QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes

Authors: OREN, ELAD - Newe Ya'Ar Research Center; TZURI, GALIL - Newe Ya'Ar Research Center; DAFNA, ASAF - Cornell University; REESE, EVAN - Cornell University; SONG, BAOXING - Cornell University; FREILICH, SHIRI - Newe Ya'Ar Research Center; ELKIND, YONATAN - Hebrew University Of Jerusalem; ISAACSON, TAL - Newe Ya'Ar Research Center; SCHAFFER, ARTHUR - Volcani Center (ARO); TADMOR, YAAKOV - Newe Ya'Ar Research Center; BURGER, JOSEPH - Newe Ya'Ar Research Center; Buckler, Edward - Ed; GUR, AMIT - Newe Ya'Ar Research Center

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2021
Publication Date: 1/19/2022
Citation: Oren, E., Tzuri, G., Dafna, A., Reese, E.R., Song, B., Freilich, S., Elkind, Y., Isaacson, T., Schaffer, A.A., Tadmor, Y., Burger, J., Buckler IV, E.S., Gur, A. 2022. QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes. Horticulture Research. https://doi.org/10.1093/hr/uhab081.
DOI: https://doi.org/10.1093/hr/uhab081

Interpretive Summary: Breeding melon varieties with desirable traits such as earliness and long-shelf-life properties is a desired and challenging goal. The negative relationship of these traits requires their dissection to discrete elements that can be used to assemble favorable genetic combinations. In this study, we mapped earliness and ripening traits to the candidate gene level, combining second and third-generation sequencing technologies in the prioritization process. We identified two main loci associated with both earliness and ethylene emission (a ripening-related gaseous hormone), explaining the inherent negative correlation between them. Additionally, we identified a third separate locus for earliness that might help breed for early melons while retaining a longer shelf life. The associations of selected candidate genes presented in this manuscript will hopefully assist in breeding early, long-shelf-life melons and contribute to reducing food waste The parental genomes de novo assemblies submitted during this work are also part of a collaborative effort in creating the melon pan-genome--an important resource for the scientific community.

Technical Abstract: Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines “Dulce” (reticulatus, climacteric) and “Tam Dew” (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.