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A novel genetic map of pomegranate based on transcript markers enriched with QTLs for fruit quality traits

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Abstract

A novel genetic map of pomegranate (Punica granatum L.) enriched with quantitative trait loci (QTLs) for seven traits was constructed using an F2 population. The population was generated from a cross between two varieties of P. granatum: “Nana” and “Black.” Phenotyping of 76 F2 plants was conducted over two seasons. The map includes 1092 SNP markers which were newly developed from de novo transcriptome assembly and a comparison of the sequences of the two varieties or accessions. The map covers 1141 centimorgans (cM) with an average of 1.17 cM between markers over 11 linkage groups. Twenty-five QTLs were identified for fruit traits and plant size. The map includes QTLs for total soluble solids (TSS), fruit weight and perimeter, seed hardness, aril color and weight, and plant height. In an effort to explore the potential of the Agricultural Research Organization (ARO) pomegranate germplasm collection to associate traits with gene markers, an association study was conducted using a set of 346 SNPs described in an earlier study. Of these SNPs, 233 were mapped on the genetic map and found to be distributed in the different linkage groups (LGs). The associated traits were anchored to the map by these common markers. The F2 population described here and the corresponding genetic map provide a useful resource for further genomics and genetic studies of pomegranate, as well as a reservoir of markers for fruit improvement.

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Acknowledgments

We thank Kamel Hatib for growing and maintaining the orchards. This research was supported by funding from the Chief Scientist Office, Ministry of Agriculture & Rural Development, http://www.science.moag.gov.il/, Agricultural Biotechnology 203-0753-09.

Authors’ contribution statement

R. H. B. conducted the phenotyping of the mapping population and the genetic and mapping analysis and wrote the paper; A. S. and R. E. conducted the sequencing, marker development, and the genotyping of the mapping population; M. R. and R. O. conducted the marker development, array and probe design, array hybridization and signal preprocessing, and genotype calling; I. B. Y conducted the phenotyping of the ARO collection and the mapping population; T. T. conducted the total RNA extraction and developed the method for DNA extraction from pomegranate; and D. H. wrote the paper and designed and supervised the study. All authors discussed the results and commented on the manuscript.

Data Archiving Statement

Data base on which this study was based was published before by Ophir et al. (2014) and deposited in GenBank (http://www.ncbi.nlm.nih.gov/sra/SRX395468[accn] and http://www.ncbi.nlm.nih.gov/sra/SRX395465[accn]).

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Authors and Affiliations

  1. Department of Fruit Tree Sciences, Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishai, P.O.Box 1021, 30095, Israel

    Rotem Harel-Beja, Irit Bar-Ya’akov, Taly Trainin & Doron Holland

  2. Department of Fruit Tree Sciences, Volcani Center, Agricultural Research Organization, Bet Dagan, Israel

    Amir Sherman, Mor Rubinstein, Ravit Eshed & Ron Ophir

  3. The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel

    Rotem Harel-Beja

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  1. Rotem Harel-Beja
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  2. Amir Sherman
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  3. Mor Rubinstein
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  8. Doron Holland
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Correspondence to Doron Holland.

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Communicated by V. Decroocq

This article is part of the Topical Collection on Complex Traits

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Harel-Beja, R., Sherman, A., Rubinstein, M. et al. A novel genetic map of pomegranate based on transcript markers enriched with QTLs for fruit quality traits. Tree Genetics & Genomes 11, 109 (2015). https://doi.org/10.1007/s11295-015-0936-0

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  • DOI: https://doi.org/10.1007/s11295-015-0936-0

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