A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

PLoS One. 2018 May 16;13(5):e0197458. doi: 10.1371/journal.pone.0197458. eCollection 2018.

Abstract

The identification of germplasm resources is an important aspect of sugarcane breeding. The aim of this study was to introduce a new method for identifying Saccharum spontaneum and its progeny. First, we cloned and sequenced nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) sequences from 20 Saccharum germplasms. Analysis of these nrDNA-ITS sequences showed a stable mutation at base 89. Primers (FO13, RO13, FI16, and RI16) were then designed for tetra-primer amplification refractory mutation system (ARMS) PCR based on mutations at base 89 of the nrDNA-ITS sequence. An additional 71 Saccharum germplasms were identified using this tetra-primer ARMS PCR method, which confirmed that the method using the described primers successfully identified Saccharum spontaneum and progeny. These results may help improve the efficiency of modern molecular breeding of sugarcane and lay a foundation for identification of sugarcane germplasms and the relationships among them.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Ribosomal Spacer / genetics*
  • Evolution, Molecular
  • Genetic Variation / genetics
  • Haplotypes / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics*
  • Saccharum / genetics*

Substances

  • DNA, Ribosomal Spacer

Grants and funding

This work was funded by the National Natural Science Foundation of China (31571730 and 31401440) and was supported by the science and technology major project of the Fujian Province of China (2015NZ0002-2) and special fund for scientific and technological innovation of the Fujian Agriculture and Forestry University (KFA17168A). This project was also supported by an open project of the Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources (SKLCUSA-b201606). These funding institutions played no role in study design, data collection or analysis, or manuscript preparation.