Comparison of three genetic similarity coefficients based on dominant markers from predominantly self-pollinating species

A. Beharav, M. Maras, M. Kitner, J. Šuštar-Vozlič, G. L. Sun, I. Doležalová, A. Lebeda, V. Meglič

Research output: Contribution to journalArticlepeer-review

Abstract

Three genetic similarity coefficients were estimated and compared for their usefulness: simple matching (SSM), Jaccard's (SJ) and Dice's (SD), all based on dominant markers data from individuals representing predominantly self-pollinating species. AFLP markers were used to analyze 139 Phaseolus vulgaris L. (common bean) and 67 Lactuca saligna L. (least lettuce) accessions, and RAPD markers were used to analyze 110 Triticum dicoccoides Koern. (wild emmer wheat) accessions. Similar discriminating structure and power based on the three genetic similarity coefficients was found for each of the three species. This discriminating power was high for both P. vulgaris and L. saligna but moderate for T. dicoccoides. With closely related individuals, as in our study, the absence of a band in two individuals should be due to an identical cause inherited from the same ancestor. Accordingly we propose the use of SSM, which alone out of the three examined coefficients involved shared absence of DNA bands, as contributing to genetic similarity. When RAPDs are employed, inferences about population structure and nucleotide divergence should be made with prudence as the nature of genetic variation uncovered by RAPDs is often unclear.

Original languageEnglish
Pages (from-to)54-60
Number of pages7
JournalBiologia Plantarum
Volume54
Issue number1
DOIs
StatePublished - Feb 2010

Bibliographical note

Funding Information:
Received 14 November 2008, accepted 25 April 2009. Abbreviations: AFLP - amplified fragment length polymorphism; CCC - cophenetic correlations coefficients; D - dissimilarity; OUT - operational taxonomic unit; RAPD - random amplified polymorphic DNA; S - similarity; UPGMA - unweighted pair group method with the arithmetic averages. Acknowledgements: The molecular work for this research was supported by grant MSM 6198959215 (Ministry of Education, Youth and Sports of the Czech Republic); in part by grant J4-9476-0401-06 from the Slovenian Research Agency; and by a postdoctoral grant from the Israeli Council of Higher Education to G.L. Sun. * Corresponding author; fax (+972) 4 8246554, e-mail: beharav@research.haifa.ac.il

Keywords

  • Closely related individuals
  • Lactuca saligna
  • Negative matches
  • Phaseolus vulgaris
  • Triticum dicoccoides

ASJC Scopus subject areas

  • Plant Science
  • Horticulture

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