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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Crop and Commodity Protection Research » Research » Publications at this Location » Publication #375283

Research Project: Detection, Control and Area-wide Management of Fruit Flies and Other Quarantine Pests of Tropical/Subtropical Crops

Location: Tropical Crop and Commodity Protection Research

Title: Taro genome assembly and linkage map reveal QTLs for resistance to Taro Leaf Blight

Author
item BELLINGER, M - University Of Hawaii
item PAUDEL, ROSHAN - University Of Hawaii
item STARNES, STEVEN - University Of Hawaii
item KAMBIC, LUKAS - University Of Hawaii
item KANTAR, MICHAEL - University Of Hawaii
item WOLFGRUBER, THOMAS - University Of Hawaii
item LAMOUR, KURT - University Of Tennessee
item Geib, Scott
item Sim, Sheina
item MIYASAKA, SUSAN - University Of Hawaii
item HELMKAMPF, MARTIN - University Of Hawaii
item SHINTAKU, MICHAEL - University Of Hawaii

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2020
Publication Date: 6/16/2020
Citation: Bellinger, M.R., Paudel, R., Starnes, S., Kambic, L., Kantar, M., Wolfgruber, T., Lamour, K., Geib, S.M., Sim, S.B., Miyasaka, S., Helmkampf, M., Shintaku, M. 2020. Taro genome assembly and linkage map reveal QTLs for resistance to Taro Leaf Blight. G3, Genes/Genomes/Genetics. 10(6). https://doi.org/10.1534/g3.120.401367.
DOI: https://doi.org/10.1534/g3.120.401367

Interpretive Summary: The taro (Colocasia esculenta), and important food staple crop in the tropics. It is threatened by a fungus-like pathogen, Phythophthora colocasiae which causes taro leaf blight. In this study, the taro genome was sequenced and assembled and represents a highly contiguous genome in the understudied plant family Araceae. The genome was then assembled into linkage groups and used to perform a QTL analysis to identify loci linked to taro leaf blight resistance. This study provides foundational genomic resources for investigating disease resistance in taro with the potential for application to directed breeding programs.

Technical Abstract: Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ~60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. Family-level (Araceae) genome features reveal repeat content of taro to be 77%, ~3x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ~391 versus ~70 (~182 and ~46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTLs) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species.