Genome-wide association study and quantitative trait loci mapping of fruit-related traits using recombinant inbred lines in watermelon

• Published in: Scientia horticulturae 2024-12, Vol.338, p.113826, Article 113826
• Main Authors: Shahwar, Durre, Park, Girim, Jang, Gaeun, Shin, Jagyeong, Park, Seoyeon, Kwon, Gibeom, Kim, Yongjae, Kim, Hoytaek, Lee, Oakjin, Yunus, Mohammad Hadi, Park, Younghoon
• Format: Article
• Language: English
• Subjects: Citrullus lanatus; Fruit traits; GWAS; QTL mapping; Watermelon
• ISSN: 0304-4238
• DOI: 10.1016/j.scienta.2024.113826

•Analyzed 130 watermelon RILs, identified FC, FF, RH, and RT correlations.•QTL mapping and GWAS discovered significant genomic regions for these traits.•WGRS of parental lines revealed putative candidate genes.•Insights into mechanisms of watermelon fruit-related traits.•Identifies molecular markers for marker-assisted selection. Watermelons (Citrullus lanatus var. lanatus), an essential cucurbit crop of the Cucurbitaceae family, displays a diverse range of fruit-related traits, including flesh color (FC), flesh firmness (FF), rind hardness (RH), and rind thickness (RT). Understanding the genetic basis of this variation has considerable implications for watermelon breeding and broader crop enhancement. Herein, we conducted a genome-wide association study (GWAS) and quantitative trait loci (QTL) analysis using genotyping-by-sequencing of 130 watermelon recombinant inbred lines to identify putative candidate genes for FC, FF, RH, and RT. Analysis of the phenotypic correlation coefficients among the four traits revealed a significant positive correlation between FF and RH, and a negative correlation between FF and RT. The QTL mapping identified major QTLs that were considerably associated with FC (qFC-4.1) on Chr.4 (LOD=40.48, R2=0.67), FF (qFF-10.1) on Chr.10 (LOD=10.37, R2=0.28), RH (qRH-10.1) on Chr.10 (LOD=13.68, R2=0.33), and RT (qRT-2.1) on Chr.2 (LOD=20.03, R2=0.50) which were confirmed consitantly by the GWAS. Whole-genome resequencing of parental lines and sequence variation detection in genomic regions of QTLs revealed candidate genes, including Cla97C04G070940 (lycopene β-cyclase, LCYB) and Cla97C02G039880 (pentatricopeptide repeat, PPR) for FC, Cla97C10G187120 (ethylene responsive transcription factor 4, ERF4) for FF and RH, and Cla97C02G044160 (MADS box transcription factor AGAMOUS) for RT. Phenotypic distribution in RILs based on the genotype validated by the candidate gene-based CAPS and SCAR markers demonstrated a clear marker-to-phenotype association, highlighting the potential applicability of these markers for marker-assisted selection (MAS). This study provides valuable data resources that are essential not only for facilitating MAS breeding efforts, but also elucidating the molecular mechanisms underlying variations in the watermelon fruit-related traits.