נגישות
menu      
Advanced Search
Syntax
Search...
Volcani treasures
About
Terms of use
Manage
Community:
אסיף מאגר המחקר החקלאי
Powered by ClearMash Solutions Ltd -
The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality
Year:
2021
Source of publication :
BMC Plant Biology
Authors :
Cohen, Yuval
;
.
Ophir, Ron
;
.
Sherman, Amir
;
.
Volume :
Co-Authors:

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 

Facilitators :
From page:
0
To page:
0
(
Total pages:
1
)
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.

Note:
Related Files :
de novo assembly
Fruit weight
Mangifera indica
QTL
Show More
Related Content
More details
DOI :
10.1186/s12870-021-02858-1
Article number:
0
Affiliations:
Database:
PubMed
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
53802
Last updated date:
02/03/2022 17:27
Creation date:
28/02/2021 22:04
Scientific Publication
The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality

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 

The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality

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.

Scientific Publication
You may also be interested in