Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus. (29th January 2018)

• Record Type: Journal Article
• Authors: Dougherty, Laura; Singh, Raksha; Brown, Susan; Dardick, Chris; Xu, Kenong
• Is Part Of: Journal of experimental botany. Volume 69:Number 7(2018)
• Page Start: 1499
• Page End: 1516
• Publication Date: 2018-01-29
• Subjects: DNA variants -- Malus -- pooled genome sequencing -- RNA-seq -- segregation types -- weeping; Botany -- Periodicals; Botany, Experimental -- Periodicals; Plant physiology -- Periodicals; 580
• DOI: 10.1093/jxb/erx490
• Languages: English
• ISSNs: 0022-0957

Abstract

Abstract : Identifying and exploiting three informative DNA variant segregation types in pooled genome sequencing analysis of the weeping phenotype in Malus empowers an effective genetic mapping strategy in out-crossing woody species. 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 <h k×h k> (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 .