Integrated QTL mapping and QTL‐seq reveal major loci for dormancy release timing and lateral bearing in walnut ( Juglans regia L.)

The timing of dormancy release and the spatial distribution of reproductive buds are crucial physiological processes for frost avoidance and yield formation in walnut ( Juglans regia L.). However, the major loci temporal stability and independent validation at high genomic resolution have not been adequately addressed in walnut. In this paper, high‐density linkage mapping, classical quantitative trait locus (QTL) analysis, and quantitative trait locus sequencing (QTL‐seq) were integrated to dissect the genetic control of leafing date (used as a field proxy for dormancy release timing) and lateral bearing in an F 1 population derived from Chandler × Kaplan‐86. High‐density parental genetic maps constructed using simple sequence repeats, single‐nucleotide polymorphisms (SNPs), and Diversity Arrays Technology markers resolved into 16 linkage groups corresponding to the haploid chromosome number of walnut. Classical QTL mapping consistently identified a major, highly consistent QTL for leafing date on linkage group 4 across four consecutive years, explaining up to ∼69% of phenotypic variance, together with several minor modifier loci. A major QTL was repeatedly detected on linkage group 8 (chromosome 11) for lateral bearing, accounting for up to ∼59% of phenotypic variance. The lateral bearing locus was independently validated by QTL‐seq through the detection of clusters of high‐confidence variants with extreme ΔSNP‐index values, which partially overlapped with the interval defined by linkage‐based QTL. This study links consistent genomic regions to dormancy release, bud development, and reproductive differentiation. It provides molecular targets for functional analyses and physiology‐informed breeding in walnut.