The ‘Tommy Atkins’ Mango Genome Reveals Candidate Genes for Fruit Quality

Authors: BELLY, IAN - Department Of Agriculture And Fisheries; BOMBARELY, AURELIANO - University Of Milan; CHAMBERS, ALAN H - University Of Florida; COHEN, YUVAL - Agricultural Research Organization, Volcani Center; DILLON, NATALIE - Department Of Agriculture And Fisheries; INNES, DAVID - Department Of Agriculture And Fisheries; ISLA-OSUNA, MARIA - Centro De Investigacion En Alimentaction Y Desarollo; KUHN, DAVID - Retired ARS Employee; MUELLER, LUKAS - Boyce Thompson Institute; OPHIN, RON - Agricultural Research Organization, Volcani Center; RAMBANI, ADITI - Boyce Thompson Institute

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/28/2021
Publication Date: 2/22/2021
Citation: Belly, I., Bombarely, A., Chambers, A., Cohen, Y., Dillon, N., Innes, D., Isla-Osuna, M., Kuhn, D., Mueller, L., Ophin, R., Rambani, A. 2021. The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality. Biomed Central (BMC) Plant Biology. (201) 21:108.
DOI: https://doi.org/10.1186/s12870-021-02858-1

Interpretive Summary: Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past breeding improvement for this species relied predominantly on planting seedlings and selecting trees that display desired traits. This process requires substantial amounts of money, space, and time to grow large trees and wait up to seven or eight years for trees to bear fruit. The combined analysis of genetic and tree/fruit traits is poised to improve mango breeding efficiency; for instance, using genetic markers to detect favorable traits in small seedlings. However, historically there has been very limited molecular information on mango. This study sequenced, assembled, and annotated the genome of the commercially important mango cultivar ‘Tommy Atkins’ using next generation sequencing techniques. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate a highly resolved genetic map using single nucleotide polymorphisms (SNPs). Two regions containing 28 candidate genes were associated with the commercially important fruit size characteristic in the mapping population. Genetic markers can be designed from the regions found associated with fruit size to screen mangos as soon as leaves appear on seedlings. With the genome now available associations with other desirable traits can be investigated to ultimately improve mango breeding efficiency. The availability of the complete ‘Tommy Atkins’ mango genome can lead to additional discoveries in the future and will aid global initiatives to study mango genetics.

Technical Abstract: 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 1,000 cultivars in the Indian subcontinent 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 ~3.3M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3,348 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.