|Table of Contents|

Relationship between Length of Soybean ESTs Sequence and Characters of EST-SSR(PDF)

《大豆科学》[ISSN:1000-9841/CN:23-1227/S]

Issue:
2009年02期
Page:
204-209
Research Field:
Publishing date:

Info

Title:
Relationship between Length of Soybean ESTs Sequence and Characters of EST-SSR
Author(s):
ZHAN Shao-hua1SHENG Xin-ying2FAN Hong-hong2CAI Yong-ping2LIN Yi2
1Chemistry and Biology Department,West Anhui University,Lu’an 237012,Anhui;
2Life Science School,Anhui Agricultural University,Hefei 230036,Anhui,China
Keywords:
SoybeanESTEST-SSRSequence lengthRepeat Conting
PACS:
S565.1
DOI:
10.11861/j.issn.1000-9841.2009.02.0204
Abstract:
The objective of this study was to research the traits of simple sequence repeats (SSR) derived from expressed sequence tags(EST) of soybean and to compare the characters of SSRs in different length of ESTs,so 20183 no redundancy EST sequences were analyzed.The EST sequences were downloaded from NCBI,and SSRs were screened using SSRIT program.The results showed 1747 ESTs (8.66%)contained one or more SSRs.According to EST sequence length over or less than 400bp,the SSRs rates were 10.05% and 4.74%,respectively.Di-nucleotide repeats (60.45%)were the most abundant type of repeats followed by Tri-nucleotide repeats(37.04%).AT,AG,AAT,AC,AAG,ACG were the most common SSR repeat motifs.In the 1798 EST-SSRs,the length of EST-SSR over 12bp accounted for 51.45 percent,and proportion of the length more than 20bp accounted for 13.35 percent.The average distance of distribution was 7.91(1/kb).123527 SSRs were deduced in EST database of NCBI,so we claimed exploration value of the EST-SSRs for the soybean molecular marker.The results would contribute to EST-SSR primer efficient design.

References:

[1]Powell W,Machray G C,Provan J.Polymorphism revealed by simple sequence repeats [J].Trends Plant Science,1996,1:215-222.

[2]杨喆,刘丽君,高明杰,等.大豆高蛋白基因分子标记及其在大豆育种中的应用[J].大豆科学,2008,27(2):186-189.(Yang Z,Liu L J,Gao M J,et al.QTL Tagging for high protein gene and using molecular marker assistant selection in soybean breeding[J].Soybean Science,2008,27(2):186-189.)
[3]王俊,王林林,刘章雄,等.大豆地方品种遗传结构及其保存研究[J].大豆科学,2008,27(3):361-365.(Wang J,Wang L L,Liu Z X,et al.Genetic structure and conservation of soybean landraces[J].Soybean Science,2008,27(3):361-365.)
[4]汤复跃,周立人,程潇,等.大豆M型细胞质雄性不育恢复基因SSR标记初步定位[J].大豆科学,2008,27(3):383-386.(Tang F Y,Zhou L R,Cheng X,et al.SSR marker location for fertility restorer gene of M-cytoplasmic male sterility in soybean[J].Soybean Science,2008,27(3):383-386.)
[5]Cordeiro G M,Casu R,McIntyre C L,et al.Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum [J].Plant Science,2001,160:1115-1123.
[6]Eujayl I,Sorrells M E,Baum M,et al.Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs[J].Euphytica,2001,119:39-43.
[7]Thiel T,Michalek W,Varshney R K,et al.Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L) [J].Theoretical and Applied Genetics,2003,106:411-422.
[8]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.
[9]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.(Li X B,Zhang M L,Cui H R.Analysis of SSR information in EST resource of oilseed rape[J].Chinese Journal of Oil Crop Sciences,2007,29(1):20-25.)
[10]金基强,崔海瑞,龚晓春,等.用EST-SSR标记对茶树种质资源的研究[J].遗传,2007,29(1):103-108.( Jin J Q,Cui H R,Gong X C,et al.Studies on tea plants (Camellia sinensis) germplasms using EST-SSR marker[J].Hereditas,2007,29(1):103-108.)
[11]林忠旭,王锦峰,张献龙.瑟伯氏棉和异常棉的陆地棉导入系的EST-SSR和gSSR分析[J].棉花学报,2008,20(4):243-248.( Lin Z X,Wang J F,Zhang X L.Characteristics of Gossypium thurberi and G.anomalum Introgression Lines of G.hirsutum Revealed by EST-SSR and gSSR[J].Cotton Science,2008,20(4):243-248.)
[12]张俊娥,李芬,孙蒙祥.烟草EST-SSR位点分析[J].武汉植物学研究,2007,25(5):427-431.(Zhang J E,Li F,Sun M X.Analysis of EST-SSR loci in tobacco (Nicotiana tabacum L.)[J].Journal of Wuhan Botanical Research,2007,25(5):427-431.)
[13]Varshney R K,Graner,A,Sorrells M E.Genic microsatellite markers in plants: features and applications[J].Trends Biotechnology,2005,23,48-55.
[14]Guo W,Cai C,Wang,C,et al.A microsatellite based gene-rich linkage map reveals genome structure,function and evolution in Gossypium[J].Genetics,2007,176:527-541.
[15]李永强,李宏伟,高丽锋,等.基于表达序列标签的微卫星标记(EST-SSRs)研究进展[J].植物遗传资源学报,2004,5 (1): 91-95.( Li Y Q,Li H W,Gao L F,et al.Progress of simple sequence repeats derived from expressed sequence tags[J].Journal of Plant Genetic Resources,2004,5 (1): 91-95.)
[16]Varshney R K,Graner A,Sorrells M E.Genic microsatellite markers in plants: features and applications[J].Trends in Biotechnology,2005,23(1): 48-55.
[17]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].BMC Genomics,2005,6: 23.
[18]Song Q J,Marek L F,Shoemaker R C,et al.A new integrated genetic linkage map of the soybean[J].Theoretical and Applied Genetics,2004,109:122-128.
[19]Temnykh S,De Clerck G,Lukashova A,et al.Computational and experimental analysis of microsatellites in rice (Oryza sativa L.) [J].Genome Research,2001,11:1441-1452.
[20]Dreisigacker S,Zhang P,Warburton M L,et al.SSR and pedigree analyses of genetic diversity among CIM-MYT wheat lines targeted to different megaenvironments [J].Crop Science,2004,44: 381-388.

Memo

Memo:
-
Last Update: 2014-10-03