Nadia HAIDER, Imad NABULSI, Nizar MIRALI

Identification of species of Vicia subgenus Vicia (Fabaceae) using chloroplast DNA data

Vicia subgenus Vicia (Fabaceae) contains several economically important food and forage legume species. Generally, the taxonomy and identification of these species have relied heavily on a few diagnostic morphological characters (e.g., the number of flowers per inflorescence). However, there are several specimens with intermediate morphological characters that make diagnosis of these species using those characters a difficult task for nonspecialists and render results that are not always accurate. The use of molecular markers, therefore, is the most attractive alternative strategy for a more accurate identification of species of the subgenus Vicia. In the present study, an attempt was made to investigate polymorphism in the chloroplast DNA of 22 species of the subgenus Vicia using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) on 9 chloroplast regions and a set of 12 consensus chloroplast simple sequence repeat (ccSSR) primer pairs for the diagnosis of the targeted species. Based on the data generated, it was possible to identify all of the species analyzed, except for 4 species that were placed in 2 groups (1, V. noeana and V. dionysiensis; and 2, V. serratifolia and V. hyaeniscyamus), each of which had a unique chloroplast type. Species-specific markers developed here are useful for the early diagnosis of targeted Vicia species and can provide essential baseline data for the evolution of systematic breeding and conservation strategies, as well as guidance for germplasm collections.

Anahtar Kelimeler:

Key words: Diagnosis, legumes, markers, taxonomy, Vicia

Identification of species of Vicia subgenus Vicia (Fabaceae) using chloroplast DNA data

Keywords:

Key words: Diagnosis, legumes, markers, taxonomy, Vicia,

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Allkin R, Goyder DJ, Bisby FA, White RJ (1986) Names and synonyms of species and subspecies in the Vicieae: Issue 3. Vicieae Database Project 7: 0263-8517.
Caputo P, Frediani M, Venora G, Ravalli C, Ambrosio M, Cremonini R (2006) Nuclear DNA contents, rDNAs, and karyotype evolution in subgenus Vicia: III. Th e heterogeneous section Hypechusa. Protoplasma 228: 167-177.
Chung SM, Decker-Walters DS, Staub JE (2003) Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses. Can J Bot 81: 814-832.
Chung SM, Staub JE (2003) Th e development and evaluation of consensus chloroplast primer pairs that possess highly variable sequence regions in a diverse array of plant taxa. Th eor Appl Genet 107: 757-767.
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
Duc G, Bao SY, Baum M, Redden B, Sadiki M, Suso MJ (2010) Diversity maintenance and use of Vicia faba L. genetic resource. Field Crops Res 115: 270-278.
Eurlings MCM, Gravendeel B (2006) Final report of CITES-fi nanced pilot project: Search for DNA markers to discriminate cultivated from wild gaharu (agarwood). CITES, Geneva. Available at: http://www.cites.org/common/com/PC/16/X- PC16-01-Inf.pdf.
Fennell SR, Powell W, Wright F, Ramsay G, Waugh R (1998) Phylogenetic relationships between Vicia faba (Fabaceae) and related species inferred from chloroplast trnL sequences. Plant Syst 212: 247-259.
Ford CS, Ayres KL, Toomey N, Haider N, van Alpen Stahl J, Kelly LJ, Wikström N, Hollingsworth PM, Duff RJ, Hoot SB, Cowan RS, Chase MW, Wilkinson MJ (2009) Selection of candidate DNA barcoding regions for use on land plants. Bot J Linn Soc 159: 1-11.
Frediani M, Caputo P, Venora G, Ravalli C, Ambrosio M, Cremonini R (2005) Nuclear DNA contents, rDNAs, and karyotype evolution in Vicia subgenus Vicia: II. Section Peregrinae. Protoplasma 226: 181-90.
Frediani M, Maggini F, Gelati MT, Cremonini R (2004) Repetitive DNA sequences as probes for phylogenetic analysis in Vicia genus. Caryologia 57: 379-386.
Gielly L, Taberlet P (1994) Th e use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol 11: 769-777.
Haider A, Hassanin BR, Mahmoud N, Madkour M (2000) Molecular characterization of some species of the genus Vicia. Arab Council for Graduate Studies and Scientifi c Research, Cairo. Available at: http://www.acgssr.org/BioTechnology/ V4N2July2001/fullpaper/p17.pdf.
Haider N (2003) Development and Use of Universal Primers in Plants. PhD thesis. Th e University of Reading, Reading, UK.
Haider N (2011) Identifi cation of plant species using traditional and molecular-based methods, pp. 1-62. In: Wild Plants: Identifi cation, Uses and Conservation (Ed. RE Davis), Nova Science Publishers, Inc., New York, USA.
Haider N (2012) Evidence for the origin of the B genome of bread wheat based on chloroplast DNA. Turk J Agric For 36: 13-25.
Haider N, Nabulsi I (2008) Identifi cation of Aegilops L. species and Triticum aestivum L. based on chloroplast DNA. Genet Resour Crop Ev 55: 537-549.
Haider N, Nabulsi I, Kamary Y (2010) Identifi cation of species of Orchidaceae in Northern West of Syria based on chloroplast DNA. Russ J Genet 46: 1067-1078.
Haider N, Wilkinson MJ (2011) A set of plastid DNA-specifi c universal primers for fl owering plants. Russ J Genet 47: 44-55.
Hosseinzadeh Z, Pakravan M, Tavassoli A (2008) Micromorphology of seed in some Vicia species from Iran. Rostaniha 9: 96-107.
İnceer H, Hayırlıoğlu Ayaz S (2005) Giemsa C-banded karyotypes of Vicia cracca L. subsp. cracca and V. bithynica L. Turk J Bot 29: 311-316.
Jaaska V (1997) Isoenzyme diversity and phylogenetic affi nities in Vicia subgenus Vicia (Fabaceae). Genet Resour Crop Ev 44: 557-574.
Jaaska V (2005) Isozyme variation and phylogenetic relationships in Vicia subgenus Cracca (Fabaceae). Ann Bot 96: 1085-1096.
Jürgen K, Weder P (2002) Species identifi cation of beans, peas and other legumes by RAPD-PCR aft er DNA isolation using membrane columns. LWT 35: 277-283.
Kupicha FK (1974) Taxonomic Studies in the Tribe Vicieae (Leguminosae). PhD thesis. University of Edinburgh, Edinburgh, UK.
Kupicha FK (1976) Th e infrageneric structure of Vicia L. Notes Roy Bot Garden Edinb 34: 287-326.
Leht M, Jaaska V (2002) Cladistic and phenetic analysis of relationships in Vicia subgenus Vicia (Fabaceae) by morphology and isozymes. Plant Syst Evol 232: 237-260.
Li WT, Peng YY, Wei YM, Baum BR, Zheng YL (2009) Relationships among Avena species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers. Genet Resour Crop Ev 56: 465-480.
Maxted N (1993) A phenetic investigation of Vicia L. subgenus Vicia (Leguminosae-Vicieae). Bot J Linn Soc 111: 155-182.
Maxted N (1995) An ecogeographical study of Vicia subgenus Vicia. Systematic and Ecogeographic Studies on Crop Genepools 8. International Plant Genetic Resources Institute, Rome, Italy. Available at: http://pdf.usaid.gov/pdf_docs/PNABU773.pdf.
Maxted N, Callimassia MA, Bennett MD (1991) Cytotaxonomic studies of eastern Mediterranean Vicia species (Leguminosae). Plant Syst 177: 221-234.
Maxted N, Khattab A, Ehram T, Bisby FA, Obari H, Sweidan Y, Goyder DJ (1993). Important collections of Vicieae from Syria. Proceedings of the 5th OPTIMA Meeting, pp. 693-699.
Maxted N, Obari H, Tan A (1990) New and interesting Vicieae from the Eastern Mediterranean. Plant Genetic Resources- Newsletter 78: 21-26.
MirAli N, El-Khouri S, Rizq F (2007) Genetic diversity and relationships in some Vicia species as determined by SDS- PAGE of seed proteins. Biol Plantarum 51: 660-666.
Navratilova A, Neumann P, Macas J (2003) Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences. Ann Bot 91: 921-6.
Piergiovanni AR, Taranto G (2005) Specifi c diff erentiation in Vicia genus by means of capillary electrophoresis. J Chromatogr A 1069: 253-260.
Ponert J (1973) Combinationes novae, stat novi et taxa nova non tantum specierum turcicarum. Feddes Repert 83: 617-644.
Potokina E, Tomooka N, Vaughan DA, Alexandrova T, Xu RQ (1999) Phylogeny of Vicia subgenus Vicia (Fabaceae) based on analysis of RAPDs and RFLP of PCR-amplifi ed chloroplast genes. Genet Resour Crop Ev 46: 149-161.
Raina SN, Ogihara Y (1994) Chloroplast DNA diversity in Vicia faba and its close wild relatives: implications for reassessment. Th eor Appl Genet 88: 261-266.
RainaSN, OgiharaY (1995) Ribosomal DNA repeat unit polymorphism in 49 Vicia species. Th eor Appl Genet 90: 477- 486.
Sakowicz T, Cieślikowski T (2006) Phylogenetic analyses within three sections of the genus Vicia. Cell Mol Biol Lett 11: 594-615.
Sakr MM, Gowayed SMH, HassanWM, Almghraby OA (2010) Identifi cation of some wild Vicia species using electrophoretic analysis of seed proteins and amino acids composition. Indian J Sci Technol 3: 490-498.
Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplifi cation of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
van de Ven WTG, Duncan N, Ramsay G, Phillips M, Powell W, Waugh R (1993) Taxonomic relationships between V. faba and its relatives based on nuclear and mitochondrial RFLPs and PCR analysis. Th eor Appl Genet 86: 71-80.
Zimniak-Przbylska Z, Przybylska J (1995) Electrophoretic seed globulin patterns and species relationships in Vicia section Faba (Fabaceae). J Appl Genet 36: 299-312.