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Population Structure and Genetic Diversity in Sweet Cassava Accessions in Paraná and Santa Catarina, Brazil

  • Vanesca Priscila Camargo RochaEmail author
  • Maria Celeste Gonçalves-Vidigal
  • Alex Henrique Tiene Ortiz
  • Giseli Valentini
  • Rebecca Caroline Ulbricht Ferreira
  • Tiago Maretti Gonçalves
  • Giselly Figueiredo Lacanallo
  • Pedro Soares Vidigal Filho
Original Paper
  • 23 Downloads

Abstract

Manihot esculenta Crantz is originally from the Amazon region of Brazil, which has the highest genetic diversity. Due to the wide adaptation of cassava to the most diverse environments, the evolutionary forces acted on the crop, resulting in a more complex genetic structure. This study evaluated the population structure and the genetic diversity through 25 SSR markers of 144 sweet cassava accessions collected in seven places in the south of Brazil. All the loci analyzed were polymorphic and showed several alleles per loci with a mean of 3.36 alleles and 38 rare alleles in the population. The mean value of polymorphism information content (PIC) was 0.488, which indicates that the markers were informative and the mean observed heterozygosity was 0.644, while the mean expected heterozygosity was 0.557. The sweet cassava accessions were divided into 10 groups based on the population structure analysis. There was a moderate genetic differentiation (PhiPT = 0.106) among the sweet cassava subpopulations. The wide genetic variability among the studied accessions of sweet cassava demonstrates the importance of the emergency in the conservation of plants in germplasm banks, because the intense change in agriculture; the expansion of areas occupied by soybeans, corn, and other crops; and also the farmers’ migration from rural areas to urban areas reduced cassava cultivation over time, and as a consequence, genetic variability has been lost.

Keywords

Manihot esculenta SSR molecular markers Germplasm bank Heterozygosity 

Notes

Acknowledgments

The authors would like to thank the graduate students from the Genetic and Breeding Program (www.pgm.uem.br) of Universidade Estadual de Maringá that collaborated to the development of the present work.

Funding Information

The authors would like to thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for the financial support given to the agronomy undergraduate students. MC Gonçalves-Vidigal and PS Vidigal Filho received scholarships from CNPq.

Supplementary material

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References

  1. Aguiar EB, Valle TL, Lorenzi JO, Kanthack RAD, Miranda Filho H, Granja NP (2011) Efeito da densidade populacional e época de colheita na produção de raízes de mandioca de mesa. Bragantia 70:561–569CrossRefGoogle Scholar
  2. Albuquerque HYG, Oliveira EJ, Brito AC, Andrade LRB, Carmo CD, Morgante CV, Vieira EA, Moura EF, Faleiro FG (2019) Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs). Sci Agric 76:328–336.  https://doi.org/10.1590/1678-992x-2017-0389 CrossRefGoogle Scholar
  3. Allem AC (2002) The origins and taxonomy of cassava. In: Hillocks RJ, Thresh JM, Bellotti AC (eds) Cassava: biology, production and utilization. CABI International, Wallingford, pp 1–16Google Scholar
  4. Asare PA, Galyuon IKA, Sarfo JK, Tetteh JP (2011) Morphological and molecular based diversity studies of some cassava (Manihot esculenta Crantz) germplasm in Ghana. Afr J Biotechnol 10:13900–13908CrossRefGoogle Scholar
  5. Beovides Y, Fregene M, Gutiérrez JP, Milián MD, Coto O, Buitrago C, Cruz JÁ, Ruiz E, Basail M, Rayas A, Rodríguez D, Santos A, López J, Medero V (2015) Molecular diversity of Cuban cassava (Manihot esculenta Crantz) cultivars assessed by simple sequences repeats (SSR). Biotechnol Agron Soc 19:364–377Google Scholar
  6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedPubMedCentralGoogle Scholar
  7. Carrasco NF, Oler JRL, Marchetti FF, Carniello MA, Amorozo MCM, Valle TL, Veasey EA (2016) Growing cassava (Manihot esculenta) in Mato Grosso, Brazil: genetic diversity conservation in small-scale agriculture. Econ Bot 70(1):15–28.  https://doi.org/10.1007/s12231-016-9331-5 CrossRefGoogle Scholar
  8. Cavalli-Sforza LL, Edwards AW (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 19:233–257PubMedPubMedCentralGoogle Scholar
  9. Ceballos H, de la Cruz GA (2002) Taxonomía y morfología de la yuca. In: CIAT (ed) La Yuca en el Tercer Milenio. pp 15–28Google Scholar
  10. Chavarriaga-Aguirre P, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, Kochert G (1998) Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theor Appl Genet 97:493–501CrossRefGoogle Scholar
  11. Costa TR, Vidigal-Filho PS, Gonçalves-Vidigal MC, Galván MZ, Lacanallo GF, da Silva LI, Kvitschal MV (2013) Genetic diversity and population structure of sweet cassava using simple sequence repeat (SSR) molecular markers. Afr J Biotechnol 12:1040–1048.  https://doi.org/10.5897/AJB12.2727
  12. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation version II. Plant Mol Biol Report 1:19–21CrossRefGoogle Scholar
  13. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361.  https://doi.org/10.1007/s12686-011-9548-7 CrossRefGoogle Scholar
  14. Elias M, Penet L, Vindry P, McKey D, Panaud O, Robert T (2001) Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Mol Ecol 10:1895–1907.  https://doi.org/10.1046/j.09621083.2001.01331.x
  15. Elias M, Mühlen GS, McKey D, Roa AC, Tohme J (2004) Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites. Econ Bot 58:242–256CrossRefGoogle Scholar
  16. El-Sharkawy MA (2004) Cassava biology and physiology. Plant Mol Biol 56:481–501.  https://doi.org/10.1007/s11103-005-2270-7 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Esuma W, Rubaihayo P, Pariyo A, Kawuki R, Wanjala B, Nzuki I, Harvey JJW, Baguma Y (2012) Genetic diversity of provitamin A cassava in Uganda. J Plant Stud 1:60–71.  https://doi.org/10.5539/jps.v1n1p60 CrossRefGoogle Scholar
  18. 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.  https://doi.org/10.1111/j.1365-294X.2005.02553.x CrossRefPubMedPubMedCentralGoogle Scholar
  19. FAO (2017) Food outlook- biannual report on global food markets. Food Outlook Biannu Rep Glob Food Mark:1–152Google Scholar
  20. Faraldo MIF, Silva RM, Ando A, Martins PS (2000) Variabilidade genética de etnovariedades de mandioca em regiões geográficas do Brasil. Sci Agr 57(3):499–505CrossRefGoogle Scholar
  21. Ferguson M, Rabbi I, Kim D, Gedil M, Lopez-Lavalle LAB, Okogbenin E (2012) Molecular markers and their application to cassava breeding: past, present and future. Trop Plant Biol 5:95–109.  https://doi.org/10.1007/s12042-011-9087-0 CrossRefGoogle Scholar
  22. Ferreira RCU, Vidigal Filho P, Gonçalves-Vidigal MC, Moiana LD, Kvitschal MV (2015) Genetic and population structure of sweet cassava (Manihot esculenta Crantz) germplasm collected from Campo Grande, Mato Grosso do Sul, Brazil. Aust J Crop Sci 9(5):458–467Google Scholar
  23. Fregene MA, Suarez M, Mkumbira J, Kulembeka H, Ndedya E, Kulaya A, Mitchel S, Gullberg U, Rosling H, Dixon AGO, Dean R, Kresovich S (2003) Simple sequence repeat marker diversity in cassava landraces genetic diversity and differentiation in an asexually propagated crop. Theor Appl Genet 107:1083–1093CrossRefGoogle Scholar
  24. Fukuda WMG, de Silva SO, Iglesias C (2002) Cassava breeding. Crop Breed Appl Biotechnol 2:617–638CrossRefGoogle Scholar
  25. Gonçalvez TM, Vidigal Filho PS, Gonçalves-Vidigal MC, Ferreira RCU, Rocha VPC, Ortiz AHT, Moiana LD, Kvitschal MV (2017) Genetic diversity and population structure of traditional sweet cassava accessions from Southern of Minas Gerais State, Brazil, using microsatellite markers. Afr J Biotechnol 16:346–358.  https://doi.org/10.5897/AJB2016.15768 CrossRefGoogle Scholar
  26. Groxko M (2017) Prognóstico Mandioca 2017/18. SEAB – Secretaria de Estado da Agricultura e do Abastecimento DERAL - Departamento de Economia Rural:1–18Google Scholar
  27. Hale ML, Burg TM, Steeves TE (2012) Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS One.  https://doi.org/10.1371/journal.pone.0045170 CrossRefGoogle Scholar
  28. Hans E (2004) Microsatellites: simple sequences with complex evolution. Nature 5:435–445.  https://doi.org/10.1038/nrg1348 CrossRefGoogle Scholar
  29. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334.  https://doi.org/10.1007/s10681-010-0286-9 CrossRefGoogle Scholar
  30. Kawuki RS, Herselman L, Labuschagne MT, Nzuki I, Ralimanana I, Bidiaka M, Kanyange MC, Gashaka G, Masumba E, Mkamilo G, Gethi J, Wanjala B, Zacarias A, Madabula F, Ferguson ME (2013) Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa. Plant Genet Resour 11:170–181.  https://doi.org/10.1017/S1479262113000014 CrossRefGoogle Scholar
  31. Kizito EB, Bua A, Fregene M, Egwang T, Gullberg U, Westerbergh A (2005) The effect of cassava mosaic disease on the genetic diversity of cassava in Uganda. Euphytica 146:45–54CrossRefGoogle Scholar
  32. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874.  https://doi.org/10.1093/molbev/msw054 CrossRefGoogle Scholar
  33. Li Y, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putativa functions, and mutational mechanism: a review. Mol Ecol 11:2453–2465.  https://doi.org/10.1046/j.1365-294X.2002.01643.x CrossRefPubMedGoogle Scholar
  34. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinforma Appl Note 21:2128–2129.  https://doi.org/10.1093/bioinformatics/bti282 CrossRefGoogle Scholar
  35. Liu J, Zheng Q, Ma Q, Gadidasu KK, Zhang P (2011) Cassava genetic transformation and its application in breeding. J Integr Plant Biol 53:552–569.  https://doi.org/10.1111/j.1744-7909.2011.01048.x CrossRefPubMedGoogle Scholar
  36. MAPA (2017) Projecões do Agronegócio Brasil 2016/17 a 2026/27: Projeções de Longo Prazo 125.Google Scholar
  37. Martins PS (2005) Dinâmica evolutiva em roças de caboclos amazônicos. Estud Av 19(53):209–220.  https://doi.org/10.1590/S0103-40142005000100013 CrossRefGoogle Scholar
  38. Mba REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J, Fregene M (2001) Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theor Appl Genet 102:21–31.  https://doi.org/10.1007/s001220051614 CrossRefGoogle Scholar
  39. Mezette TF, Carvalho CRL, Morgano MA, Silva MG, Parra ESB, Galera JMSV, Valle TL (2009) Seleção de clones-elite de mandioca de mesa visando a características agronômicas, tecnológicas e químicas. Bragantia 68:601–609CrossRefGoogle Scholar
  40. Mezette TF, Blumer CG, Veasey EA (2013) Morphological and molecular diversity among cassava genotypes. Pesqui Agropec Bras 48:510–518.  https://doi.org/10.1590/S0100-204X2013000500007 CrossRefGoogle Scholar
  41. Montero-Rojas M, Correa AM, Siritunga D (2011) Molecular differentiation and diversity of cassava (Manihot esculenta) taken from 162 locations across Puerto Rico and assessed with microsatellite markers. AoB Plants 2011:1–13.  https://doi.org/10.1093/aobpla/plr010 CrossRefGoogle Scholar
  42. Moura EF, Sousa NR, Moura MF, Dias MC, Souza ED, Farias Neto JT, Sampaio JE (2016) Molecular characterization of accessions of a rare genetic resource: sugary cassava (Manihot esculenta Crantz) from Brazilian Amazon. Genet Resour Crop Ev 63:583–593.  https://doi.org/10.1007/s10722-016-0378-z CrossRefGoogle Scholar
  43. Mühlen GS, Alves-Pereira A, Clement CR, Valle TL (2013) Genetic diversity and differentiation of Brazilian bitter and sweet manioc varieties (Manihot esculenta Crantz, Euphorbiaceae) based on SSR molecular markers on SSR molecular markers. Tipití J Soc Anthropol Lowlan South Am 11:66–73Google Scholar
  44. Nassar NMA, Ortiz R (2007) Cassava improvement: challenges and impacts. J Agric Sci 145:163–171.  https://doi.org/10.1017/S0021859606006575 CrossRefGoogle Scholar
  45. Olsen KM, Schaal BA (2001) Microsatellite variation in cassava (Manihot esculenta, Euphorbiaceae) and wild relatives: further evidence for a southern Amazonian origin of domestication. Am J Bot 88:131–142.  https://doi.org/10.2307/2657133 CrossRefPubMedGoogle Scholar
  46. Ortiz AHT, Rocha VPC, Moiana LD, Gonçalves-Vidigal MC, Galván MZ, Vidigal Filho PS (2016) Population structure and genetic diversity in sweet cassava cultivars from Paraná, Brazil. Plant Mol Biol Report 34:1153–1166.  https://doi.org/10.1007/s11105-016-0995-x CrossRefGoogle Scholar
  47. Pariyo A, Tukamuhabwa P, Baguma Y, Kawuki RS, Alicai T, Gibson P, Kanju E, Wanjala BW, Harvey J, Nzuki I, Rabbi IY, Ferguson M (2013) Simple sequence repeats (SSR) diversity of cassava in South, East and Central Africa in relation to resistance to cassava brown streak disease. Afr J Biotechnol 12:4453–4464.  https://doi.org/10.5897/AJB2013.12348 CrossRefGoogle Scholar
  48. Peakall ROD, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  49. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855.  https://doi.org/10.1111/j.1523-1739.1998.96489.x CrossRefGoogle Scholar
  50. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959.  https://doi.org/10.1111/j.1471-8286.2007.01758.x CrossRefPubMedPubMedCentralGoogle Scholar
  51. Rimoldi F, Vidigal-Filho PS, Kvitschal MV, Gonçalves-Vidigal MC, Prioli AJ, Prioli SMAP, Costa TR (2010) Genetic divergence in sweet cassava cultivars using morphological agronomic traits and RAPD molecular markers. Braz Arch Biol Technol 53:1477–1486.  https://doi.org/10.1590/S1516-89132010000600025 CrossRefGoogle Scholar
  52. Rocha VPC (2014) Caracterização morfo-agronômica e molecular de acessos tradicionais de mandioca de mesa oriundos do Paraná e de Santa Catarina. Thesis, Universidade Estadual de Maringá.Google Scholar
  53. Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants: problems and prospects. Mol Ecol 7:465–474CrossRefGoogle Scholar
  54. Siqueira MVBM, Queiroz-Silva JR, Bressan EA, Borges A, Pereira KJC, Pinto JG, Veasey EA (2009) Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats. Genet Mol Biol 32:104–110CrossRefGoogle Scholar
  55. Siritunga D, Sayre R (2004) Engineering cyanogen synthesis and turnover in cassava (Manihot esculenta). Plant Mol Biol 56(4):661–669.  https://doi.org/10.1007/s11103-004-3415-9 CrossRefPubMedGoogle Scholar
  56. Sousa SB, Silva GF, Dias MC, Clement CR, Sousa NR (2017) Farmer variety exchange along Amazonian rivers influences the genetic structure of manioc maintained in a regional Brazilian GeneBank. Genet Mol Res 16(3):gmr16039690.  https://doi.org/10.4238/gmr16039690 CrossRefGoogle Scholar
  57. Tovar E, Bocanegra JL, Villafane C, Fory L, Velásquez A, Gallego G, Moreno R (2015) Diversity and genetic structure of cassava landraces and their wild relatives (Manihot spp.) in Colombia revealed by simple sequence repeats. Plant Genet Resour 14:200–210.  https://doi.org/10.1017/S1479262115000246 CrossRefGoogle Scholar
  58. Turyagyenda LF, Kizito EB, Ferguson ME, Baguma Y, Harvey JW, Gibson P, Wanjala BW, Osiru DSO (2012) Genetic diversity among farmer-preferred cassava landraces in Uganda. Afr Crop Sci J 20:15–30.  https://doi.org/10.4314/acsj.v20i1 CrossRefGoogle Scholar
  59. Valle TL, Carvalho CRL, Ramos MTB, Mühlen GS, Villela OV (2004) Conteúdo cianogênico em progênies de mandioca originadas do cruzamento de variedades mansas e bravas. Bragantia 63:221–226.  https://doi.org/10.1590/S0006-87052004000200007 CrossRefGoogle Scholar
  60. Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M (2017) Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100- day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 12:1–14.  https://doi.org/10.1371/journal.pone.0177456 CrossRefGoogle Scholar
  61. Wikipedia (2014) Geografia do Paraná. Wikipédia: a enciclopédia livre https://pt.wikipedia.org/wiki/Geografia_do_Paran%C3%A1. Accessed 8 October 2014Google Scholar
  62. Wouw MVD, Kik C, Hintum TV, Treuren RV, Visser B (2009) Genetic erosion in crops: concept, research results and challenges. Plant Genetic Resources: Characterization and Utilization 8:1–15.  https://doi.org/10.1017/S1479262109990062 CrossRefGoogle Scholar
  63. Wright S (1978) Evolution and genetics of populations. The University of Chicago Press, Chicago, p 91Google Scholar
  64. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506–519.  https://doi.org/10.1093/molbev/msi035 CrossRefPubMedGoogle Scholar
  65. Zuin GC, Vidigal-Filho PS, Kvitschal MV, Gonçalves-Vidigal MC, Coimbra GK (2009) Divergência genética entre acessos de mandioca-de-mesa coletados no município de Cianorte, região Noroeste do Estado do Paraná. Semin-Cien Agrar 30:21–30CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Vanesca Priscila Camargo Rocha
    • 1
    Email author
  • Maria Celeste Gonçalves-Vidigal
    • 1
  • Alex Henrique Tiene Ortiz
    • 1
  • Giseli Valentini
    • 1
    • 2
  • Rebecca Caroline Ulbricht Ferreira
    • 1
  • Tiago Maretti Gonçalves
    • 1
  • Giselly Figueiredo Lacanallo
    • 1
  • Pedro Soares Vidigal Filho
    • 1
  1. 1.Programa de Pós-Graduação em Genética e Melhoramento de Plantas (PGM)Universidade Estadual de Maringá (UEM)ParanáBrazil
  2. 2.FEITEP-Faculdade de Engenharia e Inovação Técnico ProfissionalMaringáBrazil

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