Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum

doi:10.11924/j.issn.1000-6850.casb16040046

Abstract

Abstract: The objective of this study was to characterize SSR derived from the Paspalum vaginatum EST sequences and to develop EST-SSR markers for genetic diversities analysis. In total, 81220 EST sequences from Paspalum vaginatum were investigated using the software SSRIT, and the distribution and characteristics of EST-SSR were analyzed. Fifty primers were designed using the software Primer 3.0, and the validity and polymorphism of the primers were tested by PCR amplification of 10 turfgrass cultivars. The results showed that 22721 SSRs were identified from the Paspalum vaginatum 13705 EST sequences with a frequency of 16.87%. Analysis of EST-SSRs motifs revealed that tri-nucleotide and mono-nucleotide were the dominant motifs, accounted for 31.71% and 29.28%, respectively. A total of 163 EST-SSR motif types were mined, A/T was the dominant repeat motif, followed by CCG/CGG and AGC/CTG. Fifty primers of EST-SSRs primers were synthesized and 37 primer pairs could amplify clear bands using the DNA template of ‘Adalady’. The polymorphisms of the primers were tested by PCR amplification of 10 turfgrass cultivars, and 12 primer pairs showed polymorphism. The cluster analysis based on EST-SSR markers indicated that 10 turfgrass cultivars were grouped into four classes. These results showed that it is an effective and feasible way to develop EST-SSR markers from the Paspalum vaginatum EST sequences, and EST-SSR markers developed in the study could be used for genetic diversity analysis in turfgrass.

CLC Number:

S543

Li Huayong,Wang Xiansheng,Wang Yanping,Wu Yan,Shen Qi and Jia Xinping. Analysis of SSR Information in EST Resources and Development of EST-SSR Marker in Paspalum vaginatum[J]. Chinese Agricultural Science Bulletin, 2016, 32(30): 96-102.

References

[1] 解新明,卢小良.海滨雀稗种质资源的优良特性及其利用价值[J].华南农业大学学报,2004,25(Z2):64-67.
[2] Liu Y M, Du H M, He X X, et al. Identification of differentially expressed salt-responsive proteins in roots of two perennial grass species contrasting in salinity tolerance[J]. Plant Physiology, 2012,169:117-126.
[3] 贾新平,邓衍明,孙晓波,等.盐胁迫对海滨雀稗生长和生理特性的影响[J].草业学报,2015,24(12):204-212.
[4] Shahba M A, Abbas M S, Alshamary S F. Drought resistance strategies of seashore paspalum cultivars at different mowing heights[J]. HortScience, 2014,49:221-229.
[5] 孙清明,马文朝,马帅鹏,等.荔枝EST资源的SSR信息分析及EST-SSR标记开发[J].中国农业科学,2011,44(19):4037-4049.
[6] Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes[J]. Nature Genetics, 2002, 30:194-200.
[7] Powell W, Machray G C, Provan J. Polymorphism revealed by simple sequence repeats[J]. Trends in Plant Science,1996,1:215-222.
[8] Hua Y Z, Tian Z Z, Lu M Y, et al. EST-SSR sequences revealed the relationship of D-genome in diploid and tetraploid species in Gossypium[J]. Plant Science, 2009,176:397-405.
[9] 董清华,王西成,赵密珍,等.草莓EST-SSR标记开发及在品种遗传多样性分析中的应用[J].中国农业科学,2011,44(17):3603-3612.
[10] Varshney R K, Graner A, Sorrells M E. Genic microsatellite markers in plants: Features and applications[J]. Trends in Biotechnology, 2005,23:48-55.
[11] Kamel C, Varshney R K, Graner A, et al. Generation and exploitation of EST-derived SSR markers for assaying molecular diversity in durum wheat populations[J]. Genetic Resources and Crop Evolution, 2008,55(6):869-881.
[12] 李小白,张明龙,崔海瑞.油菜EST资源的SSR信息分析[J].中国油料作物学报,2007,29(1):20-25.
[13] Tan L Q, Wang L Y, Wang K, et al. Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis) [J]. PLoS One, 2013,8:e81611.
[14] 贾新平,邓衍明,孙晓波,等.鸟巢蕨EST-SSR标记的开发与应用[J].华北农学报,2015,30(6):134-139.
[15] Liu Z P, Chen T L, Ma L H, et al. Global Transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid Alfalfa[J]. PLoS One, 2013,8:e83549.
[16] 陈昆松,李摇方,徐昌杰,等.改良CTAB法用于多年生植物组织基因组DNA的大量提取[J].遗传,2004,26(4):529-531.
[17] Li D, Deng Z, Qin B, et al. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.) [J]. BMC Genomics, 2012,13:192.
[18] 王娟,陶永焕,宋尚伟.葡萄EST-SSR引物的开发及部分种质聚类分析[J].华北农学报,2014,29(2):121-126.
[19] Cardle L, Ramsay L, Milbourne D, et al. Computational and experimental characterization of physically clustered simple sequence repeats in plants[J]. Genetics, 2000, 156: 847-854.
[20] 孙湘来,陈新,文明富,等.基于EST-SSR的木薯分子标记遗传连锁图谱的构建[J].中国农学通报,2011,27(9):231-236.
[21] 刘峰,王运生,田雪亮,等.辣椒转录组SSR挖掘及其多态性分析[J].园艺学报,2012,39(1):168-174.
[22] Kantety R V, Rota M L, Matthews D E, et al. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat[J]. Plant Molecular Biology, 2002,48:501-510.
[23] Keniry A, Hopkins C J, Jewll E, et al. Identification and characterization of simple sequence repeat (SSR) markers from Fragaria×Ananassa expressed sequences[J]. Molecular Ecology Notes, 2006,6:319-322.
[24] Wang S, Wang X, He Q, et al. Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish[J]. Plant Cell Report, 2012,31:1437-1447.
[25] Liang X, Chen X, Hong Y, et al. Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species[J]. BMC Plant Biology, 2009,9:35-48.
[26] Rota L R, Kantety R V, Yu J K. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat and barley[J]. BioMed Central Genomics, 2005,6(1):23.
[27] Kumpatla S P, Mukhopadhyay S. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species[J]. Genome, 2005, 48: 985-998.
[28] 陈琛,庄木,李康宁,等.甘蓝EST-SSR标记的开发与应用[J].园艺学报,2010,37(2):221-228.
[29] Wei W L, Qi X Q, Wang L H, et al. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J]. BMC Genomics, 2011, 12: 451.
[30] Nicot N, Chiquet V, Gandon B, et al. Study of simple sequence repeat (SSRs) markers from wheat expressed sequence tags (ESTs) [J].Theoretical and Applied Genetics, 2004, 109:800-805.
[31] Thiel T, Michalek W, Varshney R, et al. Exploiting EST database for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.) [J]. Theoretical and Applied Genetics, 2003, 106:411-422.
[32] Areshchenkova T, Ganal M. Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources[J]. Theoretical and Applied Genetics, 2002, 104:229-235.
[33] 王西成,姜淑苓,上官凌飞,等.梨EST-SSR标记的开发及其在梨品种遗传多样性分析中的应用评价[J].中国农业科学,2010,43(24):5079-5087.