Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China
文献类型： 外文期刊
作者： Zhang, Yao 1 ; Liu, Xi 3 ; Li, Yuying 4 ; Liu, Xiongfang 1 ; Ma, Hong 1 ; Qu, Suping 6 ; Li, Zhenghong 1 ;
作者机构： 1.Chinese Acad Forestry, Inst Highland Forest Sci, Kunming 650224, Yunnan, Peoples R China
2.Nanjing Forestry Univ, Coll Forestry, Nanjing 210037, Peoples R China
3.Southwest Forestry Univ, Sch Geog & Ecotourism, Kunming 650224, Yunnan, Peoples R China
4.Shanxi Agr Univ, Coll Grassland Sci, Jinzhong 030801, Peoples R China
5.Natl Forestry & Grassland Adm, Key Lab Breeding & Utilizat Resource Insects, Kunming 650224, Yunnan, Peoples R China
6.Yunnan Acad Agr Sci, Flower Res Inst, Kunming 650205, Yunnan, Peoples R China
关键词： Luculia yunnanensis; transcriptome; EST-SSR markers; polymorphism; conservation genetics
期刊名称：PLANTS-BASEL （ 影响因子：4.658； 五年影响因子：4.827 ）
ISSN：
年卷期： 2022 年 11 卷 9 期
页码：
收录情况： SCI
摘要： Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of L. yunnanensis has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of L. yunnanensis was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of L. yunnanensis. The results showed that 98,389 unigenes were obtained from the L. yunnanensis flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon's information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for L. yunnanensis.
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