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Publication Overview
Abstract
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 the weeping trait, an F1 population from the cross ‘Cheal’s
Weeping’ × ‘Evereste’ was used to create two genomic DNA pools ‘weeping’ (17 progeny) and ‘standard’ (16 progeny).
Illumina pair-end (2 × 151 bp) sequencing of the pools to a 27.1× (weeping) and a 30.4× (standard) genome (742.3 Mb)
coverage allowed detection of 84562 DNA variants specific to ‘weeping’, 92148 specific to ‘standard’, and 173169
common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation
types of variants: (type I) in weeping pool-specific variants, and (type II) and (type
III) in variants common to both pools, where the first allele is assumed to be weeping linked and the allele shown in
bold is a variant in relation 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.
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