High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo
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ORIGINAL ARTICLE
High‑density NGS‑based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo Elad Oren1,3 · Galil Tzuri1 · Asaf Dafna1 · Ayala Meir1 · Ravindra Kumar1 · Nurit Katzir1 · Yonatan Elkind3 · Shiri Freilich1 · Arthur A. Schaffer2 · Yaakov Tadmor1 · Joseph Burger1 · Amit Gur1 Received: 14 November 2019 / Accepted: 17 February 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Melon is an important crop that exhibits broad variation for fruit morphology traits that are the substrate for genetic mapping efforts. In the post-genomic era, the link between genetic maps and physical genome assemblies is key for leveraging QTL mapping results for gene cloning and breeding purposes. Here, using a population of 164 melon recombinant inbred lines (RILs) that were subjected to genotyping-by-sequencing, we constructed and compared high-density sequence- and linkage-based recombination maps that were aligned to the reference melon genome. These analyses reveal the genomewide variation in recombination frequency and highlight regions of disrupted collinearity between our population and the reference genome. The population was phenotyped over 3 years for fruit size and shape as well as rind netting. Four QTLs were detected for fruit size, and they act in an additive manner, while significant epistatic interaction was found between two neutral loci for this trait. Fruit shape displayed transgressive segregation that was explained by the action of four QTLs, contributed by alleles from both parents. The complexity of rind netting was demonstrated on a collection of 177 diverse accessions. Further dissection of netting in our RILs population, which is derived from a cross of smooth and densely netted parents, confirmed the intricacy of this trait and the involvement of major locus and several other interacting QTLs. A major netting QTL on chromosome 2 co-localized with results from two additional populations, paving the way for future study toward identification of a causative gene for this trait.
Introduction
Communicated by Sanwen Huang. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03567-3) contains supplementary material, which is available to authorized users. * Amit Gur [email protected] 1
Plant Science Institute, Agricultural Research Organization, Newe Ya’ar Research Center, P.O. Box 1021, 3009500 Ramat Yishay, Israel
2
Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7507101 Rishon LeZiyyon, Israel
3
The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
Melon, a major cucurbits crop, is of worldwide relevance with 32 million tons produced globally (FAO statistics 2017, www.fao.org). Being one of the top ten fruits produced, melons are an important part of the diet of many cultures and are a valuable source of both vitami
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