Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo)

Elad Oren; Asaf Dafna; Galil Tzuri; Ilan Halperin; Tal Isaacson; Meital Elkabetz; Ayala Meir; Uzi Saar; Shachar Ohali; Thuy La; Cinta Romay; Yaakov Tadmor; Arthur A Schaffer; Edward S Buckler; Roni Cohen; Joseph Burger; Amit Gur

doi:10.1111/tpj.16021

Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo)

Plant J. 2022 Dec;112(6):1525-1542. doi: 10.1111/tpj.16021. Epub 2022 Nov 23.

Authors

Elad Oren^#¹, Asaf Dafna^#^{1

2}, Galil Tzuri¹, Ilan Halperin¹, Tal Isaacson¹, Meital Elkabetz¹, Ayala Meir¹, Uzi Saar¹, Shachar Ohali¹, Thuy La³, Cinta Romay³, Yaakov Tadmor¹, Arthur A Schaffer⁴, Edward S Buckler^{3

5}, Roni Cohen¹, Joseph Burger¹, Amit Gur¹

Affiliations

¹ Cucurbits Section, Department of Vegetable Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 3009500, Israel.
² The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel.
³ Institute for Genomic Diversity, Cornell University, Ithaca, New York, 14853, USA.
⁴ Department of Vegetable Sciences, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, Rishon LeZiyyon, 7507101, Israel.
⁵ United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853, USA.

^# Contributed equally.

Abstract

Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled and integrated with phenotypic characterization of genetic diversity. We developed a multi-parental framework for trait dissection in melon (Cucumis melo), leveraging a novel pan-genome constructed for this highly variable cucurbit crop. A core subset of 25 diverse founders (MelonCore25), consisting of 24 accessions from the two widely cultivated subspecies of C. melo, encompassing 12 horticultural groups, and 1 feral accession was sequenced using a combination of short- and long-read technologies, and their genomes were assembled de novo. The construction of this melon pan-genome exposed substantial variation in genome size and structure, including detection of ~300 000 structural variants and ~9 million SNPs. A half-diallel derived set of 300 F₂ populations, representing all possible MelonCore25 parental combinations, was constructed as a framework for trait dissection through integration with the pan-genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color intensity and pattern, fruit sugar content, and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.

Keywords: Cucumis melo; SNP; crop breeding; disease resistance; fruit-quality; genetic mapping; half-diallel; pan-genome; structural variation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Mapping
Cucumis melo* / genetics
Cucurbitaceae* / genetics
Phenotype
Plant Breeding