Development and Polymorphism Analysis of EST-SSR Markers Based on Transcriptome of Non-heading Chinese Cabbage (Brassica rapa ssp. chinensis)
YANG Dan-Qing1, HE Xiao-Li1, DU Zhi-Jie1, WANG Shu-Bin1, SUN Li-Wei1, LIN Yi-Zhang1, SHAO Gui-Rong3, ZHONG Feng-Lin1,2,*
1 College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; 2 The Vegetable Institute of Fujian Agricultural and Forestry University, Fuzhou 350002, China; 3 Fujian Jinpin Agricultural Technology Co., Ltd., Fuzhou 350002, China
Abstract：The EST-SSR markers obtained from transcriptome sequencing information have the advantages of good stability, high polymorphism, co-dominant inheritance, and simple operation, and are widely used in genetic diversity analysis of plant germplasm resources. In this study, high-throughput sequencing of the transcriptome of non-heading Chinese cabbage (Brassica rapa ssp. chinensis) was used to seek SSR loci and develop EST-SSR markers, and preliminary primer verification and polymorphism analysis were performed. A total of 17 009 SSR loci were found in the 48 817 unigene sequences of the transcriptional set of non-heading Chinese cabbage, with an occurrence frequency of 18.44% and a SSR distribution frequency of 34.84%. The SSR sites of non-heading Chinese cabbage contained 212 repeat elements whose SSR types were mainly concentrated on single, binary and trinucleotide repeats. Among them, single nucleotide repeats accounted for the most, accounting for 39.70% of the total, and the dominant repeating unit was T/A (26.83%). The EST-SSR primers designed by Primer Premier 3.0 soft were used to randomly selected for 40 pairs in batch design primers for synthesis and preliminary verification. Twenty-five pairs of primers could amplify the expected size bands in 92 non-heading Chinese cabbage germplasm resources. The average number of alleles was 3.72, and the effective number of alleles (Ne), Shannon's index (I), polymorphism information content (PIC) and gene diversity (GD) were 2.710 8, 0.999 1, 0.488 4 and 0.545 2, respectively. The obtained EST-SSR primers could provide effective molecular markers for genetic structure analysis, germplasm utilization and genetic map construction of non-heading Chinese cabbage and other Brassica plants.
杨丹青, 何晓丽, 杜志杰, 王树彬, 孙笠维, 林义章, 邵贵荣, 钟凤林. 基于不结球白菜转录组EST-SSR标记开发及多态性分析[J]. 农业生物技术学报, 2020, 28(1): 13-21.
YANG Dan-Qing, HE Xiao-Li, DU Zhi-Jie, WANG Shu-Bin, SUN Li-Wei, LIN Yi-Zhang, SHAO Gui-Rong, ZHONG Feng-Lin. Development and Polymorphism Analysis of EST-SSR Markers Based on Transcriptome of Non-heading Chinese Cabbage (Brassica rapa ssp. chinensis). 农业生物技术学报, 2020, 28(1): 13-21.
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