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Bulked segregant analysis identifies molecular markers associated with early bulking in cassava (Manihot esculenta Crantz)

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Abstract

Late root bulking is a major factor leading to rejection and abandoning of improved cassava genotypes in sub-Saharan Africa. Early bulking (EB) varieties shorten the growth period from planting to harvesting, better fit into environments with short rainy season, and reduce exposure to biotic and abiotic stresses thereby increasing productivity. This study was carried out to identify molecular markers linked to EB in cassava. Nine cassava hybrid populations (COB-1–COB-9) were developed using six elite varieties (TMS 30572, TMS 97/2205, TMS 98/0505, TMS 30555, NR 8212 and NR 8083) from the African cassava germplasm as parents. The progeny in each of the nine populations (101–272 genotypes per population) were evaluated for EB at 7 months after planting at seedling, clonal, and preliminary stages of breeding evaluation at Umudike. The parameters measured are fresh root yield, harvest index, fresh shoot weight and number of storage roots per plant. The progeny in each of the nine populations were genotyped at 542 simple sequence repeat (SSR) marker loci. Bulked segregant analysis was used to identify the SSR markers associated with EB in the populations. Nine SSR markers (SSRY 106, (ESTs)SSRY 292, SSRY 239, (ESTs)SSRY 7, NS 194, (ESTs)SSRY 47, SSRY 63, SSRY 250, and NS 323) were found to be closely linked (r = 0.3–0.5; p < 0.05) to EB in six of the nine hybrid populations. Seven of the markers with 10 % or more coefficient of determination (R2) were linked to major quantitative trait loci associated with EB in cassava. The molecular markers identified in this study provide useful materials to select for EB in cassava and for further target-traits-improvement by pyramiding.

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Abbreviations

BSA:

Bulked segregant analysis

FRY:

Fresh root yield

LB:

Late bulking

EB:

Early bulking

SSR:

Simple sequence repeat

QTL:

Quantitative trait loci

ESTs:

Expressed sequence tags

NR, TMS, COB:

Nomenclature codes for cassava genotypes/varieties

pm-p:

Polymorphic markers between two parents

pm-pb:

Polymorphic markers among two parents and two bulks of a population

References

  • Akinbo OA (2008) Introgression of high protein and pest resistance genes from inter-specific hybrids of Manihot esculenta ssp flabellifolia into cassava (Manihot esculenta Crantz). Thesis, Plant Science, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, p 263

  • Bainbridge Z, Wellings K, Westby A (1997) Village level cassava processing: distance learning package (field guide). Natural Resources Institute, Chatman

    Google Scholar 

  • Brauer MJ, Christianson CM, Pai DA, Dunham MJ (2006) Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics 173(3):1813–1816

    Article  PubMed  CAS  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142(1-2):169–196

    Article  CAS  Google Scholar 

  • Dellaporta SL, Wood J, Hicks JR (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21

    Article  CAS  Google Scholar 

  • Deutschbauer AM, Davis RW (2005) Quantitative trait loci mapped to single- nucleotide resolution in yeast. Nat Genet 37:1333–1340

    Article  PubMed  CAS  Google Scholar 

  • Dixon AGO, Okechukwu RU, Akoroda MO, Ilona P, Ogbe F, Egesi CN, Kulakow P, Ssemakula G, Maziya-Dixon B, Iluebbey P, Yomeni MO, Geteloma C, James B, Eke-Okoro ON, Sanni L, Ntawuruhunga P, Tarawali G, Mahungu N, Lemchi J, Ezedinma CI, Okoro E, Kanju E, Adeniji AA, Nwosu K (2010) Improved cassava variety handbook. IITA Integrated Cassava Project, Ibadan, p 129

    Google Scholar 

  • FAO (Food and Agriculture Organization of the United Nations) (2008) www.fao.org. Investing in cassava research and development could boost yields and industrial uses. http://www.ugent.be/we/genetics/ipbo/en/research/cassava.htm. Accessed 7 Jul 2013

  • FAO (2010) www.fao.org. Accessed 21 Feb 2012

  • FAOSTAT (Food and Agriculture Organization of the United Nations) (2005) Statistical database of the Food and Agricultural Organisation of the United Nations. FAO, Rome. http://faostat.fao.org. Accessed 2 Apr 2007

  • FAOSTAT (2008) Statistical database of the Food and Agricultural Organisation of the United Nations. FAO, Rome from http://faostat.fao.org. Accessed 26 Jan 2011

  • FAOSTAT (2010) www.faostat.fao.org. Accessed 21 Feb 2012

  • Gomez SM, Narayana M, Schubert AM, Ayers JL, Baring MR, Burow MD (2009) Identification of QTLs for pod and kernel traits in cultivated peanut by bulked segregant analysis. Electron J Biotechnol 12.2:10 p. https://en.wikipedia.org/wiki/Marker-assisted_selection. Accessed 7 Jul 2013

  • Huang J, Bachem C, Jacobsen E, Visser RGF (2001) Molecular analysis of differentially expressed genes during post-harvest deterioration in cassava (Manihot esculenta Crantz) tuberous root. Euphytica 120:85–93

    Article  CAS  Google Scholar 

  • Lin HX, Qian HR, Zhuang JY, Lu J, Min SK, Xiong ZM, Huang N, Zheng KL (1996) RFLP mapping of QTL for yield and related characters in rice (Oryza sativa L.). Theor Appl Genet 92:920–927

    Article  PubMed  CAS  Google Scholar 

  • Mace ES, Phong DT, Upadhyaya HD, Chandra S, Crouch JH (2006) SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases. Euphytica 152(3):317–330

    Article  Google Scholar 

  • Mackay IJ, Caligari PDS (2000) Efficiencies of F2 and backcross generations for bulked segregant analysis using dominant markers. Crop Sci 40:626–630

    Article  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease- resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    Article  PubMed  CAS  Google Scholar 

  • Nweke FI, Dixon AGO, Asiedu R, Folayan SA (1994) Cassava variety needs of farmers and potential for production growth in Africa. Collaborative study of cassava in Africa (COSCA). Working paper 10:40–41

    Google Scholar 

  • Okogbenin E (2004). Quantitative trait loci mapping of root quality traits, morphological characters, and early bulking in cassava (Manihot esculenta Crantz). Thesis, Agronomy, Agriculture and Forestry, University of Ibadan, Ibadan p 220

  • Okogbenin E, Marin J, Fregene M (2006) An SSR-based molecular genetic map of cassava. Euphytica 147(3):433–440

    Article  CAS  Google Scholar 

  • Olasanmi B (2010) Marker-assisted selection (MAS) for improvement of traits associated with high and early root productivity in cassava (Manihot esculenta Crantz). Thesis, Agronomy, Agriculture and Forestry, University of Ibadan, Ibadan p 168

  • Sarma JS, Kunchai D (1989) Trends and prospects for cassava in the third World. Summary proceedings of a workshop on trends and prospects of cassava in the Third World. IFPRI, Washington DC pp 20–35

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This study was conducted with funding support from Kirkhouse Trust Foundation, UK and with support from University of Ibadan, Nigeria; International Center for Tropical Agriculture (CIAT), Cali, Colombia; National Root Crops Research Institute (NRCRI), Umudike; and Generation Challenge Programme (GCP).

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Authors and Affiliations

  1. Department of Agronomy, University of Ibadan, Ibadan, Nigeria

    B. Olasanmi & M. O. Akoroda

  2. International Centre for Tropical Agriculture (CIAT), Cali, Colombia

    B. Olasanmi, J. Guitierrez, H. Ceballos, J. Tohme & M. Fregene

  3. National Root Crops Research Institute (NRCRI), Umudike, Nigeria

    B. Olasanmi, E. Okogbenin, C. Egesi, S. S. Kahya, O. Onyegbule & F. Ewa

  4. Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA

    M. Fregene

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  1. B. Olasanmi
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  2. M. O. Akoroda
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  3. E. Okogbenin
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  4. C. Egesi
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  5. S. S. Kahya
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  6. O. Onyegbule
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  7. F. Ewa
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  9. H. Ceballos
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  10. J. Tohme
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  11. M. Fregene
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Correspondence to B. Olasanmi.

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Olasanmi, B., Akoroda, M.O., Okogbenin, E. et al. Bulked segregant analysis identifies molecular markers associated with early bulking in cassava (Manihot esculenta Crantz). Euphytica 195, 235–244 (2014). https://doi.org/10.1007/s10681-013-0991-2

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