The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality.
Mango Genome Consortium, Ian S E Bally, Aureliano Bombarely, Alan H Chambers, Yuval Cohen, Natalie L Dillon, David J Innes, María A Islas-Osuna, David N Kuhn, Lukas A Mueller, Ron Ophir, Aditi Rambani, Amir Sherman, Haidong Yan
Author Information
Ian S E Bally: Department of Agriculture and Fisheries, Horticulture and Forestry Science, 28 Peters St, Mareeba, QLD, 4880, Australia.
Aureliano Bombarely: Department of Bioscience, University of Milan, Via Celoria 26, 20133, Milan, Italy.
Alan H Chambers: Tropical Research and Education Center, Horticultural Sciences Department, University of Florida, 18905 SW 280th St, Homestead, FL, 33031, USA. ac@ufl.edu. ORCID
Yuval Cohen: Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel.
Natalie L Dillon: Department of Agriculture and Fisheries, Horticulture and Forestry Science, 28 Peters St, Mareeba, QLD, 4880, Australia.
David J Innes: Department of Agriculture and Fisheries, Horticulture and Forestry Science, EcoSciences Precinct, 41 Boggo Rd, Dutton Park, QLD, 4102, Australia.
María A Islas-Osuna: Centro de Investigación en Alimentación y Desarrollo, A.C, Carretera Gustavo Enrique Astiazarán Rosas 46, Col. La Victoria, 83304, Hermosillo, Sonora, Mexico.
David N Kuhn: Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Cutler Rd, Coral Gables, FL, 33158, USA.
Lukas A Mueller: Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA.
Ron Ophir: Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel.
Aditi Rambani: Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA.
Amir Sherman: Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel.
Haidong Yan: School of Plants and Environmental Sciences, Virginia Tech, Ag Quad Lane, Blacksburg, VA, 24061, USA.
BACKGROUND: Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. RESULTS: This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. CONCLUSIONS: The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.
