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Molecular Characterization of Cultivated Species of the Genus Pachyrhizus Rich. ex DC. by AFLP Markers: Calling for More Data

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Abstract

Yam beans (Pachyrhizus DC.) are legume root crops that have attracted scientific interest because of high contents of starch, protein, and iron in their roots. In this study, 58 accessions of three cultivated Pachyrhizus species were characterized by amplified fragment length polymorphism (AFLP) molecular markers in order to estimate genetic diversity and interspecific relationships. To complement molecular marker information, individuals from each accession were analyzed in order to confirm ploidy levels. Eight AFLP primer combinations detected 136 (68.7 %) polymorphic bands. Shannon’s diversity indices (Hs) for each species were 1.04 (P. ahipa), 1.07 (P. tuberosus), and 2.42 (P. erosus), while the total diversity index was 2.45. Phylogenetic analysis, principal coordinate analysis and analysis of molecular variance (F ST = 0.796) all showed significant species differentiation. All accessions were diploid (2n = 2x = 22), which is characteristic of the tribe Phaseoleae. Finally, a misclassified accession of P. tuberosus was identified. Molecular characterization of accessions is necessary for efficient management of germplasm collections.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

CIP:

International Potato Center

AMOVA:

Analysis of molecular variance

DM:

Dry matter

RAPD:

Random amplified polymorphic DNA

PCoA:

Principal coordinates analysis

References

  • Abbott R, Brennan A (2014) Altitudinal gradients, plant hybrid zones and evolutionary novelty. Phil Trans R Soc B 369:20130346

    Article  PubMed  Google Scholar 

  • Anderson M, Willis T (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84(2):511–525

    Article  Google Scholar 

  • Catteau L, Lautié E, Koné O, Coppée M, Hell K, Bertrand C, Quetin-Leclercq J (2013) Degradation of rotenone in Yam Bean seeds (Pachyrhizus sp.) through food processing. J Agric Food Chem 61:11173–11179

    Article  CAS  PubMed  Google Scholar 

  • Chavez AL, Bedoya JM, Sánchez T, Iglesias C, Ceballos H, Roca W (2000) Iron, carotene, and ascorbic acid in cassava roots and leaves. Food Nutr Bull 21(4):410–413

    Google Scholar 

  • Delêtre M, Soengas B, Utge J, Lambourdière J, Sørensen M (2013) Microsatellite markers for the Yam bean Pachyrhizus (Fabaceae). Appl Plant Sci 1(7):1200551

    Google Scholar 

  • Døygaard S, Sørensen M (1998) Principal component analysis of morphological characters in the genus Pachyrhizus DC. In: Sørensen et al. (eds) Proceedings of Second International Symposium on Tuberous Legumes, Celaya-Mexico pp 33–42

  • Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15

    Google Scholar 

  • Doyle JJ, Doyle JL (1993) Chloroplast DNA phylogeny of the Papilionoid legume tribe Phaseoleae. Syst Bot 18(2):309–327

    Article  Google Scholar 

  • Doyle J, Doyle J, Harbison C (2003) Chloroplast-expressed glutamine synthetase in Glycine and related Leguminosae: phylogeny, gene duplication, and ancient polyploidy. Syst Bot 28(03):567–577

    Google Scholar 

  • Espert S, Sede S, Ruiz L, Fortunato R, Poggio L (2008) New chromosome reports in the subtribes Diocleinae and Glycininae (Phaseoleae: Papilionoideae: Fabaceae). Bot J Linn Soc 158:336–341

    Article  Google Scholar 

  • Estrella J, Phillips S, Abbott R, Gillies A, Sørensen M (1998) Genetic variation and relationships in agronomically important species of Yam Bean (Pachyrhizus DC.) based on RAPD markers. In: Sørensen et al. (eds) Proceedings of Second International Symposium on Tuberous Legumes, Celaya-Mexico, pp 43–59

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinforma 1:47–50

    CAS  Google Scholar 

  • Garcia A, Benchimol L, Barbosa A, Geraldi I, Souza C Jr, Souza A (2004) Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genet Mol Biol 27(4):579–588

  • Ghislain M, Zhang DP, Herrera MR (1999) Molecular biology laboratory protocols: plant genotyping. CIP (eds) Lima, Perú

  • Grum M (1994) Breeding of new yam bean (Pachyrhizus Rich. ex DC.). Cultivars in Tonga involving interspecific hybrids. In: Sørensen M (ed.) Proceedings of the First International Symposium on Tuber Legumes, pp.315–320. Guadeloupe, FWI 21–24 April 1992. Jordbrugsforlaget, Copenhagen, Denmark

  • Grüneberg WJ, Goffman FD, Velasco L (1999) Characterization of Yam Bean (Pachyrhizus spp.) seeds as potential sources of high palmitic acid oil. J Am Oil Chem Soc 76(11):1309–1312

    Article  Google Scholar 

  • Grüneberg WJ, Freynhagen-Leopold P, Delgado-Váquez O (2003) A new yam bean (Pachyrhizus spp.) interspecific hybrid. Genet Resour Crop Evol 50:757–766

  • Hammer K, Heller J, Engels J (2001) Monographs on underutilized and neglected crops. Genet Resour Crop Evol 48:3–5

  • Heider B, Tumwegamire S, Tukamuhabwa P, Ndirigwe J, Bouwe G, Bararyenya A, Hell K, Leclercq J, Lautié E, Wassens R, Burgos G, Zum T, Thiele G, Grüneberg W (2011) Nutritional improvement of yam bean and sustainability of farming systems in Central and West Africa. Afr Crop Sci 10:93–95

  • Ipek M, Ipek H, Simon P (2003) Comparison of AFLPs, RAPD markers and isozymes for diversity assessment of garlic and detection of putative duplicates in germplasm collections. J Am Soc Hortic Sci 128(2):245–252

    Google Scholar 

  • Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390

    Article  CAS  Google Scholar 

  • Karuniawan A, Anas I, Kale P, Heinzenmann J, Becker HC, Grüneberg WJ (2003) Status of under- utilised tuber legumes Yam Bean and wild Cow Pea in Indonesia. In: Wollny et al. (eds) Technological and Institutional Innovations for Sustainable Rural Development. Book of Abstracts, Göttingen

  • Kosman E, Leonard KJ (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol Ecol 14:415–424

    Article  CAS  PubMed  Google Scholar 

  • Lackey J (1980) Chromosome numbers in the Phaseoleae (Fabaceae: Faboideae) and their relation to taxonomy. Am J Bot 67(4):595–602

    Article  Google Scholar 

  • Lautié E, Rozet E, Hubert P, Quetin Leclercq J (2012) Quantification of rotenone in seeds of different species of yam bean (Pachyrhizus sp.) by a SPE HPLC-UV method. Food Chem 131:1531–1538

    Article  Google Scholar 

  • Lautié E, Rozet E, Hubert P, Vandelaer N, Billard F, Zum Felde T, Grüneberg WJ, Quetin Leclercq J (2013) Fast method for the simultaneous quantification of toxic polyphenols applied to the selection of genotypes of yam bean (Pachyrhizus sp.) seeds. Talanta 117:94–101

    Article  PubMed  Google Scholar 

  • Lee J, Hymowitz T (2001) A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA RPS16 intron sequences. Am J Bot 88(11):2064–2073

    Article  CAS  PubMed  Google Scholar 

  • Malice M, Baudoin J (2009) Genetic diversity and germplasm conservation of three minor Andean tuber crop species. Biotechnol Agron Soc Environ 13(3):441–448

    Google Scholar 

  • Masterson J (1994) Stomatal size in fossil plants—evidence for polyploidy in the majority of angiosperms. Science 264:421–424

    Article  CAS  PubMed  Google Scholar 

  • Maughan PJ, Saghai Maroof MA, Buss GR, Huestis GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near- isogenic line analysis. Theor Appl Genet 93:392–401

    Article  CAS  PubMed  Google Scholar 

  • Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Tree 14:10

    Article  Google Scholar 

  • Oré-Balbin I, Delgado O, Mejía K, Sørensen M, Kvist PL (2005) El cultivo de Chuin: una alternativa para la seguridad alimentaria y la recuperación de suelos degradados en la Amazonía Peruana. Peruvian Amazon Research Institute (IIAP). Iquitos, Perú

  • Oré-Balbin I, Sørensen M, Kvist PL, Delgado O (2007) Review of the Pachyrhizus tuberosus (Lam.) Spreng. Cultivar groups in Peru. PGR Newsl FAO Biodivers 151:2–13

    Google Scholar 

  • Orjeda G (1990) Desarrollo y uso de híbridos interespecíficos entre Ipomoea batatas Lam. (2n = 6x = 90) e I. trifida (H.B.K.) G. Don. (2n = 2x = 30) como probadores de especies silvestres diploides y tetraploides. Dissertation, Universidad Nacional Agraria La Molina (UNALM)

  • Ørting B, Grüneberg WJ, Sørensen M (1996) Ahipa (Pachyrhizus ahipa (Wedd.) Parodi) in Bolivia. Genet Resour Crop Evol 43:435–446

  • Padonou SW, Houyèvou AK, Ahounou JL, Houssou AP, Fandohan P, Aïhou K, Adjanohoun A, Hell K, Adégbola PY, Mensah GA, Koundandé DO (2013) Yam bean (Pachyrhizus erosus) tuber processing in Benin: production and evaluation of the quality of yam bean-gari and yam bean-fortified gari. Int J Biol Chem Sci 7(1):247–259

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon et al. (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier, pp 43–76

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/

  • Ramanatha V, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Org 68:1–19

    Article  Google Scholar 

  • Ratanadilok M, Suriyawan K, Thanaisawanrayangkura S (1996) Yam Bean (Pachyrhizus erosus (L.) Urban) and its economic potential. In: Sørensen et al. (eds) Proceedings of Second International Symposium on Tuberous Legumes, Celaya-Mexico 261

  • Rizky WH, Hasani S, Karuniawan A (2013) Tuber yield and quality of nine genotypes Yam Bean (Pachyrhizus spp.) due to sink-reproductive pruning. Horticulture 62:445–448

    Google Scholar 

  • Roach DA, Wulff RD (1987) Maternal effects in plants. Annu Rev Ecol Syst 18:209–235

    Article  Google Scholar 

  • Sharma AK, Sharma A (1980) Chromosome techniques. Butterworth & Co, London

    Google Scholar 

  • Sørensen M (1988) A taxonomic revision of the genus Pachyrhizus Rich. ex DC. nom. cons. Nord J Bot 8(2):167–192

    Article  Google Scholar 

  • Sørensen M (1990) Observations on distribution, ecology and cultivation of the tuber-bearing legume genus Pachyrhizus Rich. ex DC. (Fabaceae: Phaseoleae). Agric Univ Wageningen Pap 90–3:1–38

  • Sørensen M (1991) Cross breeding experiments: Compatibility, pollen fertility, and germination percentages of interspecific hybrids, F1, F2 & F3 in the genus Pachyrhizus Rich. ex DC. (Fabaceae: Phaseolae). In: Degras, L. (eds) 1991. Caribbean Food Crops Society, Twenty-Fifth Annual Meeting, Vol 25. Publication INRA, Guadeloupe, pp 597–624

  • Sørensen M (1996) Yam bean (Pachyrhizus DC.). Promoting the conservation and use of underutilized and neglected crops. 2. Institute of Plant Genetics and Crop Plant Research, Gatersleben/ International Plant Genetic Resources Institute, Rome

  • Sørensen M, Døygaard S, Estrella EJ, Kvist LP, Nielsen PE (1997) Status of the South American tuberous legume Pachyrhizus tuberosus (Lam.) Spreng. Biodivers Conserv 6(12):1581–1625

    Article  Google Scholar 

  • Talledo D, Escobar C (1999) Comparativo de la acción de los inhibidores de la mitosis en especies vegetales nativas del Perú. Scientia 1(1):129–157

    Google Scholar 

  • Talledo D, Escobar C, Arenas N (1999) Citogenética de Pachyrhizus tuberosus y Pachyrhizus ahipa: ciclo celular y número cromosómico. In: Fairlie et al. (eds) Raíces y tubérculos andinos, avances de investigación, vol I. CIP CONDESAN Lima, Peru, pp 139–161

  • Tapia CG (1998) Caracterización morfológica y molecular de la diversidad genética de la colección de Pachyrhizus tuberosus (LAM.) SPRENG. Del CATIE. Dissertation, Tropical Agricultural Research and Higher Education Center (CATIE)

  • Tapia CG, Sørensen M (2003) Morphological characterization of the genetic variation existing in a Neotropical collection of yam bean, Pachyrhizus tuberosus (Lam.) Spreng. Genet Resour Crop Evol 50:681–692

  • Tumwegamire S, Kapinga R, Rubaihayo PR, La Bonte DR, Grüneberg WJ, Burgos G, zum Felde T, Carpio R, Pawelzik E, Mwanga ROM (2011) Evaluation of dry matter, protein, starch, sucrose, β-carotene, iron, zinc, calcium, and magnesium in East African sweetpotato [Ipomoea batatas(L.) Lam] germplasm. HortScience 46(3):348–357

  • Villar MLD, Valio IFM (1994) Rotenone and pachyrhizin in P. tuberosus: effect of endogenous rotenone and pachyrhizin on early growth of Pachyrhizus tuberosus (Lam.) Spreng. In: Sørensen M (ed) Proceedings of the first international symposium on tuber legumes. FWI, Guadalupe

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Weising K, Nybom H, Wolff K, Kahl G (2005) DNA fingerprinting in plants, principles, methods and applications, 2nd edn. CRC Press, Boca Ratón

    Book  Google Scholar 

  • Zanklan A, Ahouangonou S, Becker HC, Pawelzik E, Grüneberg WJ (2007) Evaluation of the storage root-forming legume Yam Bean (Pachyrhizus spp.) under West African conditions. Crop Sci 47:1934–1946

    Article  Google Scholar 

  • Zeven AC (1998) Landraces: A review of definitions and classifications. Euphytica 104:127–139

    Article  Google Scholar 

  • Zohary D (2007) Unconscious selection and the evolution of domesticated plants. Econ Bot 58(1):5–10

    Article  Google Scholar 

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Acknowledgments

This study was conducted within in the framework of the project “Enhancing the nutrient-rich yam bean (Pachyrhizus spp.) to improve food quality and availability and sustainability of farming systems in Central and West Africa.” Financial support from the Belgian Development Cooperation (D43/JK: Belgian CIP Project Yam-bean) is gratefully acknowledged.

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Authors and Affiliations

  1. International Potato Center (CIP), Av. La Molina 1895, Lima, 12, Peru

    Monica Santayana, Genoveva Rossel, Jorge Núñez, Ronald Robles, Victor Fernández, Wolfgang J. Grüneberg & Bettina Heider

  2. Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 21, 1958, Frederiksberg, Denmark

    Marten Sørensen

  3. Muséum National d’Histoire Naturelle, Département Hommes Natures Sociétés, UMR 7206 Eco-anthropologie et ethnobiologie, CP 135, 57 rue Cuvier, Cedex 05, 75231, Paris, France

    Marc Delêtre

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  1. Monica Santayana
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  2. Genoveva Rossel
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  3. Jorge Núñez
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  4. Marten Sørensen
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  9. Bettina Heider
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Correspondence to Monica Santayana.

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Communicated by: Paulo Arruda

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Santayana, M., Rossel, G., Núñez, J. et al. Molecular Characterization of Cultivated Species of the Genus Pachyrhizus Rich. ex DC. by AFLP Markers: Calling for More Data. Tropical Plant Biol. 7, 121–132 (2014). https://doi.org/10.1007/s12042-014-9143-7

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