Abstract Detail

Economic Botany Section

Boutain, Jeffrey [1], Nickum, Mark [2].

Phylogenetic Profiling Hawaii Avocado Cultivars Using a Genome Surfing Approach.

Introduction: The avocado (Persea americana Mill., Lauraceae) is an important world commodity with production exceeding 3.5 million tonnes of this exceptionally nutritious ‘superfood.’ Recent climate changes in the world’s avocado growing regions have decreased this year’s supply while demands continue to increase. Within the unique environments of the Hawaiian Islands, a year round supply of locally adapted avocado cultivars is possible. Little is known about the genetic composition of the Hawaii cultivars due to introgression with known cultivars and locally discovered hybrids with unknown parentage. An approach similar to ‘navigating the tip of the genomic iceberg’ is ‘surfing the genome’ for those adapted to subtropical and tropical latitudes. Thus, the primary goal of this research is to determine the maternal lineage of select Hawaii avocado cultivars using high-throughput sequencing and a chloroplast genome (plastome) phylogeny. Methods: Leaf material was collected from the University of Hawaii Waiakea Experiment Station in Hilo, Hawaii Island. DNA was extracted using E.Z.N.A. HP Plant DNA Mini Kit (Omega Bio-Tek) and prepared for 300 PE reads of v3 sequencing on a MiSeq as follows: 1) DNA was sheared at 30 seconds on /30 seconds off for 15 cycles at 4°C (Diagenode Bioruptor NGS), 2) DNA fragments between 150-500bp were collected using E.Z.N.A. Size Select-It Kit (Omega Bio-Tek), and 3) Illumina libraries were prepared using the NEBNext Ultra DNA Library Prep Kit and the corresponding NEBNext Multiplex Oligos for Illumina. Bioinformatics included developing a draft plastome of Persea borbonia (SRR837436) for reference mapped assemblies to each Hawaii cultivar using CLC Genomics Workbench. The draft plastomes of the avocados were aligned with MAFFT7 online server, and a Maximum Likelihood phylogeny was constructed with MEGA5.2. Results: The three horticultural races were identified, which correlates to the presumed centers of origin (i.e., Mexican, Guatemalan, and West Indian). Hybrid cultivars clustered to their respective clades, and possible maternal lineages were discovered. Conclusion: Phylogenomics, particularly using a single locus like the maternally inherited plastome as a DNA barcode, can clarify breeding lines of crop cultivars of unknown origins. With this study as a model, the identity of local avocados in the Hawaiian Islands can be determined for future agronomic research and development.

Related Links:
Tropical Fruit and Nut Crops Program

1 - University of Hawaii at Manoa, Botany Department and Department of Tropical Plant and Soil Sciences, 3190 Maile Way, Honolulu, HI, 96822, United States
2 - University of Hawaii at Manoa, Department of Tropical Plant and Soil Sciences, 3190 Maile Way, Room 102, Honolulu, HI, 96822, United States

Keywords:
avocado
Persea americana
Hawaii
High-Throughput Sequencing
chloroplast
plastome
phylogenomics.

Presentation Type: Oral Paper:Papers for Sections
Session: 5
Location: River Fork/Grove
Date: Monday, July 28th, 2014
Time: 11:30 AM
Number: 5012
Abstract ID:892
Candidate for Awards:Economic Botany Section best student paper