Distribution and Properties of SSR in Transcriptome of <i>Nymphaea</i> Paul Stetson Flowers

MAO Liyan; HUANG Qiuwei; YU Yanping; DING Liqiong; CAI Yuanbao; HUANG Xinyi; QIN Qian; SU Qun; NONG Xiaohui; ZHU Tianlong; LONG Lingyun

doi:10.19303/j.issn.1008-0384.2024.07.004

Volume 39 Issue 7

Jul. 2024

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Article Navigation > Fujian Journal of Agricultural Sciences > 2024 > 39(7): 775-784

MAO L Y, HUANG Q W, YU Y P, et al. Distribution and Properties of SSR in Transcriptome of Nymphaea Paul Stetson Flowers [J]. Fujian Journal of Agricultural Sciences，2024，39（7）：775−784 doi: 10.19303/j.issn.1008-0384.2024.07.004

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MAO L Y, HUANG Q W, YU Y P, et al. Distribution and Properties of SSR in Transcriptome of Nymphaea Paul Stetson Flowers [J]. Fujian Journal of Agricultural Sciences，2024，39（7）：775−784 doi: 10.19303/j.issn.1008-0384.2024.07.004

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Distribution and Properties of SSR in Transcriptome of Nymphaea Paul Stetson Flowers

doi: 10.19303/j.issn.1008-0384.2024.07.004

1.
Guangxi Subtropical Crops Research Institute/Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits, Nanning, Guangxi　530001, China
2.
Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi　530007, China
3.
Guangxi Pingguo Hualian Science and Technology Research Institute, Pingguo, Guangxi 531400
4.
Hainan Fodu Lianyuan Ecological Agriculture Co., Ltd., Haikou, Hainan　570100, China

Received Date: 2024-01-22
Rev Recd Date: 2024-05-29

Available Online: 2024-08-15

Publish Date: 2024-07-01

Abstract

Abstract

Objective SSRs in the transcriptome of Nymphaea Paul Stetson flowers were studied to generate new markers for evaluating germplasms and facilitating breeding of tropical waterlilies. Method SSR loci were retrieved from the transcriptomes of floral pistils, stamens, and petals of Nymphaea Paul Stetson using MISA. Characteristics of the loci were analyzed by Excel, and primers designed by Primer 3.0 and screened by TP-M13-SSR PCR. Result There were 12365 SSR loci found in the 39079 unigenes of the transcriptome at the frequency of 31.64% averaging one SSR locus per 5.79 kb. Most of the SSR loci had dinucleotide repeat motifs comprising 71.85% of total with AG/CT being the dominant unit that made up 61.34% of the motifs. Trinucleotide repeat motifs accounted for 26.10% of the sites with AAG/CTT being dominant at 8.30%. The repeating frequency was 5–20 times with a sequence of 12–30 bp averaging 18.38 bp long. Of the 9212 pairs of primers designed, 100 were randomly selected for a validation by PCR amplification to arrive at 9 pairs with high polymorphism being used as the markers. Subsequently, the 12 germplasms were clustered into 3 branches under a genetic similarity coefficient of 0.7375. Conclusion The SSR loci in the Nymphaea Paul Stetson transcriptome were high on distribution frequency, rich in diversity, greatly polymorphic, and desirable for applications. The 9 pairs of SSR primers identified in this study extended the existing marker repertoire facilitating effective germplasm differentiation on waterlilies.
- tropical waterlily,
- transcriptome,
- SSR,
- sequence analysis

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References(34)

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