Abstract:

This study developed a genome-wide InDel marker map of Jinlan pummelo（Citrus maxima）genome. The next generation sequencing（NGS）technology was applied to produce the deep resequencing data of the individual，and was mapped to the reference genome using BWA-MEM. The pipeline with strict parameters improved accuracy and effectiveness of heterozygous InDel markers. The primers designment was performed by using Primer 3.0. The agarose gel electrophoresis of polymerase chain reaction（PCR）product was used to validate the effectiveness of primers. A total of 81 effective paired primers were identified. The corresponding markers covered nearly the whole genome of Jinlan pummelo，with an average number of nine InDel markers per chromosome. Of these markers，24 markerswere succussed in distinguishing the 48 pummelo individuals，which showed that two paired markers could distinguish Jinlan pummelo and other 47 pummelo individuals. Finally，UPGMA was used to construct the phylogeny of 48 pummelo，which was divided into three groups at threshold 0.611 of genetic similarity coefficient. This study suggested that the genome-wide InDel markers developed using deep resequencing was suitable for the identification of the different germplasms of pummelo，and provides a basis in variety protection and origin traceability management.

Key words: pummelo, re-sequencing, InDel marker