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An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz)

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Abstract

Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina’s GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences’ KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.

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Acknowledgments

The authors appreciate the financial support from the BioSciences eastern and central Africa Network (BecANet), the Generation Challenge Program (GCP) and the International Institute of Tropical Agriculture (IITA). We would like to thank Jim Lorenzen of IITA and Steve Rounsley (University of Arizona and Dow AgroSciences) for the fruitful discussions that led to the improvement of the manuscript. We sincerely thank the two anonymous reviewers and the associated editor for their useful comments that has also led to further improvement of this paper.

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Authors and Affiliations

  1. International Institute of Tropical Agriculture (IITA), PMB 5320 Oyo Road, Ibadan, Nigeria

    Ismail Yusuf Rabbi

  2. Ukiriguru Agricultural Research Institute, P.O. Box 1433, Mwanza, Tanzania

    Heneriko Philbert Kulembeka

  3. Sugarcane Research Institute, P.O. Box 30031, Kibaha, Tanzania

    Esther Masumba

  4. BIO5 Institute, University of Arizona, Tucson, AZ, USA

    Pradeep Reddy Marri

  5. IITA c/o ILRI, P.O. Box 30709 00100, Nairobi, Kenya

    Morag Ferguson

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  1. Ismail Yusuf Rabbi
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  2. Heneriko Philbert Kulembeka
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  3. Esther Masumba
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  4. Pradeep Reddy Marri
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  5. Morag Ferguson
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Correspondence to Ismail Yusuf Rabbi.

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Communicated by A. Bervillé.

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122_2012_1836_MOESM1_ESM.pdf

Online Resource 1 Comparison of order of markers of the present one-step map and the SSR-based map of Whankaew et al. (2011) shows clear co-linearity in the two linkage maps (PDF 106 kb)

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Rabbi, I.Y., Kulembeka, H.P., Masumba, E. et al. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz). Theor Appl Genet 125, 329–342 (2012). https://doi.org/10.1007/s00122-012-1836-4

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