Advertisement

Plant Systematics and Evolution

, Volume 300, Issue 6, pp 1337–1347 | Cite as

Genetic structure and diversity analysis revealed by AFLP on different Echinochloa spp. from northwest Turkey

  • Hilal Betul Kaya
  • Mehmet Demirci
  • Bahattin TanyolacEmail author
Original Article

Abstract

Rice is one of the most economically important cereal crops in the world. The genus Echinochloa is the most competitive and difficult to control weeds in the rice fields. Improving the knowledge on the genetic diversity and structure of Echinochloa spp. can supply crucial information for designing effective management strategies for weed control in rice breeding. In the study, 28 Echinochloa spp. genotypes were subjected to the analysis of genetic diversity using four amplified fragment length polymorphism selective primer combinations. The number of polymorphic fragments per primer combination detected ranged from 28 to 50 bands with an average of 41.5 bands. Average polymorphic information content (PIC) was 0.26 in overall primer combinations. EACA-MCAG primer combination showed the highest PIC (0.52) which can be a good candidate primer combination to verify genetic diversity in Echinochloa spp. The unweighted pair-group method of the arithmetic average and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of two populations. The accessions were clearly assigned to a single population in which >70 % of their inferred ancestry was derived from one of the model-based populations. However, three genotypes (10.7 %) in the sample were categorized as having admixed ancestry. The study showed that genetic variation and population structure are determined among genotypes collected from different locations. High level of genetic variation in both intra and inter species was detected.

Keywords

Echinochloa spp. AFLP Genetic structure and diversity Principal coordinate analysis 

Notes

Acknowledgments

We would like to acknowledge Melis Zeybek and Agah Kozan for their kind help in calculating principal components and some evaluations.

References

  1. Aoki D, Yamaguchi H (2008) Genetic relationship between Echinochloa crus-galli and Echinochloa oryzicola accessions inferred from internal transcribed spacer and chloroplast DNA sequences. Weed Biol Manag 8:233–242CrossRefGoogle Scholar
  2. Asins MJ, Carretero JL, Del Busto A, Carbonell EA, De Barreda D (1999) Morphologic and isozyme variation in barnyardgrass (Echinochloa) weed species. Weed Technol 13:209–215Google Scholar
  3. Botstein D, White RL, Skolmick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Amer J of Hum Genet 32:314–332Google Scholar
  4. Cao Q, Lu BR, Xia H, Rong J, Sala F, Spada A, Grassi F (2006) Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers. Ann Bot 98:1241–1252PubMedCentralPubMedCrossRefGoogle Scholar
  5. Carretero JL (1981) El ge’nero Echinochloaen el Grande Suroeste de Europa. An Jard Bot Madrid 38:91–108Google Scholar
  6. Carvalho RC, Guedes-Pinto H, Igrejas G, Stephenson P, Scwwarzacher T, Heslop-Harrison JS (2004) High levels of genetic diversity throughout the range of the Portuguese wheat landrace ‘Barbela’. Ann Bot 94:699–705CrossRefGoogle Scholar
  7. Chandi A, Milla-Lewis SR, Jordan DL, York AC, Burton JD, Zuleta MC, Whitaker JR, Culpepper AS (2013) Use of AFLP markers to assess genetic diversity in Palmer Amaranth (Amaranthus palmeri) populations from North Carolina and Georgia. Weed Sci 61:136–145CrossRefGoogle Scholar
  8. Danquah EY, Hanley SJ, Brookes RC, Aldam C, Karp A (2002) Isolation and characterization of microsatellites in Echinochloa (L.) Beauv. spp. Mol Ecol Notes 2:54–56CrossRefGoogle Scholar
  9. Davis PH (1985) Flora of Turkey and the East Aegean Islands, vol 9. Edinburgh University Press, EdinburghGoogle Scholar
  10. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  11. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  12. Fukao T, Paterson AH, Hussey MA, Yamasue Y, Kennedy RA, Rumpho ME (2004) Construction of a comparative RFLP map of Echinochloa crus-galli toward QTL analysis of flooding tolerance. Theor Appl Genet 108(6):993–1001PubMedCrossRefGoogle Scholar
  13. Gonzalez-Andres F, Pita JM, Ortiz JM (1996) Caryopsis isoenzymes of Echinochloa weed species as an aid for taxonomic discrimination. J Hortic Sci 71:187–193Google Scholar
  14. Goolsby JA, De Barro PJ, Makinson JR, Pemberton RW, Hartley DM, Frohlich DR (2006) Matching the origin of an invasive weed for selection of a herbivore haplotype for a biological control program. Mol Ecol 15:287–297 (INSS: 1365-294X)PubMedCrossRefGoogle Scholar
  15. Ho CL, Julaveerasingam H, Kandasamy KI, Chin CF, Rahman SSA (2003) Variation in turfgrasses demonstrated by amplified fragment length polymorphism (AFLP). Asia Pac J Mol Biol Biotech 11:51–55Google Scholar
  16. Jaccard P (1908) Nouvelles recherchers sur la distribution florale. Bull Vaud Soc Nat 44:233–270Google Scholar
  17. Jasieniuk M, Maxwell BD (2001) Plant diversity: new insights from molecular biology and genomics technologies. Weed Sci 49:257–265CrossRefGoogle Scholar
  18. Karam D, Westra P, Nissen SJ, Ward SM, Figueiredo JEF (2004) Genetic diversity among proso millet (Panicum miliaceum) biotypes assessed by Aflp technique. Planta Daninha. Viçosa-MG 22(2):167–174Google Scholar
  19. Kendig A, Williams B, Smith CW (2003) Rice weed control, chapter 3.7. In: Smith CW, Dilday RH (eds) Rice, origin, history, technology and production. John Wiley and Sons Inc., Hoboken, pp 457–472Google Scholar
  20. Kim DS, Kim DH, Yoo JH, Kim BD (2006) Cleaved amplified polymorphic sequence and amplified fragment length polymorphism markers linked to the fertility restorer in chilli pepper (Capsicum annuum L.). Mol Cells 21:135–140PubMedCrossRefGoogle Scholar
  21. Loh JP, Kiew R, Hay A, Kee A, Gan LH (2000) Intergeneric and interspecific relationships in araceae tribe caladieae and development of molecular markers using amplified fragment length polymorphism (AFLP). Ann Bot 85:371–378CrossRefGoogle Scholar
  22. Lopez-Martinez N, Salva AP, Finch RP, Marshall G, De Prado R (1999) Molecular markers indicate intraspecific variation in the control of Echinochloa spp. with quinclorac. Weed Sci 47:310–315Google Scholar
  23. Mangolin CA, de Oliveira Junior RS, de Fatima PS, Machado M (2012) Genetic diversity in weeds, herbicides––environmental impact studies and management approaches. In: Ruben Alvarez-Fernandez (ed), ISBN: 978-953-307-892-2, InTech. http://www.intechopen.com/books/herbicides-environmental-impact-studies-and-management-approaches/genetic-diversity-and-structure-of-weed-plant-populations
  24. Maun MA, Barrett SCH (1986) The biology of Canadian weeds, Echinochloa crus-galli (L.) Beauv. Can J Plant Sci 66:739–759CrossRefGoogle Scholar
  25. McRoberts N, Sinclair W, McPherson A, Franke AC, Saharan RP, Malik RK, Singh S, Marshall G (2005) An assessment of genetic diversity within and between populations of Phalaris minor using ISSR markers. Weed Res 45:431–439CrossRefGoogle Scholar
  26. Mennan H, Kaya-Altop E (2012) Molecular techniques for discrimination of late watergrass (Echinochloa oryzicola) and early watergrass (Echinochloa oryzoides) species in Turkish rice production. Weed Sci 60:525–530CrossRefGoogle Scholar
  27. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117PubMedCrossRefGoogle Scholar
  28. Michael PW (1983) Taxonomy and distribution of Echnichloa species with special reference to their occurrence as weeds in rice. In: Weed control in rice. International Rice Research Institute, Manila, pp 291–306Google Scholar
  29. Michael P (2001) The taxonomy and distribution of Echinochloa species (barnyard grasses) in the Asian-Pacific region, with a review of pertinent biological studies. In:Proceedings of the 18th APWSS conference (Beijing, China, 28 May-2 June 2001). Standard Press of China, Beijing, pp 57–66Google Scholar
  30. Nakayama Y, Umemoto S, Yamaguchi H (1999) Identification of polyploidy groups in the genus Echinochloa. J Weed Sci Technol 44:205–217Google Scholar
  31. Ni H, Moody K, Robles RP, Paller EC, Lales JS, Cosico WC (1996) Effect of nitrogen rate on competition of two rice cultivars against Echinochloa crus-galli. Philip J Weed Sci 24:53–62Google Scholar
  32. Nissen SJ, Masters RA, Lee DJ, Rowe ML (1995) DNA-based marker systems to determine genetic diversity of weedy species and their application to biocontrol. Weed Sci 43:504–513Google Scholar
  33. O’Hanlon PC, Peakall R, Briese DT (1999) A review of new PCR-based genetic markers and their utility to weed ecology. Weed Res 40:239–254CrossRefGoogle Scholar
  34. Pester AP, Ward SM, Fenwick AL, Westra P, Nissen SJ (2003) Genetic diversity if jointed goatgrass (Aegilops cylindrica) determined with RAPD and AFLP markers. Weed Sci 51:287–293CrossRefGoogle Scholar
  35. Pignatti S (1982) Flora d’Italia, vol III. Agricole, Bologna, p 2324Google Scholar
  36. Portis E, Mauromicale G, Barchi L, Mauro R, Lanteri S (2005) Population structure and genetic variation in autochthonous globe artichoke germplasm from Sicily Island. Plant Sci 168:1591–1598CrossRefGoogle Scholar
  37. Powell W, Morgante M, Andre C (1996) The comparison of RFLP, RAPD, AFLP, and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238CrossRefGoogle Scholar
  38. Pritchard KJ, Wen W (2004) Documentation for structure software. The University of Chicago Press, ChicagoGoogle Scholar
  39. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  40. Roy S, Simon JP, Lapointe FJ (2000) Determination of the origin of the cold-adapted populations of barnyardgrass (Echinochloa crus-galli) in eastern North America: a total evidence approach using RAPD DNA and DNA sequences. Can J Bot 78:1505–1513Google Scholar
  41. Ruiz-Santaella JP, Bastida F, Franco AR, de Prado R (2006) Morphological and molecular characterization of different Echinochloa spp. and Oryza sativa populations. J Agric Food Chem 54:1166–1172PubMedCrossRefGoogle Scholar
  42. Rutledge J, Talbert RE, Sneller CH (2000) RAPD analysis of genetic variation among propanil resistant and -susceptible Echinochloa crus-galli populations in Arkansas. Weed Sci 46:669–674CrossRefGoogle Scholar
  43. Slotta TAB (2008) What we know about weeds: insights from genetic markers. Weed Sci 56(2):322–326 (ISSN 0043–1745)CrossRefGoogle Scholar
  44. Slotta TAB, Rothhouse J, Horvath DP, Foley ME (2006) Genetic diversity of Cirsium arvense (Canada thistle) in North Dakota. Weed Sci 54:1080–1085CrossRefGoogle Scholar
  45. Smith RJ (1983) Weeds of major economic importance in rice and yield losses due to weed competition. In: Proceedings of the conference on weed control in rice, International Rice Research Institute, Los Banos, pp 19–36Google Scholar
  46. Tabacchi M, Mantegazza R, Spada A, Ferrero A (2006) Morphological traits and molecular markers for classification of Echinochloa species from Italian rice fields. Weed Sci 54:1086–1093CrossRefGoogle Scholar
  47. Tajdoost S, Khavari-Nejad RA, Meighani F, Zand E, Noormohammadi Z (2013) Evaluation of genetic diversity and differentiation of Cuscuta campestris (field dodder) ecotypes using ISSR markers. Food Agric Environ 11(1):1072–1075Google Scholar
  48. Tasrif A, Juraimi AS, Kadir J, Soetikno SS (2004) Genetic diversity of Echinochloa crus-galli var. crus-galli (L.) Beauv (Barnyard grass: Poaceae) ecotypes in Malaysia and Indonesia as revealed by RAPD markers. Asian J Plant Sci 3:231–238CrossRefGoogle Scholar
  49. Tsuji R, Fischer AJ, Yoshino M, Roel A, Hill JE, Yamasue Y (2003) Herbicide-resistant late watergrass (Echinochloa phyllopogon): similarity in morphological and amplified fragment length polymorphism traits. Weed Sci 51:740–747CrossRefGoogle Scholar
  50. Van Devender KW, Costello TA, Smith RJ (1997) Model of rice (Oryza sativa), yield reduction as a function of weed interference. Weed Sci 45:218–224Google Scholar
  51. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414PubMedCentralPubMedCrossRefGoogle Scholar
  52. Wang T, Chen G, Zan Q, Wang C, Su Y (2012) AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the ınvasive weed mikania micrantha. PLoS One 7(7):e41310. doi: 10.1371/journal.pone.0041310 PubMedCentralPubMedCrossRefGoogle Scholar
  53. Wassom PJ, Tranel JJ (2005) Amplified fragment length polymorphism-based genetic relationships among weedy Amaranthus species. J Hered 96:410–416PubMedCrossRefGoogle Scholar
  54. Yabuno T (1966) Biosystematic study of the genus Echinochloa. Jpn J Bot 19:277–323Google Scholar
  55. Yabuno T (1975) The classification and geographical distribution of genus Echinochloa. Weed Res Japan 20:97–104Google Scholar
  56. Yamaguchi H, Utano A, Yasuda K, Yano A, Soejima A (2005) A molecular phylogeny of wild and cultivated Echinochloa in East Asia inferred from non-coding region sequences of trnT-L-F. Weed Biol Manag 5:210–218CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2014

Authors and Affiliations

  • Hilal Betul Kaya
    • 1
  • Mehmet Demirci
    • 2
  • Bahattin Tanyolac
    • 1
    Email author
  1. 1.Department of BioengineeringEge UniversityBornova-IzmirTurkey
  2. 2.Agrobest GroupKemalpaşa-IzmirTurkey

Personalised recommendations