Horticulture, Environment, and Biotechnology

, Volume 57, Issue 1, pp 69–78 | Cite as

Complete chloroplast genome sequence of Solanum nigrum and development of markers for the discrimination of S. nigrum

Research Report Genetics and Breeding
First Online:
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Abstract

Solanum nigrum is a wild non-tuber-bearing species that serves as an excellent resource in potato breeding due to its resistance potential against biotic and abiotic stresses. However, sexual hybrids between S. nigrum and S. tuberosum are difficult to produce because these species are highly incompatible. Therefore, somatic hybridization is used to introduce various traits from this wild species into potato. After somatic hybridization, it is essential to select fusion products often the aid of molecular markers. In this study, we obtained the chloroplast genome sequence of S. nigrum by next-generation sequencing technology and compared it with those of four other Solanaceae species to develop specific markers for S. nigrum. The chloroplast genome has a total sequence length of 155,432 bp. Its size, gene content, order and orientation are similar to those of the four other Solanaceae species, but there are some structural variations at repeat and junction areas. Phylogenic analysis revealed that S. nigrum is located in the same clade as Nicotiana tabacum and S. tuberosum is the least closely related species. After detailed comparisons of the chloroplast genome sequences of the five Solanaceae species, we identified 76 InDels (Insertion/Deletions), including 47 insertions and 29 deletions in the intergenic and intragenic regions. Based on these InDels, we developed seven markers for discriminating S. nigrum from other Solanum species. The results obtained in this study can be used to select somatic fusion products and accelerate breeding using S. nigrum.

Additional key words

InDel late blight resistance molecular marker potato Solanum tuberosum 
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Copyright information

© Korean Society for Horticultural Science and Springer-Verlag GmbH 2016

Authors and Affiliations

  1. 1.Highland Agriculture Research InstituteNational Institute of Crop Science, RDAPyeongchangKorea
  2. 2.Department of Horticulture and Institute of Life and EnvironmentDaegu UniversityGyeongsanKorea

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