Characterization and development of EST-SSR markers in sweet potato (Ipomoea batatas (L.) Lam).

Jin-Hee Kim,Kyung-Min Kim,Il Kyung Chung,Won-Sam Jo,Jun-Hoi Kim,Jeong-Gwan Ham

doi:10.1007/s13205-016-0565-9

Abstract

In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.

Highlights

Sweet potato [Ipomoea batatas (L.) Lam.] is a hexaploid (2n = 6x = 90) plant that belongs to the family Convolvulaceae (Ting and Kehr 1953; Martin 1970)
More variations of sweet potato will be needed for its breeding, because despite its importance, this hexaploid crop is difficult to breed owing to the complexity of its genetics and the lack of genomic resources (Kriegner et al 2003; Cervantes-Flores et al 2008)
Molecular markers have great potential to speed up the process of developing improved cultivars; a little effort has been devoted to the development and application of molecular marker technology for the genetic improvement of sweet potato (Kriegner et al 2003)

Summary

Introduction

Sweet potato [Ipomoea batatas (L.) Lam.] is a hexaploid (2n = 6x = 90) plant that belongs to the family Convolvulaceae (Ting and Kehr 1953; Martin 1970). More variations of sweet potato will be needed for its breeding, because despite its importance, this hexaploid crop is difficult to breed owing to the complexity of its genetics and the lack of genomic resources (Kriegner et al 2003; Cervantes-Flores et al 2008). Molecular markers have great potential to speed up the process of developing improved cultivars; a little effort has been devoted to the development and application of molecular marker technology for the genetic improvement of sweet potato (Kriegner et al 2003). The randomly amplified polymorphic DNA (RAPD) technique developed in 1990 is a powerful molecular marker technique in genetics and plant breeding

Methods

Results

Conclusion