Journal Article

Analysis of genetic differences underlying chilling stress tolerance using whole genome Re-Sequencing in walnut (Juglans regia L.)

Sang, Yaxin, Zhang, Junpei, Wang, Hongxia, Ji, Lianlian, Liu, Feng, Liang, Dejun, Li, Yang, Liu, Kai, Zhang, Ruifen

2025

Overview

Walnut ( Juglans regia L.) is prized worldwide for both its nutritional value and economic importance, yet it remains vulnerable to cold stress, with significant differences in tolerance among varieties. This study combined physiological analyses with whole-genome resequencing (WGS) to evaluate the cold stress responses of two varieties, ‘Qingxiang’ and ‘Liaoning No.8’. Under chilling stress (0 °C), we measured electrolyte leakage and antioxidant enzyme activity, applying both exogenous methyl jasmonate (MeJA) and the jasmonate inhibitor DIECA. Genomic variations were analyzed using WGS. Results showed that ‘Liaoning No.8’ exhibited superior cold tolerance. Application of MeJA reduced electrolyte leakage by 37% and MDA accumulation by 52% on average, whereas DIECA exacerbated stress-related damage. WGS achieved 16.24–16.26× coverage and identified 2.73–2.78 million SNPs, 378–382k InDels, 25–26k SVs, and 7.2–7.9k CNVs. Twenty genes containing sequence variants showed transcriptional responses under cold stress that were significantly correlated with mutation density ( r  = 0.62, P  < 0.01). One gene, XM_018985465.2, which lacked SNPs in ‘Liaoning No.8’, was expressed 4.2 times more in this variety, suggesting cis-regulatory influence. These findings highlight the role of jasmonic acid signaling in enhancing cold tolerance in walnut and offer genomic insights into its underlying adaptive mechanisms.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Antioxidants / Biomedical and Life Sciences / Biosynthesis / Chilling stress / Cold / Cold tolerance / Cold tolerance and adaptation / Cooling / Cultivars / Diseases and pests / DNA sequencing / Economic importance / Electrolyte leakage / Enzymatic activity / Enzyme activity / Enzymes / Fatty acids / Food quality / Gene sequencing / Genes / Genetic analysis / Genetic aspects / Genomes / Genomics / Growth / Hardiness / Health aspects / Jasmonic acid / Jasmonic acid signaling / Juglans regia / Leakage / Life Sciences / Methyl jasmonate / Microarrays / Microbial Genetics and Genomics / Mutation / Mutation detection / Nucleotide sequencing / Nutritive value / Plant Genetics and Genomics / Plants / Polymorphism / Proteomics / Quality control / Single-nucleotide polymorphism / Stress response / Walnut / Whole genome re-sequencing