Abstract Detail

Comparative Genomics/Transcriptomics

Ryan, Gillian [1], Ashwal, Eli [2], Turgman-Cohen, Salomon [3], Cohen, Jim [4].

Intraindividual genomic variation and mutation in apple (Malus x domestica).

Due to the modular nature of plant growth, plants can develop the same type of organ independently and at different times during their lifetime. This development leads to intraindividual genetic variation that can influence 1) the diversity of gametes (sperm and egg) and offspring (seeds and spores) from a plant, 2) herbivore and pathogen resistance within a plant, and 3) environmental adaptation in different parts of a plant. Despite its utility in crop production and selection, genomic intraindividual variation within a single plant has yet to be empirically investigated. Using a combination of genomic sequencing and modeling, intraindividual variation within one apple tree (Malus x domestica Baumg.) was investigated. Eight leaf samples from across one ca. 35-year-old apple tree were collected and DNA isolated, which was subsequently sequenced with 100 bp paired-end reads using an Illumina HiSeq 2000. The resulting reads were mapped to the apple genome (ca. 750 Mb), and single nucleotide polymorphisms (SNPs) were identified. Depending on the genome version and the mapping and SNP calling criteria, 600,000 SNPS to 1,800,000 SNPs were identified as variant among the eight samples, resulting in ca. 0.01-0.025% variation across the genome of the apple tree. Five of the samples showed little genetic variation from each other, while the other three demonstrated more variation. Interestingly, ca. 50% of the mutations were missense mutations, and the other ca. 50% were silent mutations. Most of the mutations are in non-coding regions of the genome, but ca. 10% are in coding regions. A stochastic model of tree growth is developed to further investigate the influences of the modular plant growth and of the accumulation of individual mutations on the overall genetic variation across the tree. Although simple theoretical predictions of the expected numbers of mutations and branches in any tree may be inferred from average mutation and branching rates, stochastic simulations allow for the sampling of the variation in these values. Preliminary results from the model indicate that variation in the number of total mutations per branch across a population of clonal trees grown under identical conditions decreases with age, consistent with the Central Limit Theorem. However, as the number of mutations increases with age, the number of permutations, or unique ways to distribute those mutations across the genome, increases faster than exponential growth.

1 - Kettering University, Applied Physics, 1700 University Ave., Flint, MI, 48504, USA
2 - Kettering University, 1700 University Ave., Flint, MI, 48504, USA
3 - Kettering University, Chemical Engineering, 1700 University Ave., Flint, MI, 58504, USA
4 - Kettering University, Applied Biology, 1700 University Ave., Flint, MI, 48504, USA

Keywords:
Malus
Apple
genetic diversity
variation
Rosaceae
Mutation.

Presentation Type: Poster
Session: P, Comparative Genomics and Transcriptomics
Location: Exhibit Hall/Omni Hotel
Date: Monday, June 26th, 2017
Time: 5:30 PM This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PGT004
Abstract ID:269
Candidate for Awards:None