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A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size

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Abstract

To breed a new variety of coffee (Coffea arabica) requires approximately 25 years due to the long generation time (5–6 years) of this perennial plant and the fact that it takes at least five generations of selection to obtain superior individuals. One way to reduce the number of generations is to use marker-assisted selection (MAS). To implement MAS, it is necessary to develop a genetic map and to identify markers associated with quantitative trait loci (QTLs) governing traits of interest. The objective of this study was to identify QTLs associated with yield, plant height, and bean size. An F2 mapping population consisting of 278 individuals was developed from a cross between Caturra × CCC1046. A total of 338 SSR were used to construct a framework linkage map. Subsequently, SNP markers were added to construct a more robust genetic map. R/qtl software was used to integrate SSR and SNP markers. The integrated linkage map consists of 22 linkage groups populated by 848 SSR and SNP markers, with a total map length of 3800 cM. F3 progenies of the mapping population were planted in five locations and evaluated for yield, plant height, and bean size. A major yield QTL was significant at two locations and a second was significant at one location. Two QTL were each detected for plant height and bean size.

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Acknowledgments

We thank the Experimentation Unit at Cenicafe for valuable assistance in collecting field data, and Cenicafe and Ministry of Agriculture and Rural Development of Colombia (Agreements No. 100 of 2004, 015 of 2006, 067 of 2007, and 102 of 2011) for financial support. We are grateful to the US National Science Foundation for a PhD fellowship for JS and for research support under Plant Genome Research Program award #1026555 to SMc.

Data archiving statement

Primer sequences of the SSR markers are provided in Table ESM 1

SNP markers sequences and polymorphism are provided in Table ESM 2.

Genotypic data for SSR and SNP markers in the F2 coffee population are provided in Table ESM 3.

Author information

Authors and Affiliations

  1. Department of Plant Breeding, National Coffee Research Center—Cenicafe—A.A. 2427, Manizales, Colombia

    Maria Del Pilar Moncada, Eduardo Tovar, Juan Carlos Montoya & Alexandra González

  2. Department of Plant Breeding, Cornell University, Ithaca, NY, USA

    Jennifer Spindel & Susan McCouch

Authors
  1. Maria Del Pilar Moncada
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  2. Eduardo Tovar
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  3. Juan Carlos Montoya
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  4. Alexandra González
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  5. Jennifer Spindel
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  6. Susan McCouch
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Corresponding author

Correspondence to Maria Del Pilar Moncada.

Additional information

Communicated by D. Grattapaglia

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table ESM 1

(XLS 706 kb)

Table ESM 2

(XLSX 198 kb)

Table ESM 3

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Appendix

Appendix

Fig. 7
figure 7

Genetic map of C. arabica consisting of 21 linkage groups and 185 SSR markers. Marker names are to the right of each linkage group; genetic distances (cM) are on the left. Loci with distorted segregation (0.01 < p < 0.05) are indicated with an asterisk (*)

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Moncada, M., Tovar, E., Montoya, J.C. et al. A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size. Tree Genetics & Genomes 12, 5 (2016). https://doi.org/10.1007/s11295-015-0927-1

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