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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #339266
Title: Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus

Author
item DOUGHERTY, LAURA - Cornell University
item SINGH, RAKSHA - Cornell University
item BROWN, SUSAN - Cornell University
item Dardick, Christopher - Chris
item XU, KENONG - Cornell University

Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2017
Publication Date: 3/24/2018
Citation: Dougherty, L., Singh, R., Brown, S., Dardick, C.D., Xu, K. 2018. Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus. Journal of Experimental Botany. 69(7):1499-1516.

Interpretive Summary: New DNA sequencing technologies have enabled powerful approaches for gene discovery in genetically complex crop plant species such as trees. However, the use of these technologies is still limited in species that have complex genomes. Here, the genetic control of a weeping branch growth trait in Apple (Malus domestica) was mapped using a novel strategy that relied on identifying different types of DNA variants dubbed Type-I, Type-II, and Type-III that have different segregation patterns in the progeny of a population of apples. Type-II and Type-III variants were found to provide significantly better resolution for genetic mapping in out-crossing woody species which led to a much improved mapping method. We found a major locus for apple Weeping (W) on chromosome 13 and other minor genes on chromosomes 10 (W2), 16 (W3) and 5 (W4). Identification of the gene(s) responsible for weeping in apple are ongoing.

Technical Abstract: In recent years, next generation sequencing (NGS) based bulked segregant analysis (BSA) has become a powerful approach for allele discovery in non-model plant species. However, challenges remain, particular for out-crossing species with complex genomes. Here, the genetic control of a weeping branch growth trait in Apple (Malus domestica) was mapped from an F1 population derived from cross ‘Cheal’s Weeping’ (weeping) × ‘Evereste’ (standard) using a bulk segregant strategy. Two genomic DNA pools ‘weeping (17 progeny)’ and ‘standard (16 progeny)’ were subject to Illumina pair-end (2 x 151 bp) sequencing to 27.1 x and a 30.4 x genome (742.3Mb) coverage, respectively. DNA variants were identified specific to ‘weeping’ (84,542), ‘standard’ (92,148) and in common to both pools (173,169). A detailed analysis of the DNA variant genotypes in the two 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. (Note: the first allele is assumed to be linked to weeping and the allele in bold is a variant to the reference genome). Variant allele frequency and density based mapping revealed four genomic regions of significant association with the weeping trait: 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 much noisier and less certain than those from Type-II and Type-III variants, demonstrating that although Type-I variants are considered preferable, Type-II and Type-III variants provide better resolution for genetic mapping in out-crossing woody species.