## 2 Results and Discussion
### Development and Detection of Genic SSR Markers  
Genic SSR markers are regarded as having great potential for genetic diversity analysis and chromosome mapping in crop species because of their specificity and high degree of conservation [29,30]. Due to the steady decrease in cost and the increase in throughput data, NGS technology has become a powerful approach for the high-throughput discovery of genes and the generation of a large amount of sequence data for the identification of molecular markers [31,32]. Therefore, the identification and development of genic SSR markers based on NGS is an efficient and cost-effective strategy.  
In this study, a total of 2710 unigenes were used to design primers, and according to the standard, a total of 2512 unigenes (92.69%) were successfully designed, which obtained 2525 primers. A total of 311 (12.32%) primer pairs located in 307 unigenes were randomly selected from 2525 primers (Table S2) to perform the preliminary test, which consisted of 217 primers (69.77%) for the trinucleotide repeats, 50 (16.08%) for the dinucleotide repeats, and 38 (12.22%) and six (1.93%) for the tetranucleotide and pentanucleotide repeats, respectively. Furthermore, the remaining 2214 primers, located in 2205 unigenes, are presented in table S1 for reference.  
In the preliminary test, a total of 165 (53.05%) primers generated stable and clear bands, out of which 91 (29.26%) polymorphic primer pairs were reliable (Table S3). Among these genic SSR markers, the majority were trinucleotide repeats (69.23%), followed by dinucleotide repeats (19.78%), and tetranucleotide repeats (10.99%). The result was consistent with the order of SSR motif frequency.  
\begin{table}
\begin{tabular}{c c c} \hline
**No.** & **Materials** & **Origin** \\ \hline
1 & “Yuanzang” & Japan \\
2 & “HanLvDaZhu” & Korea \\
3 & “WuYeQi”1 & Hebei, China \\
4 & “WuYeQi”2 & Tianjin, China \\
5 & “GaoBaiQingCaiCong” & Hebei, China \\
6 & “ZhongYingTeDa” & Henan, China \\
7 & “SanYu” & Shandong, China \\
8 & “YeFuYiHao” & Shandong, China \\
9 & “ZhangQiuDaCong” & Shandong, China \\
10 & “ErShengZi” & Shandong, China \\
11 & “Zao134” & Shandong, China \\
12 & “ShanXiFenCong” & Shanxi, China \\
13 & “Qi110” & Shandong, China \\
14 & “ZhongHuaJuCong” & Shandong, China \\
15 & “WuYeQi”3 & Shanxi, China \\
16 & “ShanXiYunChengKeXingYiHao” & Shanxi, China \\
17 & “HeBeiInXianDaCong” & Hebei, China \\
18 & “Shou1105” & Shandong, China \\
19 & “LiaoNingChaoYangLinCong” & Liaoning, China \\
20 & “XiYeWanShengCong” & Japan \\
21 & “SongBenYiBenTaiCong” & Japan \\
22 & “7722” & Guangdong, China \\ \hline \end{tabular}
\end{table}
Table 3: List of 22 _Allium_ accessions used in the polymorphism analysis.  
Compared with the bulb onion, the Welsh onion is suitable for genetic studies because it has a 28% smaller genome [33], but some of the genic SSR markers used in many genetic studies of the construction of a chromosome map and cultivar identification in Welsh onion [8,10,11] are derived from the bulb onion. The genic SSR marker in the Welsh onion has been far less developed than that in the bulb onion because less attention is currently being paid to the Welsh onion. Therefore, due to the limited number of SSR markers, we explored more SSR markers based on transcriptome sequencing to enrich the research into molecular marker-assisted selection and genetic diversity in the Welsh onion.