二态性InDel位点的鉴定和分子标记开发

Biallelic InDel loci detection and molecular marker development in maize

随着下一代测序技术(Next generation sequencing,NGS)的发展,可以利用高通量测序数据挖掘基因组特异的插入/缺失(In Del)位点,这使In Del分子标记的开发成为可能。本研究利用327份玉米自交系的测序数据,通过全基因组结构变异评估发现分布于10条染色体上的25 847个In Del位点。利用PIC值≥0.30的3 304个位点进行系统发育树构建和群体结构分析,其结果与利用SNP位点分析获得的结果高度一致,说明这些多态性较高的In Del位点可以作为代表性标记用于玉米遗传组成的差异分析。采用53对PCR引物进行扩增试验,发现这些In Del引物具有位点专化特征并且其杂交种鉴定的平均杂合率为0.569 2,表明这些标记能准确鉴定出玉米杂交种的杂合度。

Next generation sequencing （NGS） technology revolutionized the throughput of sequence data generation and enabled genome-wide identification of insertion and deletion variation （InDel） ,which could provide potential informa-tion for molecular marker development. However,large scale characterization of InDel in maize genome was poorly under-stood. Here,we evaluated 327 maize inbreed lines genomes and detected more than 25 847 biallelic InDel loci across ten chromosomes. 3 304 InDel loci with relative high PIC values were used to construct the genetic dendrogram,which was consistent with the results concluding from all called SNP loci, suggesting that these biallelic InDel loci could indiscrimi-nately describe maize genome variations. To explore the application of the InDel loci,we developed 53 InDel markers for PCR validation. The results exhibited that the newly developed molecular markers were not only locus specific, but had the capabilities for identifying the hybrid seed heterozygosity. Taken together,our results will particularly facilitate the develop-ment of biallelic molecular marker for studies in genetics and have potential for marker-assisted breeding.