## 2 Results and Discussion  
### Frequency and Distribution of Genic SSRs in the Welsh Onion Transcriptome  
Since the RNA-Seq NGS technology allows for lower cost and higher throughput transcriptome sequencing than traditional Sanger sequencing, it has been widely used in many non-model organisms, including _Tapiscia sinensis_, _Cucurbita moschata_, and _Larix kaempfer_[20, 21, 22]. In this study, a total of 6766 SSR loci containing 1-5 bp repeat motifs were found in 6206 unigenes of the Welsh onion. Of these, 5497 (88.6%) contained a single SSR locus; 486 (7.8%) contained more than one SSR, and 275 (4.4%) possessed compound SSRs. Moreover, 6486 SSR loci (except for 280 compound SSRs) located in 5983 unigenes were counted and presented based on the transcriptome data (Table 1). The repeat motifs among the 6486 SSR loci included a total of 186 types, and the number of repeats varied from five to 24. The frequency and number of each SSR motif and the percentage of the primary repeat motifs were evaluated in Tables 1 and 2. The most abundant motif was mononucleotide (52.33%) followed by trinucleotide (31.96%), dinucleotide (14.57%), tetranucleotide (1.02%), and pentanucleotide (0.12%), and the most common class was \(n=10\) (32.25%), which was mostly composed of mononucleotide repeats. In addition, the most common class of dinucleotide was \(n=6\), and other types of repeat motif were \(n=5\). A/T was the most common motif, representing 98.29% of the mononucleotide repeat motifs and 51.43% of the total repeat motifs. Additionally, the dominant repeat motifs were AG/CT (34.29%), AT/AT (33.65%), and AC/GT (31.11%) among the dinucleotides, and AAG/CTT (26.44%) and AAAAT/ATTT (33.33%) among the trinucleotides and tetranucleotides, respectively. \begin{table}
\begin{tabular}{c c c c c c c c c c c c} \hline \hline \multirow{2}{*}{**SSR Motif**} & \multicolumn{8}{c}{**Repeat Number**} & \multirow{2}{*}{**Total**} & \multirow{2}{*}{**Percentage (\%)**} \\ \cline{2-2} \cline{4-11}  & & & & & & & & & & & & \\ \hline Mononucleotide & 0 & 0 & 0 & 0 & 0 & 2060 & 548 & 297 & 489 & 3394 & 52.33 \\ Dinucleotide & 0 & 478 & 212 & 119 & 57 & 32 & 37 & 10 & 0 & 945 & 14.57 \\ Trinucleotide & 1328 & 510 & 188 & 47 & 0 & 0 & 0 & 0 & 0 & 2073 & 31.96 \\ Tetranucleotide & 52 & 14 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 66 & 1.02 \\ Pentanucleotide & 8 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 8 & 0.12 \\ Total & 1388 & 1002 & 400 & 166 & 57 & 2092 & 585 & 307 & 489 & 6486 & 100 \\ Percentage (\%) & 21.40 & 15.45 & 6.17 & 2.56 & 0.88 & 32.25 & 9.02 & 4.73 & 7.54 & 100 & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Frequencies of the different SSR repeat motif types observed in the Welsh onion transcriptome. Among the dinucleotide repeat motifs based on the 6468 SSR loci, the frequency of GA as a primary nucleotide (5.00%) was higher than GT (4.53%) in the Welsh onion transcriptome sequences (Table 3), and this result agreed with [PERSON] _et al._, (GA 22.1%, GT 15.4%) [10]. Similar results were also obtained for the bulb onion expressed sequence tags (ESTs) (GA 10.1%, GT 9.2%) [17], but GT repeats were much richer than GA repeats in the bulb onion genome [23], which was also the case in Welsh onion [9, 15]. According to the above results, the ratio of (GT)\({}_{n}\):(GA)\({}_{n}\) may be different in the transcribed and non-transcribed regions of the genome. Additionally, the GA dinucleotide repeat motif can stand for multiple codons resting within the reading frame that can be translated into different amino acids, and GA may be present in the Ala and Leu codons, which have the highest number of proteins [24]. In addition, AT was the most abundant repeat motif among the dinucleotides and was more frequent than GC in the Welsh onion (Table 1). A similar result was reported in [PERSON] _et al._, (AT 25.6%, GC 0.5%) [10] and, based on transcriptome sequencing, the same result that the AT repeat motif was more common than GC, has been obtained in many plant species, such as bulb onion, radish, mung bean, pear, Levant cotton, and so on [16, 17, 25, 26, 27].