Abstract
To study the SSR loci information and develop molecular markers, a total of 435,858 unigenes in transcriptome of Polygonatum sibiricum were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MISA software, and SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 112,728 SSR loci were found in the transcriptome of Polygonatum sibiricum, which distributed in 435,858 unigenes with a distribution frequency of 25.86%. Mo-nucleotide and Di-nucleotide repeat were the main types, accounted for 83.83% of all SSRs. The repeat motifs of A/T and AC/GT were the predominant repeat types of Mo-nucleotide and Di-nucleotide, respectively. A total of 113,305 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. One hundred and fifty-four of the 500 randomly selected primers not only produced fragments with expected molecular size but also had high polymorphism, which could accurately separate the tested varieties. The gene function of unigenes containing SSR was mostly related to the molecular function of Polygonatum sibiricum. The SSR markers in transcriptome of Polygonatum sibiricum show rich type, strong specificity, and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. The developed markers can also provide technical methods for molecular identification of intraspecific species of Polygonatum Mill. and maker-assisted breeding of superior varieties of Polygonatum Mill.
Highlights
Polygonatum sibiricum was a perennial herb in Liliaceae, more than 60 species globally, mainly distributed among the north temperate zone and the north subtropical zone [1]
A total of 112,728 SSR loci were found in 435,858 unigenes of P. sibiricum transcriptome by MISA
The total number of SSR loci more than 12 bp in the transcriptome of P. sibiricum was 105,186, of which 37,290 were more than 20 bp and 67,896 were 12-20 bp. These results indicated that the SSR loci of P. sibiricum transcriptome were moderately polymorphic
Summary
Polygonatum sibiricum was a perennial herb in Liliaceae, more than 60 species globally, mainly distributed among the north temperate zone and the north subtropical zone [1]. In China, 31 species of Polygonatum Mill. With the clarification of the effective components of Polygonatum, its medicinal value and economic value have been gradually recognized by the market. Unreasonable logging and habitat destruction have become more and more serious, resulting in the loss of Polygonatum germplasm resources, and some Polygonatum germplasm resources are on the verge of extinction [3]. It was necessary to systematically collect and protect Polygonatum Mill. Germplasm resources, so as to provide effective reference for its germplasm resources, improved variety breeding, classification basis, and protection strategies. The traditional procedure for identifying Polygonatum Mill. plants depended on the morphological characteristics such as the length-width ratio of Polygonatum leaves, the presence or absence of short hairs on the back of leaves, the length of pedicels, and the upper
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