RAD sequencing for the development of microsatellite markers for identification of Malaysian taro cultivars

Abstract

The progress in next-generation sequencing (NGS) has transformed the discovery and development of microsatellite markers, particularly for understudied species. In this study, one of the NGS platforms adopted was restriction site-associated DNA sequencing (RAD-seq) to identify and develop microsatellite markers for taro. A total of 8,490,604 clean reads were generated and assembled into 222,445 contigs with only 3,280 contigs found to contain a total of 3454 repeats. From this total, only 1,790 repeats were successfully designed as a flanking primer, and 14 microsatellites were selected at random for cultivar identification of Malaysian taro. The analysis of 14 novel simple sequence repeat (SSR) markers only showed that twelve SSR markers were polymorphic with the remaining two SSR markers, CesSSR9 and CesSSR11, monomorphic. The analysis of polymorphic SSR markers revealed the presence of 50 alleles ranging between two (CesSSR5) and seven (CesSSR13) having an average of 4.17 alleles per locus. The values of the polymorphic information content ranged from 0.05 (CesSSR5) to 0.59 (CesSSR7) with an average of 0.33 per locus. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed that cultivar MINYAK was unable to be differentiated from cultivar PUTIH. As such, these newly developed microsatellite markers will provide a tool for molecular identification in taro and provide necessary information for future biodiversity conservation and gene bank management of taro.

Keywords:

• NGS sequencing
• RAD sequencing
• SSR marker
• Taro

Acknowledgement

The authors would like to acknowledge anyone who indirectly involved in this project.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability

All data that support the findings reported in this study are available from the corresponding author upon reasonable request.

Additional information

Funding

This research was funded by Malaysian government under NKEA EPP14 project.