Development of DNA Markers to Identify Sport Cultivar ‘Summer Red’ of Fig (Ficus carica L.) by Whole-genome Resequencing

Abstract

In this study, we performed whole-genome resequencing analysis and developed DNA markers to distinguish between the fig cultivar ‘Masui Dauphine’ and sport cultivar ‘Summer Red.’ WGS short-read data for both ‘Masui Dauphine’ and ‘Summer Red’ were aligned using the genome of Horaishi_ver.1 as a reference. The alignment data were then variant-called for mapping software, and Single Nucleotide Variants (SNVs) specific to ‘Summer Red’ were extracted. Finally, cross-filtering was performed to eliminate SNVs common to variant data from two mapping softwares: BWA-MEM and Bowtie 2. Before cross-filtering, there were 6,194 and 28,790 SNVs between ‘Masui Dauphine’ and ‘Summer Red’ detected by Bowtie 2 and BWA-MEM, respectively; after cross-filtering, there were 131. Among these 131 SNVs, two Cleaved Amplified Polymorphic Sequences (CAPS) markers, s752 and s61, were developed. Both of these CAPS markers were effective at distinguishing between the two varieties grown in Aichi Prefecture.