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

Shan Yang,Fei Huang,Yongji Huang,Jiayun Wu,Rukai Chen,Zuhu Deng,Qinnan Wang,Xinlong Liu,Xueting Li,Muqing Zhang,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0197458

Shan Yang, Fei Huang + Show 9 more

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https://doi.org/10.1371/journal.pone.0197458

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Journal: PloS one	Publication Date: May 16, 2018
Citations: 12	License type: CC BY 4.0

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.

Highlights

Sugarcane is an important sugar and energy crop worldwide
We found for the first time that base 89 was a stable base mutation in the nrDNA-Internal transcribed spacers (ITS) sequence of the Saccharum genus and was present in S. spontaneum genetic material
The primers FO13, RO13, FI16, and RI16 were found to be suitable for identification of S. spontaneum genetic material and its progeny

Summary

Introduction

Sugarcane is an important sugar and energy crop worldwide. Sugarcane plants belong to the grass family Gramineae, genus Saccharum, and related plants in this family include Miscanthus, Sclerostachya, Erianthus, and Narenga. The Saccharum genus consists of six species, including Saccharum officinarum (2n = 80), S. sinense (2n = 112–120), S. barberi (2n = 82– 124), S. edule (2n = 60, 70, 80), and two wild species, S. robustum (2n = 60–120) and S. spontaneum (2n = 40–128) [1]. S. barberi and S. sinense are secondary species derived from hybridization of S. officinarum and S. spontaneum [2]. S. sinense, S. barberi, S. robustum, S. spontaneum, and S. officinarum are important parental resources in sugarcane breeding [3].

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