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KMID : 0381120170390101139
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Genes and Genomics
2017 Volume.39 No. 10 p.1139 ~ p.1156
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Development of EST-SSR markers through de novo RNA sequencing and application for biomass productivity in kenaf (Hibiscus cannabinus L.)
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Jeong Sang-Wook
Kwon Soon-Jae
Ryu Jai-Hyunk
Kim Jin-Baek
Ahn Joon-Woo
Kim Sang-Hoon
Jo Yeong-Deuk
Choi Hong-Il
Im Seung-Bin
Kang Si-Yong
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Abstract
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Kenaf is a multipurpose crop, but a lack of genetic information hinders genetic and molecular research. In this study, we aimed to develop EST-SSR markers from mutant and wild-type cultivars, and to assess the genetic diversity of the kenaf resources. A total of 33 Gb of sequence data comprising 130,480 unigenes was assembled by de novo RNA-sequencing of six kenaf cultivars, and 5619 SSRs were identified. Tri-nucleotide motifs occurred most frequently (82.67%) followed by di-, tetra-, and penta-motifs. In total, 515 polymorphic EST-SSRs were derived by pairwise comparisons of the cultivars based on in silico analyses. Of these, 70 markers were successfully validated among six cultivars. We used the six cultivars, together with 39 kenaf accessions from worldwide to assess genetic diversity and to characterize the EST-SSRs. The number of alleles per locus ranged from 2 to 8. PIC and genetic diversity values ranged from 0.08 to 0.79 and 0.08?0.82, respectively. The phylogenetic and population structure showed that the 45 accessions could be clearly divided into three groups based on different days to flowering (DTF). Genetic differentiation among the DTF groups showed a proportionally high level of variance. Association analysis between the DTF and the markers revealed three significant associations. Furthermore, using a multiplex PCR with three markers, DTF could be perfectly discriminated. These markers will be useful in marker-assisted selection after further validation with segregating populations of kenaf.
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KEYWORD
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Kenaf, Mutation breeding, De novo RNA sequencing, Expressed sequence tag (EST)-simple sequence repeat (SSR), Biomass, Association analysis
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