To unlock the power of next generation sequencing-based bulked segregant analysis in allele discovery in out-crossing woody species, and to understand the genetic control of weeping trait, an F1 population from cross 'Cheal's Weeping' × 'Evereste' was used to create two genomic DNA pools 'weeping (17 progeny)' and 'standard (16 progeny)'. Illumina pair-end (2x151bp) sequencing of the pools to a 27.1x (weeping) and a 30.4x (standard) genome (742.3Mb) coverage allowed detection of 84,562 DNA variants specific to 'weeping', 92,148 specific to 'standard' and 173,169 common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation types of variants: <lm x mm> (Type-I) in weeping pool specific variants, and <lm x ll> (Type-II) and <hk x hk> (Type-III) in variants common to both pools. Note: the first allele is assumed weeping linked and the allele in bold is a variant to the reference genome. Conducting variant allele frequency and density-based mappings revealed four genomic regions with a significant association with weeping: a major locus Weeping (W) on chromosome 13 and others on chromosomes 10 (W2), 16 (W3) and 5 (W4). The results from Type-I variants were noisier and less certain than those from Type-II and Type-III variants, demonstrating that although Type-I variants are often the first choice, Type-II and Type-III variants represent an important source of DNA variants that can be exploited for genetic mapping in out-crossing woody species. Confirmation of the mapping of W and W2, investigation into their genetic interactions, and identification of expressed genes in the W and W2 regions provided insight into the genetic control of weeping and its expressivity in Malus.