InDel Locus Identification and Molecular Marker Development in Cyperus esculentus Based on Whole Genome Re-sequencing
Four different types of Cyperus esculentus germplasm resources were selected for whole genome resequencing,and Cyperus esculentus InDel sites were identified at the whole genome level,and effective molecular markers were developed according to the polymorphic InDel site sequence information.A total of 321 271 InDel loci were identified by GATK and SAMtools based on the sequence comparison between the resequencing data and the reference genome of the Cyperus esculen-tus,showing high density distribution on each scaffold,and more than 93％of the loci showed hetero-zygous types.According to the polymorphism analysis of InDel sites among four Cyperus esculentus germplasm species,98％of InDel sites were found to be non-polymorphic,and 6 036 polymorphic InDel sites were identified.Based on the insertion/deletion sequence length analysis of polymorphic InDel sites,829 polymorphic InDel sites with insertion/deletion sequence length greater than 20 bp were selected,which was suitable for the development of InDel molecular markers that could be detected by agarose gel electrophoresis.Eight polymorphic sites were selected for InDel molecular marker development and agarose gel electrophoresis test.The results showed that the identified polymorphic InDel sites were real and reliable,and the developed InDel molecular markers were suitable and available.In this study,a large number of polymorphic InDel sites were identified by different types of Cyperus esculentus germplasm,and suitable,accurate and effective InDel molecular markers could be developed,which greatly enriched the molecular marker resources of Cyperus escu-lentus germplasm,and provided reliable technical support for more accurate evaluation,identification and utilization of Cyperus esculentus germplasm resources.
万方数据
维普
