CicArMiSatDB: The chickpea microsatellite database

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Doddamani, Dadakhalandar ^a   Katta, Mohan A V S K ^a   Khan, Aamir W ^a   Agarwal, Gaurav ^a   Shah, Trushar M ^a   Varshney, Rajeev K ^a  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

Author keywords

Chickpea; cicer; Database; Microsatellite; Plant genomics; SSR

Indexed keywords

CROPS; DNA SEQUENCES; GENES; GENETIC ENGINEERING;

CHICKPEA; CICER; MICRO SATELLITE; PLANT GENOMICS; SSR;

DATABASE SYSTEMS;

CICER; CICER ARIETINUM;

MICROSATELLITE DNA;

ARTICLE; BREEDING; CHROMOSOME MAP; CICER; COMPUTER INTERFACE; GENETIC DATABASE; GENETICS; GENOMICS; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; BREEDING; CHROMOSOME MAPPING; CICER; DATABASES, GENETIC; GENOMICS; INTERNET; MICROSATELLITE REPEATS; USER-COMPUTER INTERFACE;

EID: 84902703590     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-212     Document Type: Article

References (34)

1. FAOSTAT. http://faostat.fao.org/site/567/default.aspx#ancor.
2. Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M. Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 2012, 7(12):e52443. 10.1371/journal.pone.0052443, 3531472, 23300670.
3. Pittaway JK, Robertson IK, Ball MJ. Chickpeas may influence fatty acid and fiber intake in an ad libitum diet, leading to small improvements in serum lipid profile and glycemic control. J Amer Dietetic Assoc 2008, 108(6):1009-1013.
4. Saxena RK, Penmetsa RV, Upadhyaya HD, Kumar A, Carrasquilla-Garcia N, Schlueter JA, Farmer A, Whaley AM, Sarma BK, May GD, Cook DR, Varshney RK. Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res 2012, 19(6):449-461. 10.1093/dnares/dss025, 3514856, 23103470.
5. Bohra A, Dubey A, Saxena RK, Penmetsa RV, Poornima KN, Kumar N, Farmer AD, Srivani G, Upadhyaya HD, Gothalwal R, Ramesh S, Singh D, Saxena K, Kishor PB, Singh NK, Town CD, May GD, Cook DR, Varshney RK. Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biol 2011, 11:56. 10.1186/1471-2229-11-56, 3079640, 21447154.
6. Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi M, Pandey MK, Rami JF, Fonceka D, Gowda MV, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 2013, 20(2):173-184. 10.1093/dnares/dss042, 3628447, 23315685.
7. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2012, 30(1):83-89.
8. Varshney RK, Thiel T, Stein N, Langridge P, Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 2002, 7(2A):537-546.
9. Gupta PK, Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 2000, 113(3):163-185.
10. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jungling R, Singh J, Kishor PB, Sivaramakrishnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor Appl Genet 2010, 120(7):1415-1441. 10.1007/s00122-010-1265-1, 2854349, 20098978.
11. Varshney RK, Graner A, Sorrells ME. Genomics-assisted breeding for crop improvement. Trends Plant Sci 2005, 10(12):621-630. 10.1016/j.tplants.2005.10.004, 16290213.
12. Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, Kavikishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 2011, 6(11):e27275. 10.1371/journal.pone.0027275, 3216927, 22102885.
13. Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD Varshney RK. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 2011, 9(8):922-931. 10.1111/j.1467-7652.2011.00625.x, 3437486, 21615673.
14. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB. Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 2005, 110(3):492-510. 10.1007/s00122-004-1857-8, 15712010.
15. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 2013, 31(3):240-246. 10.1038/nbt.2491, 23354103.
16. Sarika Arora V, Iquebal MA, Rai A, Kumar D. PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome. Database 2013, 2013:bas054. 3567484, 23396298.
17. Jayashree B, Punna R, Prasad P, Bantte K, Hash CT, Chandra S, Hoisington DA, Varshney RK. A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation. In Silico Biol 2006, 6(6):607-620.
18. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D. CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics 2006, 7:132. 10.1186/1471-2164-7-132, 1539020, 16737546.
19. Primer sequences for SSR markers. http://www.icrisat.org/gt-bt/ICGGC/sup_files/Table17.html.
20. Chickpea genome. http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip.
21. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 2005, 5:16. 10.1186/1471-2229-5-16, 1215491, 16107212.
22. Choudhary S, Sethy NK, Shokeen B, Bhatia S. Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes 2006, 6(1):93-95.
23. Choudhary S, Sethy NK, Shokeen B, Bhatia S. Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 2009, 118(3):591-608. 10.1007/s00122-008-0923-z, 19020854.
24. Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 2011, 12:117. 10.1186/1471-2164-12-117, 3050819, 21329497.
25. Sethy NK, Shokeen B, Edwards KJ, Bhatia S. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 2006, 112(8):1416-1428. 10.1007/s00122-006-0243-0, 16534564.
26. Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KH, Town CD, Hoisington DA. A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 2009, 10:523. 10.1186/1471-2164-10-523, 2784481, 19912666.
27. Winter P, Pfaff T, Udupa SM, Huttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G. Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 1999, 262(1):90-101. 10.1007/s004380051063, 10503540.
28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
29. BLAST executables. ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/.
30. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12(10):1599-1610. 10.1101/gr.403602, 187535, 12368253.
31. Generic Model Organism Database Project. http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/.
32. GFF (General Feature Format) specifications document. http://www.sanger.ac.uk/resources/software/gff/spec.html.
33. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106(3):411-422.
34. Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, Sibly RM. Likelihood-based estimation of microsatellite mutation rates. Genetics 2003, 164(2):781-787. 1462577, 12807796.