Simple sequence repeat (SSR) analysis in relation to calcium transport and signaling genes reveals transferability among grasses and a conserved behavior within finger millet genotypes

Plant Systematics and Evolution

Volumn 300, Issue 6, 2014, Pages 1561-1568

  Yadav, Shambhavi ^a   Gaur, Vikram Singh ^a   Jaiswal, J P ^a   Kumar, Anil ^a  

^a G B PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

Author keywords

Calcium; Conservation; Eleusine coracana; Finger millet; Genic SSRs; Transferability

Indexed keywords

ELEUSINE CORACANA; POACEAE; SORGHUM (GENUS);

EID: 84902012984     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-014-0982-3     Document Type: Article

References (51)

1. +2 medium. Physiol Plant 123: 92-99.
2. Akhunov ED, Goodyear JA, Geng S, Qi L, Echalier B, Gill BS, Lazo G, Chao S, Anderson OD, Linkiewicz AM et al (2003) The organization and rate of evolution of the wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 5: 753-763.
3. Anderson JA, Ogihara Y, Sorrells ME, Tanksley SD (1992) Development of a chromosomal arm map for wheat based on RFLP markers. Theor Appl Genet 83: 1035-1043.
4. Argumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208.
5. Asp T, Frei UK, Didion T, Nielsen KK, Lubberstedt T (2007) Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biol 7: 36.
6. Bandopadhyay R, Sharma S, Rustgi S, Singh R, Kumar A, Balyan HS, Gupta PK (2004) DNA polymorphism among 18 species of Triticum-Aegilops complex, using wheat EST-SSRs. Plant Sci 166: 349-356.
7. Barbeau WE, Hilu KW (1993) Protein, calcium, iron and amino acid content of selected wild and domesticated cultivars of finger millet. Plant Foods Hum Nutr 43: 97-104.
8. Bisht MS, Mukai Y (2001a) Genomic in situ hybridization identifies genome donor of finger millet (Eleusine coracana). Theor Appl Genet 102: 825-832.
9. Bisht MS, Mukai Y (2001b) Identification of genome donors to the wild species of finger millet, Eleusine africana by genomic in situ hybridization. Breed Sc 51: 263-269.
10. Chabane K, Ablett GA, Cordeiro GM, Valkoun J, Henry RJ (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Resour Crop Evol 52: 903-909.
11. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Park WD, Ayres N, Cartinhour S, McCouch SR (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 713-722.
12. Dayod M, Tyerman SD, Leigh RA, Gilliham M (2010) Calcium storage in plants and the implications for calcium biofortification. Protoplasma 247: 215-231.
13. Dida MM, Srinivasachary RS, Bennetzen JL, Gale MD, Devos KM (2007) The genetic map of finger millet, Eleusine coracana. Theor Appl Genet 114: 321-332.
14. Dida MM, Wanyera N, Dunn MLH, Bennetzen JL, Devos KM (2008) Population structure and diversity in finger millet (Eleusine coracona) germplasm. Trop Plant Biol 1: 131-141.
15. Dubcovsky J, Luo M-C, Zhong G-Y, Bransteiter R, Desai A, Kilian A, Kleinhofs A, Dvorak J (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143: 983-999.
16. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140: 1183-1191.
17. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8: 967-974.
18. Gao L, Tang J, Li H, Jia J (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12(3): 245-261.
19. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163-185.
20. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270: 315-323.
21. Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed sequences of barley and wheat. Mol Breed 9: 63-71.
22. 2+ pump (ACA2) located in the endoplasmic reticulum of Arabidopsis. Proc Natl Acad Sci USA 97: 6224-6229.
23. Jensen LB, Holm PB, Lubberstedt T (2007) Cross-species amplification of 105 Lolium perenne SSR loci in 23 species within the Poaceae. Mol Ecol Notes 7: 1155-1161.
24. Kashi Y, Soller M (1999) Functional roles of microsatellites and minisatellites. In: Goldstein DB, Schlötterer C (eds) Microsatellites: evolution and applications. Oxford University Press, New York, pp 10-23.
25. Klimecka M, Muszynska G (2007) Structure and functions of plant calcium-dependent protein kinases. Acta Biochim Pol 54(2): 219-233.
26. La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4(1): 34-46.
27. Lawson MJ, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7: R14.
28. Maniatis T, Sambrook J, Fritsch EF (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
29. Maser P, Thomine S, Schroeder JI et al (2001) Phylogenetic relationships within cation transporter families of Arabidopsis. Plant Physiol 126: 1646-1667.
30. McAinsh MR, Pittman JK (2009) Shaping the calcium signature. New Phytol 181: 275-294.
31. Mian MAR, Saha MC, Hopkins AA, Wang ZY (2005) Use of tall fescue EST SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48: 637-647.
32. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8: 4321-4326.
33. Nagata T, Iizumi S, Satoh K, Ooka H, Kawai J, Carninci P, Hayashizaki Y, Otomo Y, Murakami K, Matsubara K, Kikuchi S (2004) Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data. Mol Biol Evol 21(10): 1855-1870.
34. National Research Council (1996) Lost crops of Africa vol 1: grains. Board on Science and Technology for international development. National Academy Press, Washington.
35. Neves SS (2011) Eleusine. Wild crop relatives: genomics and breeding resources, millets and grasses. 3: 113-133.
36. Panwar P, Nath M, Yadav VK, Kumar A (2010) Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.). J Genet 89(2): 121-133.
37. Parida SK, Kumar Anand Raj, Dalal K, Singh NKV, Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112: 808-817.
38. Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109: 783-791.
39. Shigaki T, Hirschi KD (2006) Diverse functions and molecular properties emerging for CAX. Plant Biol 8(4): 419-429.
40. Sim SC, Yu JK, Jo Y, Sorrells ME, Jung G (2009) Transferability of cereal EST-SSR markers to ryegrass. Genome 52: 431-437.
41. Srinivasachary DMM, Gale MD, Devos KM (2007) Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet 115: 489-499.
42. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST database for the development and characterization of gene derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
43. Thorup GL, Kearsey FD (2000) The principles of QTL analysis (a minimal mathematics approach). J Exp Bot 49: 1619-1623.
44. Upadhyaya HD, Gowda CLL, Reddy VJ (2007) Morphological diversity in finger millet germplasm introduced from Southern and Eastern Africa. SAT e J 3: 1.
45. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.
46. Wang ML, Barkley NA, Yu JK, Dean RE, Newman ML, Sorrells ME, Pederson GA (2004) Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet Resour 3: 45-57.
47. Yadav OP, Mitchell SE, Zamora A, Fulton TM, Krasovich S (2007) Development of new simple sequence repeat markers for pearl millet. SAT e Journal Vol 3.
48. Yu JK, Dake TM, Singh S, Benscher D, Li WL, Gill B, Sorrells ME (2004) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47: 805-818.
49. +2-deficient conditions. Plant Mol Biol 47: 633-640.
50. Zeid M, Yu JK, Goldowitz I, Denton ME, Costich DE, Jayasuriya CT, Saha M, Elshire R, Benscher D, Breseghello F, Munkvold J, Varshney RK, Belay G, Sorrells ME (2010) Cross-amplification of EST-derived markers among 16 grass species. Field Crops Res 118: 28-35.
51. Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111: 677-687.