Analysis on the Conservation of Dinucleotide SSR Flanking Sequences in Soybean(Glycine max)(PDF)

《大豆科学》[ISSN:1000-9841/CN:23-1227/S]

Issue:

2010年02期

Page:

195-198

Research Field:

Publishing date:

Info

Title:

Analysis on the Conservation of Dinucleotide SSR Flanking Sequences in Soybean(Glycine max)

Author(s):

ZHAN Shao-hua¹; SHENG Xin-ying² ; FAN Hong-hong² ; CAI Yong-ping² ; LIN Yi²

1.Chemistry and Biology Department, West Anhui University, Lu’an 237012;

2.Life Science School, Anhui Agricultural University, Hefei, 230036, Anhui, China

Keywords:

Soybean;  Simple Sequence Repeat;  Conservation of Sequence;  Flanking Sequence;  Primer

PACS:

S565.1

DOI:

10.11861/j.issn.1000-9841.2010.02.0195

Abstract:

The soybean EST and GSS sequences were downloaded from NCBI, and the 100 nt SSR flanking sequences were extracted as analyzing material. The number of SSRs and the base composition of the flanking sequences were calculated. Meanwhile, the multiple sequence alignment and the blast scanning were conducted. The results showed distribution frequency of soybean SSRs was 1/6.67kb, GC content of the flanking sequences was 37.83%, and the dinucleotide was major type of the motif. The multiple sequence alignment revealed polymorphic types flanking sequences were in any kind of motif. The same type flanking sequences were highly conserved, but different type flanking sequences had less similarity. Especially，the blast analyzing showed the SSR flanking sequences may exist in no SSR regions. So we claimed no SSR fragments may be amplified by SSR primer pairs, and new type SSR could stem from translocation, which is one kind of chromosomal variations. The analyzing could contribute to efficient design of SSR primers and to further illuminate formative mechanism of simple sequence repeats.

References:

[1]Nakamura Y, Leppert M, O’Connell P, et al. Variable number tandem repeat(VNTR) markers for human gene mapping [J]. Science, 1987, 235:1616-1622.

[2]Jacob H J, Lindpaintner K, Lincoln S E, et al. Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat [J]. Cell, 1991,67:213-224.

[3]Litt M, Luty J A. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene [J]. American Journal of Human Genetics,1989, 44:397-401.

[4]Weber J L,May P E. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction [J]. American Journal of Human Genetics, 1989, 44: 388-396.

[5]Tautz D .Hypervariability of simple sequences as a general source of polymorphic DNA markers [J]. Nucleic Acids Researcn. 1989, 17:6463-6471.

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

[7]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.)

[8]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.)

[9]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.)

[10]Akkaya M S, Shoem aker R C, Specht J E,et al. Length polymorphism of simple sequence repeat DNA in soybean [J]. Genetic, 1992, 132:1131-1139.

[11]王彪,邱丽娟.大豆SSR技术研究进展[J].植物学通报,2002,19(1):44-48.(Wang B,Qiu L J. Current advance of simple sequence repeats in soybean [J].Chinese Bulletin of Botany, 2002,19(1):44-48.)

[12]詹少华,盛新颖,樊洪泓,等.大豆EST序列长度与SSR特性的关系[J].大豆科学,2009,28(2):204-208.(Zhan S H,Sheng X Y, Fan H H, et al. Relationship between the length of soybean ESTs sequence and characters of EST-SSR[J]. Soybean Science, 2009,28(2):204-208.)

[13]Jeffreys A J, Wilson V, Thein S L. Hypervariable “minisatellite” regions in human DNA [J]. Nature, 1985, 314: 67-73.

[14]Crow J F, William F D. Anecdotal, historical and critical commentarieson genetics: Unequal crossing over then and now [J].Genetics, 1988, 120: 1-6.

Memo

Memo:

-

Common functions