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A global overview of cassava genetic diversity


Autoři: Morag E. Ferguson aff001;  Trushar Shah aff001;  Peter Kulakow aff002;  Hernan Ceballos aff003
Působiště autorů: International Institute of Tropical Agriculture, Nairobi, Kenya aff001;  International Institute of Tropical Agriculture, Ibadan, Nigeria aff002;  International Center for Tropical Agriculture, Cali, Colombia aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0224763

Souhrn

Although numerous studies of diversity have been conducted in cassava, there is no comprehensive assessment of global genetic diversity. Here we draw on previous studies and breeders’ knowledge to select diversity sets from the International Institute of Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT) genebanks and breeders’ germplasm, as well as elite germplasm and landraces from eastern, southern and central (ESC) Africa to make a global assessment of diversity in cassava, using a SNP based GoldenGate (Illumina Inc.) assay. A synthesis of results from genetic distance and ADMIXTURE analysis essentially revealed four populations (i) South American germplasm characterised by relatively higher genetic diversity with hypothetical ancestral founder genotypes from Brazil, (ii) a smaller group of African introduction germplasm which is more distantly related to all other germplasm, (iii) West Africa germplasm dominated by IITA breeding lines, containing sources of cassava mosaic disease resistance, and IITA genebank accessions from West Africa, both characterised by slightly lower diversity, and (iv) a less cohesive group of African germplasm, termed ‘Other’, with moderate levels of diversity and a majority of germplasm from ESC Africa. This study highlights opportunities for heterosis breeding, purging of duplicates in genebanks and the need for conservation of ESC Africa landraces.

Klíčová slova:

Africa – Heterozygosity – Molecular genetics – Plant breeding – Population genetics – Species diversity – Cassava


Zdroje

1. FAOSTAT. Statistical database of the Food and Agriculture Organisation of the United Nations. Accessed June 2019 (2017 statistics). Available from: http://www.fao.org/faostat/en/#home

2. Olsen KM and Schaal B. Evidence on the origin of cassava: Phylogeography of Manihot esculenta. Proc. Natl. Acad. Sci. USA 1999; 96: 5586–5591. doi: 10.1073/pnas.96.10.5586 10318928

3. Olsen KM 2004. SNPs, SSRs and inferences on cassava’s origin. Plant Mol. Biol. 2004: 56: 517–526.

4. Rossel G. Gewas innovaties in Gabon van prehistorie tot koloniale tijd. MSc Thesis. Wageningen Agricultural University. 1987.

5. Carter S, Fresco L, Jones P, Fairbaim J. An Atlas of Cassava in Africa: Historical, agroecological and demographic aspects of crop distribution. CIAT, Cali, Colombia; 1992.

6. Jones W. Manioc in Africa. Stanford University Press, Stanford, California; 1959.

7. Legg J, Owor B, Sseruwagi P, Ndunguru J. Cassava mosaic virus disease in East and Central Africa: epidemiology and management of a regional pandemic. Adv Virus Res 2006; 67: 355–418. doi: 10.1016/S0065-3527(06)67010-3 17027685

8. Mbanzibwa D, Tian Y, Tugume A, Mukasa S, Tairo F, Kyamanywa S et al. Genetically distinct strains of Cassava brown streak virus in the Lake Victoria basin and the Indian Ocean coastal area of East Africa. Arch. Virol. 2009; 154:353–359. doi: 10.1007/s00705-008-0301-9 19184340

9. Winter S, Koerbler M, Stein B, Pietruszka A, Paape M, Butgereitt A (2010) Analysis of cassava brown streak viruses reveals the presence of distinct virus species causing cassava brown streak disease in East Africa. Journal of General Virology 2010; 91:1365–1372. doi: 10.1099/vir.0.014688-0 20071490

10. Wang HL, Cui XY, Wang XW, Liu SS, Zhang ZH, Zhou XP. First report of Sri Lankan cassava mosaic virus infecting cassava in Cambodia. Plant Dis. 2016; 100: 1029–1029.

11. Sheat S, Fuerholzner B, Stein B, Winter S. Resistance against Cassava Brown Streak Viruses from Africa in cassava germplasm from South America. Front. Plant Sci. 2019; 10:567–. doi: 10.3389/fpls.2019.00567 31134114

12. Kawuki RS, Herselman L, Labuschagne MT, Nzuki I, Ralimanana I, Bidiaka M et al. Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa. Plant Genet Resour-C. 2013; 11:170–181

13. Hurtado P, Ospina C, Marin J, Buitrago C, Castelblanco W, Correa A, et al. Assessment of the diversity in global cassava genetic resources based on simple sequence repeat (SSR) markers. In: First Scientific Meeting of the Global Cassava Partnership GCP-1. 21-25th July 2008, Ghent, Belgium.

14. Igartua E, Gracia MP, Lasa JM, Medina B, Molina-Cano JL, Montoya JL et al. The Spanish barley core collection. Genet Resour Crop Ev 1998; 45:475–481

15. Bhattacharjee R, Dumet D, Ilona P, Folarin S, Franco J. Establishment of a cassava (Manihot esculenta Crantz) core collection based on agro-morphological descriptors. Plant Genet Resour-C. 2012; 10:119–127.

16. R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. 2018. URL https://www.R-project.org

17. Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 2006; 6: 288–295.

18. Peakall R. Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics 2012; 28: 2537– 2539. doi: 10.1093/bioinformatics/bts460 22820204

19. Ferguson M, Hearne S, Close T, Wanamaker S, Moskal W, Town C et al. Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava. Theor Appl Genet 2012; 124: 685–695 doi: 10.1007/s00122-011-1739-9 22069119

20. Perrier X, Jacquemoud-Collet J. DARwin software. 2006. http://darwin.cirad.fr/darwin.

21. Yu G, Smith D, Zhu H, Guan Y, Lam TT. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 2017; 8: 28–36. doi: 10.1111/2041-210X.12628

22. Jombart T. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 2008; 24:1403–1405. doi: 10.1093/bioinformatics/btn129 18397895

23. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009; 19: 1655–1664. = doi: 10.1101/gr.094052.109 19648217

24. Akano A, Dixon A, Mba C, Barrera E, Fregene M. Genetic mapping of a dominant gene conferring resistance to cassava mosaic disease. Theor Appl Genet. 2002; 105: 521–525. doi: 10.1007/s00122-002-0891-7 12582500

25. Fregene M, Okogbenin E, Mba C, Angel F, Suarez MC, Janneth G et al. Genome mapping in cassava improvement: challenges, achievements and opportunities. Euphytica 2001; 120:159–165.

26. Nichols RFW. Breeding cassava for virus resistance. East Afr. Agric. J. 1947; 12:184–194.

27. Jennings DL. Breeding for resistance to African cassava mosaic geminivirus in East Africa. Trop. Science 1994; 34:110–122.

28. Hahn SK, Terry ER, Leuschner K. Breeding cassava for resistance to cassava mosaic disease. Euphytica 1980; 29: 673–683.

29. Hahn SK, John C, Isoba C, Ikotun T. Resistance breeding in root crops at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. Crop Protection 1989; 8:147–168.

30. Eke-okoro ON, Njoku DN. A Review of Cassava Development in Nigeria from 1940–2010. ARPN J Agric Biol Sci. 2012; 7: 59–65.

31. Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E. et al. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat Biotech 2016; 34: 562–570.

32. Mahungu NM, Dixon AGO, Kumbira JM. Breeding cassava for multiple pest resistance in Africa. Afric. Crop Science J. 1994; 2: 539–552.


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