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Spatially structured morphological and molecular diversity among Dioscorea cayenensis and D. rotundata yam accessions

Published online by Cambridge University Press:  03 February 2016

L. R. G. Silva ,
T. F. Mezette ,
W. F. Nascimento ,
E. F. Silva  and
E. A. Veasey
L. R. G. Silva
Affiliation:
Faculdades Gammon de Ensino, Rua Prefeito Jayme Monteiro, 791, CEP 197000-000 Paraguaçu Paulista, São Paulo, Brazil
T. F. Mezette
Affiliation:
Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, CEP 13418-900 Piracicaba, São Paulo, Brazil
W. F. Nascimento
Affiliation:
Centro de Ciências Agrárias e Ambientais, Universidade Federal do Maranhão, BR-222, KM 04, s/n, Boa Vista, CEP 65500-000 Chapadinha, Maranhão, Brazil
E. F. Silva
Affiliation:
Departamento de Biologia, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900 Recife, Pernambuco, Brazil
E. A. Veasey*
Affiliation:
Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, CEP 13418-900 Piracicaba, São Paulo, Brazil
*
*Corresponding author. E-mail: eaveasey@usp.br
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Abstract

Yams (Dioscorea spp.) are one of the main root and tuber crops in the world, especially within the species complex Dioscorea cayenensis/D. rotundata. Few studies have been conducted in Brazil with these species, including genetic diversity. The objective of this study was to characterize the genetic diversity of local varieties of D. cayenensis and D. rotundata using morphological and molecular markers, and provide information on the management and use of the crop by family farmers from different regions in Brazil. Thus, yam tubers were sampled from several municipalities in the South, Southeast and Northeast regions. Eighteen morphological traits and ten microsatellite loci were used to analyse 47 yam accessions (23 D. cayenensis and 24 D. rotundata). Species identification was carried out after field morphological evaluation. Spatial genetic analysis indicated significant structure among the local varieties, mostly between regions and species. Both cluster and Bayesian analyses showed a separation of the accessions into two distinct groups: group I with accessions originated from the Southeast region and group II with accessions originated from the Northeast region, while accessions from the South region were intermediate or included in either group. The results showed a separation between D. cayenensis and D. rotundata accessions in Brazil, and that D. cayenensis occurs predominantly in the Southeast region, while D. rotundata occurs in the Northeast region. Further studies with larger sampling would be welcome in order to confirm these findings. Also, this study highlights the importance of family farmers in the genetic diversity conservation of these species in Brazil.

Keywords

Dioscoreafamily agriculturegenetic diversitylocal varietiesmicrosatellitesmorphological traits
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 4 , August 2017 , pp. 296 - 309
Copyright
Copyright © NIAB 2016 

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References

Agarwal, M, Shrivastava, N and Padh, H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports 27: 617–631.CrossRefGoogle ScholarPubMed
Amorozo, MCM (2008) Maintenance and management of agrobiodiversity in small-scale. Functional Ecosystems and Communities 2: 11–20.Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. American Journal of Human Genetics 32: 314–331.Google Scholar
Brasil(2015) Guia Internet Brazil. Brasil – Clima. Available at: http://www.guianet.com.br/brasil/mapaclima.htm (accessed 21 September 2015).Google Scholar
Bressan, EA, Veasey, EA, Peroni, N, Felipim, AP and Santos, KMP (2005) Collecting yam (Dioscorea spp.) and sweet potato (Ipomoea batatas) germplasm in traditional agriculture small-holdings in the Vale do Ribeira, São Paulo, Brazil. Plant Genetic Resources Newsletter 144: 8–13.Google Scholar
Bressan, EA, Briner Neto, T, Zucchi, MI, Rabello, RJ and Veasey, EA (2014) Genetic structure and diversity in the Dioscorea cayenensis/D. rotundata complex revealed by morphological and isozyme markers. Genetics and Molecular Research 13: 425–437.CrossRefGoogle ScholarPubMed
Creste, S, Tulmann Neto, A and Figueira, A (2001) Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Molecular Biology Reporter 19: 299–306.CrossRefGoogle Scholar
Dansi, A, Mignouna, HD, Zoundjihekpon, J, Sangare, A, Asiedu, R and Quin, FM (1999) Morphological diversity, cultivar groups and possible descent in the cultivated yams (Dioscorea cayenensis/D. rotundata) complex in Benin Republic. Genetic Resources and Crop Evolution 46: 371–388.CrossRefGoogle Scholar
Dansi, A, Mignouna, HD, Zoundjihékpon, J, Sangare, A, Asiedu, R and Ahoussou, N (2000) Using isozyme polymorphism to assess genetic variation within cultivated yams (Dioscorea cayenensis/Dioscorea rotundata complex) of the Republic of Benin. Genetic Resources and Crop Evolution 47: 371–383.CrossRefGoogle Scholar
Dansi, A, Mignouna, HD, Pillay, M and Zok, S (2001) Ploidy variation in the cultivated yams (Dioscorea cayenensis–Dioscorea rotundata complex) from Cameroon as determined by flow cytometry. Euphytica 119: 301–307.CrossRefGoogle Scholar
Dansi, A, Dantsey-Barry, H, Dossou-Aminon, I, N'Kpenu, EK, Agré, AP, Sunu, YD, Kombaté, K, Loko, YL, Dansi, M, Assogba, P and Vodouhè, R (2013) Varietal diversity and genetic erosion of cultivated yams (Dioscorea cayenensis Poir–D. rotundata Lam complex and D. alata L.) in Togo. International Journal of Biodiversity and Conservation 5: 223–239.Google Scholar
Doyle, JJ and Doyle, JL (1990) Isolation of plant DNA fresh tissue. Focus 12: 13–15.Google Scholar
Dufie, WMF, Oduro, I, Ellis, WO, Asiedu, R and Maziya-Dixon, B (2013) Potential health benefits of water yam (Dioscorea alata). Food & Function 4: 1496–1501.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574–578.CrossRefGoogle ScholarPubMed
FAOSTAT(2013) Database. Available at: http://faostat.fao.org/site/567/default.aspx#ancor (accessed 16 April 2014).Google Scholar
Girma, G, Hyma, KE, Asiedu, R, Mitchell, SE, Gedil, M and Spillane, C (2014) Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of guinea yams. Theoretical and Applied Genetics 127: 1783–1794.CrossRefGoogle ScholarPubMed
IPGRI/IITA(1997) Descritores para el ñame (Dioscorea spp.). Ibadan, Nigeria: International Institute of Tropical Agriculture/Rome, Italy: International Plant Genetic Resources Institute.Google Scholar
Lebot, V (2009) Tropical Root and Tuber Crops: Cassava, Sweet Potato, Yams and Aroids. London: CABI.Google Scholar
Loko, YL, Adjatin, A, Dansi, A, Vodouhe, R and Sanni, A (2015) Participatory evaluation of Guinea yam (Dioscorea cayenensis Lam.–D. rotundata Poir. complex) landraces from Benin and agro-morphological characterization of cultivars tolerant to drought, high soil moisture and chips storage insects. Genetic Resources and Crop Evolution 62: 1181–1192.CrossRefGoogle Scholar
Mahalakshmi, V, Ng, Q, Atalobhor, J, Ogunsola, D, Lawson, M and Ortiz, R (2007) Development of a West African yam Dioscorea spp. core collection. Genetic Resources and Crop Evolution 54: 1817–1825.CrossRefGoogle Scholar
Mantel, N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27: 202–209.Google Scholar
Marchetti, FF, Massaro-Junior, LR, Amorozo, MC and Butturi-Gomes, D (2013) Maintenance of manioc diversity by traditional farmers in the state of Mato Grosso, Brazil: a 20-year comparison. Economic Botany 67: 313–323.CrossRefGoogle Scholar
Martin, FW (1978) The relationship of Dioscorea cayenensis and D. rotundata . Tropical Agriculture 55: 193–206.Google Scholar
Melo Filho, PA, Santos, RC, Mafra, RC, Santos, JW and Anunciação Filho, CJ (2000) Classificação de germoplasma de Dioscorea sp. através da análise dos componentes principais. Ciência Rural 30: 619–623.CrossRefGoogle Scholar
Mengesha, WA, Demissew, S, Fay, MF, Smith, RJ, Nordal, I and Wilkin, P (2013) Genetic diversity and population structure of Guinea yams and their wild relatives in South and South West Ethiopia as revealed by microsatellite markers. Genetic Resources and Crop Evolution 60: 529–541.CrossRefGoogle Scholar
Mignouna, HD, Dansi, A and Zok, S (2002) Morphological and isozymic diversity of the cultivated yams (Dioscorea cayenensis/Dioscorea rotundata complex) of Cameroon. Genetic Resources and Crop Evolution 49: 21–29.CrossRefGoogle Scholar
Mignouna, HD, Abang, MM and Fagbemi, SA (2003) A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata) germplasm characterization. Annals of Applied Biology 142: 269–276.CrossRefGoogle Scholar
Nascimento, WF, Rodrigues, JF, Koehler, S, Gepts, P and Veasey, EA (2013) Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil. Genetic Resources and Crop Evolution 60: 2405–2420.CrossRefGoogle Scholar
Obidiegwu, JE, Kolesnikova-Allen, M, Ene-Obong, EE, Muoneke, CO and Asiedu, R (2009) SSR markers reveal diversity in Guinea yam (Dioscorea cayenensis/D. rotundata) core set. African Journal of Biotechnology 8: 2730–2739.Google Scholar
Onyilagha, JC (1986) Numerical analysis of variation among Nigerian Dioscorea rotundata accessions. Euphytica 35: 413–419.CrossRefGoogle Scholar
Peroni, N, Kageyama, PY and Begossi, A (2007) Molecular differentiation, diversity, and folk classification of “sweet” and “bitter” cassava (Manihot esculenta) in Caiçara and Caboclo management systems (Brazil). Genetic Resources and Crop Evolution 54: 1333–1349.CrossRefGoogle Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software. Available at: http://darwin.cirad.fr/darwin (accessed 20 November 2011).Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Ramser, J, Weising, K, Lopez-Peralta, C, Terhalle, W, Terauchi, R and Kahl, G (1997) Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata–D. cayenensis). Genome 40: 903–915.CrossRefGoogle ScholarPubMed
Rohlf, J (1992) NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 1.70 (Software). New York: Stony Brook.Google Scholar
Salako, VK, Fandohan, B, Kassa, B, Assogbadjo, AE, Idohou, AFI, Gbedomon, RC, Chakeredza, S, Dulloo, ME and Kakaı, RG (2014) Home gardens: an assessment of their biodiversity and potential contribution to conservation of threatened species and crop wild relatives in Benin. Genetic Resources and Crop Evolution 61: 313–330.CrossRefGoogle Scholar
Sartie, A, Asiedu, R and Franco, J (2012) Genetic and phenotypic diversity in a germplasm working collection of cultivated tropical yams (Dioscorea spp.). Genetic Resources and Crop Evolution 59: 1753–1765.CrossRefGoogle Scholar
Scarcelli, N, Daïnou, O, Agbangla, C, Tostain, S and Pham, JL (2005) Segregation patterns of isozyme loci and microsatellite markers show the diploidy of African yam Dioscorea rotundata (2n = 40). Theoretical and Applied Genetics 111: 226–232.CrossRefGoogle ScholarPubMed
Scarcelli, N, Tostain, S, Vigouroux, Y, Agbangla, C, Daïnou, O and Pham, JL (2006) Farmers’ use of wild relative and sexual reproduction in a vegetatively propagated crop. Molecular Ecology 15: 2421–2431.CrossRefGoogle Scholar
Scarcelli, N, Tostain, S, Vigouroux, Y, Luong, V, Baco, MN, Agbangla, C, Daïnou, O and Pham, JL (2011) Genetic structure of farmer-managed varieties in clonally-propagated crops. Genetica 139: 1055–1064.CrossRefGoogle ScholarPubMed
Scarcelli, N, Couderc, M, Baco, MN, Egah, J and Vigouroux, Y (2013) Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata). BMC Plant Biology 13: 178.CrossRefGoogle ScholarPubMed
Schneeberger, CA and Farago, LA (2003) Minimanual compacto de geografia do Brasil: teoria e prática. São Paulo: Rideel.Google Scholar
Schneider, S, Roessli, D and Excoffier, L (2000) Arlequin: a software for population data analysis. Version 2000. University of Geneva, Genetic and Biometry Laboratory, Geneva. Available at: http://anthropologie.unige.ch/arlequin (accessed 14 October 2012).Google Scholar
Silva, LRG, Bajay, MM, Monteiro, M, Mezette, TF, Nascimento, WF, Zucchi, MI, Pinheiro, JB and Veasey, EA (2014) Isolation and characterization of microsatellites for an important tuber crop (Dioscorea cayenensis) and cross-amplification in D. rotundata (Dioscoreaceae). Genetics and Molecular Research 13: 2766–2771.CrossRefGoogle Scholar
Siqueira, MVBM, Bonatelli, ML, Günther, T, Gawenda, I, Schmid, KJ, Pavinato, VAC and Veasey, EA (2014) Water yam (Dioscorea alata L.) diversity pattern in Brazil: an analysis with SSR and morphological markers. Genetic Resources and Crop Evolution 61: 611–624.CrossRefGoogle Scholar
Tamiru, M, Becker, HC and Maass, BL (2008) Diversity, distribution and management of yam landraces (Dioscorea spp.) in Southern Ethiopia. Genetic Resources and Crop Evolution 55: 115–131.CrossRefGoogle Scholar
Tostain, S, Scarcelli, N, Brottier, P, Marchand, JL, Pham, JL and Noyer, JL (2006) Development of DNA microsatellite markers in tropical yam (Dioscorea sp.). Molecular Ecology Notes 6: 173–175.CrossRefGoogle Scholar
Tostain, S, Agbangla, C, Scarcelli, N, Mariac, C, Dainou, O, Berthaud, J and Pham, JL (2007) Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir) in Benin using simple sequence repeat (SSR) markers. Plant Genetic Resources 5: 71–81.CrossRefGoogle Scholar
Veasey, EA, Siqueira, MVBM, Gomes, LR, Nascimento, WF, Ferreira, AB, Silva, DM, Silva, EF, Ming, LC, Peroni, N and Santos, AH (2012) Ocorrência e diversidade de espécies cultivadas do gênero Dioscorea em diversos agroecossistemas brasileiros. In: Ming, LC, Amorozo, MCM and Kffuri, CW (eds) Agrobiodiversidade no Brasil, 2nd edn. Recife, Brazil: NUPPEA, pp. 45–74.Google Scholar
Yeh, FC, Yang, RC, Boyle, TBJ, Ye, ZH and Mao, JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Edmonton, Alberta: Molecular Biology and Biotechnology Centre.Google Scholar
Zannou, A, Agbicodo, E, Zoundjihékpon, J, Struik, PC, Ahanchédé, A, Kossou, DK and Sanni, A (2009) Genetic variability in yam cultivars from the Guinea–Sudan zone of Benin assessed by random amplified polymorphic DNA. African Journal of Biotechnology 8: 26–36.Google Scholar
Zizumbo-Villarreal, D, Colunga-Garciamarín, P, Cruz, EP, Delgado-Valerio, P and Gepts, P (2005) Population structure and evolutionary dynamics of wild–weedy–domesticated complexes of common bean in a Mesoamerican region. Crop Science 45: 1073–1083.CrossRefGoogle Scholar
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