Identification of phenological QTLs using a combination of high- and low-coverage whole genome sequencing in Japanese plum (Prunus salicina Lindl.)

Abstract

The genetic control of phenological traits in Japanese plum (Prunus salicina Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F₁ populations: ‘Black Splendor’ × ‘Pioneer’ (BS×PIO), ‘Red Beaut’ × ‘Black Splendor’ (RB×BS), and ‘Red Beaut’ × ‘Santa Rosa Precoz’ (RB×SRP), comprising 121, 103, and 103 seedlings, respectively. Whole-genome sequencing (~80×) was conducted for the four parents, and progenies were genotyped using a cost-efficient reduced-representation sequencing strategy. SNPs heterozygous in one parent and homozygous in the other were used to build six parental linkage maps. Phenological traits, including beginning, full, and end of flowering (BF, FF, EF), flowering intensity (FI), ripening date (RD), fruit development period (FDP), and productivity (P), were evaluated over three years. A total of 53 QTLs were identified for flowering stages, 16 for RD, 18 for FDP, 10 for FI, and 16 for P. Many QTLs were stable across years. Major QTLs for flowering traits were mapped to LG1, LG2, LG4, and LG6, with a strong QTL for FF on LG6 of ‘Black Splendor’. In BS×PIO, BF was uncorrelated with FF and EF, indicating distinct genetic control likely inherited from ‘PIO’, a low-chill cultivar. RD and FDP were consistently associated with LG4, while productivity QTLs were detected on LG1, LG2, and LG4, often overlapping, suggesting pleiotropic or tightly linked loci. In addition, candidate genes within stable QTLs were detected, providing immediate targets for functional studies. This study provides one of the first genome-wide QTL analyses of phenology in Japanese plum using low-coverage whole genome sequencing and offers valuable tools for marker-assisted breeding in this species.

Acknowledgements

We gratefully acknowledge the CEBAS-CSIC/IMIDA Japanese plum breeding program, directed by Dr. Ruiz and Dr. Guevara, for providing the plant material used in this study. This work was supported by the project number 48675: Genetic improvement of agricultural species of interest to the Region of Murcia, Subproject: GI Fruit trees, financed by ERDF21-27 and by the AGROALNEXT programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Fundación Séneca with funding from Comunidad Autónoma Región de Murcia (CARM). María Nicolás-Almansa was supported by a PhD fellowship (FPU16/03896) from the Spanish Ministry of Economy, Industry and Competitiveness (MINECO).

Authors contributions

MNA, PJMG, and DR designed the project and edited the first draft of the manuscript. MNA and AG collected data. MNA performed statistical and genetic analyses. PJMG performed the genome and genetic analyses. PJB performed the resequencing analysis. MR, PJB, AG, DR, and PMG wrote and revised the manuscript. MNA and PJMG revised and finalized the manuscript. All authors contributed to the article and approved the submitted version.

Data availability

The genome sequencing data for this publication have been deposited to the NCBI BioProject database (http://www.ncbi.nlm.nih.gov/bioproject/1282032) under accession number PRJNA1282032.

Conflicts of interest statement

No competing interest is declared.

Supplementary material

Supplementary material is available at Horticulture Research online.

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