The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

Abstract

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.

Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission

“…This is especially true given the identification of an atypical PIP T version of the mango IDA/IDL protein. The recent release of different mango genome sequences [48,49], opens now new avenues to explore the mango IDA-HAE/HSL2-like module. As such, a BLAST search using 'Tommy Atkins' mango genome led us to identifying three HAESA-like predicted proteins.…”

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

“…Polyembrony in mango was found to be associated to linkage group 8, along with a possible linkage of SNP markers to vegetative traits such as bloom and blush characters and fruit traits such as beak shape and pulp colour [ 8 ]. Whole genome assembly of mango using different high throughput sequencing techniques has been attempted by various research groups [ 97 , 234 , 235 , 236 ]. Integration of RNA sequence information with the genome assembly paved the way for identification of non-coding RNAs, two QTLs for fruit weight and chalcone synthase genes involved in flavanoid biosynthesis.…”

Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species

“…In cases where little to no genomic information is available, information should be extrapolated from existing genomic resources of closely related species, an approach Lemmon et al (2018) used to target domestication traits in the orphan crop "groundcherry." Though genome size and ploidy level often cause challenges in genome assembly, reference genomes do exist for several tropical crops (Ming et al, 2008;Argout et al, 2011;Prochnik et al, 2012;Xiao et al, 2017;Lantican et al, 2019;Sahu et al, 2020;Wang et al, 2020;Bally et al, 2021;Strijk et al, 2021). Pan-genomes, FIGURE 1 | when they do not exist for the varietal of interest but do exist for a different genotype or related species (C).…”

“…Another important workflow component is an annotated reference genome, which allows for quick identification of target sequences and homologous sites for genome editing ( Bortesi and Fischer, 2015 ). In cases where little to no genomic information is available, information should be extrapolated from existing genomic resources of closely related species, an approach Lemmon et al (2018) used to target domestication traits in the orphan crop “groundcherry.” Though genome size and ploidy level often cause challenges in genome assembly, reference genomes do exist for several tropical crops ( Ming et al, 2008 ; Argout et al, 2011 ; Prochnik et al, 2012 ; Xiao et al, 2017 ; Lantican et al, 2019 ; Sahu et al, 2020 ; Wang et al, 2020 ; Bally et al, 2021 ; Strijk et al, 2021 ). Pan-genomes, if available, offer a more robust view of a cultivar’s genetic variation since they consist of a core genome shared by all sequenced individuals, and reveal genetic variations that are present or absent in re-sequenced genomes ( Kyriakidou et al, 2018 ; Marschall et al, 2018 ).…”