Transferability of barley and wheat EST-microsatellite markers in some Poaceae members

Öz

The cross species transferability of  barley and wheat microsatellite markers developed from expressed sequence tag (EST) libraries constructed under Fusarium infection conditions were detected among 17 species including 8 from Aegilops, 6 from Triticum, Zea mays, Avena sativa, Oryza sativa.

Transferability rates of barley microsatellite primer pairs ranged from 29% to 100%. A maximum of 100% cross-genera transferability noticed with Avena followed by Zea (92%), Triticum (83%), Aegilops (68%), and Oryza (8%). Primer pairs were highly transferable within species of Triticum (100% in T. turgidum durum durum, 92% in T. turgidum durum dicoccon and T. monococcum aegilopoides, 83% in T.timopheevii timopheevii and T. turgidum dicoccoides, 67% in T. timopheevii armeniacum). Only one primer pairs (contig624) showed 100 % cross-species/genera amplification in all materials studied.

Considering wheat microsatellites, the microsatellite primer pairs were highly transferable within species of Triticum (ranged from %100 to %70) and but low transferable in the allied cereals (15% in Avena, 50% in Oryza, 45% in Zea, 60% in Hordeum). Two primer pairs have shown transferability only in some Triticum species, while two others showed amplication only in species of Aegilops and Triticum. Only one primer pairs showed 100 % cross-species/genera amplification in all materials studied.

This higher cross-species transferability of EST microsatellite markers indicated a high level of conservation of DNA sequences belonging to the transcribed region of the genome and its suitability in comparative genome mapping, genetic diversity and phylogenetics analysis.

Anahtar Kelimeler

• Microsatellite markers,transferability

Bazı Poaceae üyelerinde arpa ve buğday EST-mikrosatellit markırlarının aktarılabilirliği

Öz

Fusariım enfeksiyon koşulları altında oluşturulmuş eksprese olan dizi (EST) kütüphanelerinden geliştirilen arpa ve buğday mikrosatellit markırlarının türler/cinsler arası aktarılabilirlikleri, 8 Aegilops, 6 Triticum türü ile, Zea mays, Avena sativa ve Oryza sativa ‘yı içeren 17 türde belirlenmiştir. Arpa mikrosatellit primerleri için aktarılabilirlik oranı %29 ila %100 arasında değişmiştir. Cinsler arası en yüksek (%100) aktarılabilirlik  Avena da not edilmiş, bunu Zea (%92) , Triticum (%83), Aegilops (68%) ve Oryza (%8) takip etmiştir. Primer çiftleri,  Triticum türleri içerinde oldukça yüksek aktarılabilirdir (T. turgidum durum durum da %100, T. turgidum durum dicoccon ve T. monococcum aegilopoides da %92,T.timopheevii timopheevii ve T. turgidum dicoccoides de %83, T. timopheevii armeniacum da %67). Yalnızca bir primer çifti (contig624) çalışılan tüm materyallerde, %100 tür/cinsler arası çoğaltım göstermiştir.

Buğday mikrosatellitleri değerlendirildiğinde, mikrosatellit primer çiftleri Triticum türleri içinde oldukça aktarılabilirdir (%70 ila %100 arasında) ancak akraba tahıllarda düşük aktarılabilirdir (Avena da 15%, Oryza da 50%, Zea da 45%, Hordeum da 60%). İki primer çifti yalnızca bazı Triticum türlerinde aktarılabilirlik göstermişken, diğer iki primer çifti sadece Aegilops ve Triticum türlerinde çoğaltım göstermiştir.

EST mikrosatellite markırlarının bu yüksek tür/cinsler arası aktarılabilirliği, genomun ifade edilen bölgesine ait DNA diziliminin yüksek derecede korunduğunu ve bunların karşılaştırılmalı genom haritalamalarında, genetik çeşitlilikte ve filogenetik analizlerde uygunluklarını göstermektedir.

Anahtar Kelimeler

• mikrosatellit marker,aktarılabilirlik,tahıl

Kaynakça

1. Badaeva ED, Dedkova OS, Gay G, Pukhalskyi VA, Zelenin AV,Bernard S, Bernard M, 2007. Chromosomal rearrangements in wheat: their types and distribution, Genome, 50: 907
2. Bennetzen JL, Ma J, 2003. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis, Curr. Opin. Plant. Biol., 6: 128–133.
3. Kalia KR, Rai MK, Kalia S, Singh R, Dhawan AK, 2010. Microsatellite markers: an over¬view of the recent progress in plants, Euphytica, 177: 309–334.
4. Mardis ER, 2008. The impact of next–generation sequencing technology on genetics, Trends Genet., 24: 133–141.
5. Eujayl I, Sorrells M, Baum M., Wolters P, Powel W, 2002. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat, Theor. Appl. Genet., 104: 399–407.
6. Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH, 2002. Development and mapping of SSR markers for maize, Plant Mol. Biol., 48(5-6): 463-81.
7. Varshney RK, Thiel T, Stein N, Langridge P, Graner A, 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species, Cell Mol Biol Lett., 7: 537–546.
8. Chen H, Li L, Wei X, Li S, Lei T, Hu H, Wang H, Zhang X, 2005. Development, chromosome location and genetic mapping of EST-SSR markers in wheat, Chin. Sci. Bull., 20: 2328–2336.

9. Salem KFM. Varshney RK, Röder MS, Börner A, 2010. EST-SSR based estimates on functional genetic variation in a barley (Hordeum vulgare L.) collection from Egypt. Genet. Resour. Crop. Evol., 57(4): 515-521.
10. Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, DograV, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, Datta S, Singh MN, Bashasab F, Kulwal P, Wanjari KB, Varshney RK, Cook DR, Singh NK, 2011. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea (Cajanus cajan (L.) Millspaugh), BMC Plant Biol., 11: 17.
11. 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(3): 163–185.
12. Gong L, Deng Z, 2010. EST-SSR markers for gerbera (Gerbera hybrida), Mol. Breding, 26:125-132
13. Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS, 2009. Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.), BMC Plant Biol., 9:53.
14. Singh RK, Jena N, Khan S,Yadav S,Banarjee N, Raghuvanshi S, Bhardwaj V, Kattamajumder S, Kapur R, Solomon S, Swapna M, Srivastava S, Tyagi AK, 2013. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane, Gene, 524(2): 309–329.
15. Varshney RK, Graner A, Sorrells ME, 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol, 23:48–55
16. Sim SC, Yu JK, Jo YK, Sorrells ME, Jung G, 2009. Transferability of cereal EST-SSR markers to ryegrass, Genome, 52(5): 431-437.
17. Gupta PK, Rustgi S, Sharma S, 2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat, Mol. Genet. Genom., 270(4): 315-323.
18. Zhou Q, Luo D, Ma L, Xie W, Wang Y, Wang Y, Liu Z, 2016. Development and cross-species transferability of EST-SSR markers in Siberian wild rye (Elymus sibiricus L.) using Illumina sequencing. Scientific Reports, 6, doi.10.1038/srep20549
19. 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(4): 677–687.
20. Yıldırım, A, Kandemir N, Ateş Sönmezoğlu Ö, Eserkaya Güleç T, 2009. Transferability of microsatellite markers among cool season cereals. Biotechnol. Biotechnol. Equip., 23(3): 1299-1302.
21. Barbara T, Palma-Silva C, Paggi GM, Bered F, Fay MF and Lexer C, 2007. Cross-species transfer of nuclear microsatellite markers: potential and limitations, Mol. Ecol., 16: 3759–3767.
22. Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni AF, Stover EW, Bell RL, Wisniewski ME, Korban SS, 2009. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species, Mol Breeding 23: 397. doi:10.1007/s11032-008-9243-x
23. Heesacker A, Kishore VK, Gao W, Tang S, Kolkman JM, Gingle A, Matvienko M, Kozik A, Michelmore RM, Lai Z, Rieseberg LH, Knapp SJ, 2008. SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor. Appl. Genet., 117(7): 1021-1029.
24. Noor MAF, Feder JL, 2006. Speciation genetics: evolving approaches, Nat. Rev. Genet. doi:10.1038/nrg1968
25. Wang BH. Zhu P, Yuan YL, Wang CB, Yu CM, Zhang HH, Zhu XY, Wang W, Yao CB. Zhuang ZM, Li P, 2014. Development of EST-SSR markers related to salt tolerance and their application in genetic diversity and evolution analysis in Gossypium. Genet. Mol. Res., 13(2): 3732-3746.
26. Zhang M, Mao W, Zhang G, Wu F, 2014. Development and Characterization of Polymorphic EST-SSR and Genomic SSR Markers for Tibetan Annual Wild Barley, Plos One, doi:10.1371/journal.pone.0094881
27. Zhou Q, Chen T, Wang Y, Liu Z, 2014. The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa, Biochem. Sys. Ecol., 57: 227-230.
28. Kalia, RK, Rai MK, Kalia S, Singh R, Dhawan AK, 2011. Microsatellite markers: an overview of the recent progress in plants, Euphytica, 177: 309. doi:10.1007/s10681-010-0286-9
29. Song W, Henry RJ, 1995. Molecular analysis of the DNA polymorphism of wild barley (Hordeum spontaneum) germplasm using the polymerase chain reaction, Genet. Resour. Crop. Evol., 42: 273–280.
30. Cordeiro GM, Taylor GO, Henry RJ, 2000. Characterization of microsatellite markers from sugarcane (Saccharum spp.) a highly polyploidy species, Plant Sci., 155: 161–168. doi: 10.1016/S0168-9452(00)00208-9.
31. Thiel T, Michalek W, Varshney RK, Graner A, 2003. Exploiting EST databases for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.), Theor. Appl. Genet., 106: 411–422.
32. Eujayl I, Sledge MK, Wang L, May GD, Chekhovsky K, Zwonitzer JC, Milan MAR, 2004. Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet., 108: 414-422.
33. 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 Science, 166: 349–356.
34. Holton TA, Christopher JT, McClure L, Harker N, Henry RJ, 2002. Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat, Mol. Breed., 9: 63–71.
35. Konstantinos GT, Bebeli PJ, 2010. Genetic Diversity of Greek Aegilops Species Using Different Types of Nuclear Genome Markers, Mol. Phylogenet. Evol, 56 (3): 951-961.