Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L

被引:10
作者
Chand, Subodh Kumar [1 ]
Nanda, Satyabrata [1 ]
Rout, Ellojita [1 ]
Joshi, Raj Kumar [1 ]
机构
[1] Siksha O Anusandhan Univ, Ctr Biotechnol, Funct Genom Lab, Bhubaneswar 751003, Orissa, India
关键词
Allium sativum; expressed sequences tags; EST-SSRs; SSR motifs;
D O I
10.6026/97320630011145
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsEST-SSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.
引用
收藏
页码:145 / 150
页数:6
相关论文
共 26 条
[1]   Advances in molecular marker techniques and their applications in plant sciences [J].
Agarwal, Milee ;
Shrivastava, Neeta ;
Padh, Harish .
PLANT CELL REPORTS, 2008, 27 (04) :617-631
[2]  
[Anonymous], MOL BREED
[3]   Garlic as an antioxidant: The good, the bad and the ugly [J].
Banerjee, SK ;
Mukherjee, PK ;
Maulik, SK .
PHYTOTHERAPY RESEARCH, 2003, 17 (02) :97-106
[4]  
Cardle L, 2000, GENETICS, V156, P847
[5]   Maize simple repetitive DNA sequences: Abundance and allele variation [J].
Chin, ECL ;
Senior, ML ;
Shu, H ;
Smith, JSC .
GENOME, 1996, 39 (05) :866-873
[6]   NEW MICROSATELLITE MARKERS FOR GARLIC, ALLIUM SATIVUM (ALLIACEAE) [J].
Cunha, Camila P. ;
Hoogerheide, Eulalia S. S. ;
Zucchi, Maria I. ;
Monteiro, Mariza ;
Pinheiro, Jose B. .
AMERICAN JOURNAL OF BOTANY, 2012, 99 (01) :E17-E19
[7]  
DaMaia, 2008, INT J PLANT GENOM, V1, P9
[8]   Genome-wide genetic marker discovery and genotyping using next-generation sequencing [J].
Davey, John W. ;
Hohenlohe, Paul A. ;
Etter, Paul D. ;
Boone, Jason Q. ;
Catchen, Julian M. ;
Blaxter, Mark L. .
NATURE REVIEWS GENETICS, 2011, 12 (07) :499-510
[9]   EST-SSRs as a resource for population genetic analyses [J].
Ellis, J. R. ;
Burke, J. M. .
HEREDITY, 2007, 99 (02) :125-132
[10]   Peroxyl-Radical-Scavenging Activity of Garlic: 2-Propenesulfenic Acid versus Allicin [J].
Galano, Annia ;
Francisco-Marquez, Misaela .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (49) :16077-16081