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Experimental Pipeline for SNP and SSR Discovery and Genotyping Analysis of Mango (Mangifera indica L.)
Year:
2016
Source of publication :
Bio-Protocol
Authors :
Cohen, Yuval
;
.
Eshed, Ravit
;
.
Ish-Shalom, Mazal
;
.
Ophir, Ron
;
.
Rosen, Ada
;
.
Rubinstein, Mor
;
.
Schwager, Michal Sharabi
;
.
Sherman, Amir
;
.
Volume :
6 (issue 16 - August 20)
Co-Authors:
Facilitators :
From page:
1
To page:
12
(
Total pages:
12
)
Abstract:

Establishing a reservoir of polymorphic markers is an important key for marker-assisted breeding. Many crops are still lack of such genomic infrastructure. Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are useful as markers because they are widespread over the genome and many technologies were developed for high throughput genotyping. We present here a pipeline for developing a reservoir of SNP and SSR markers for Mangifera indica L. as an example for fruit tree crops having no genomic information available. Our pipeline includes de novo assembly of reference transcriptome with MIRA and CAP3 based on reads produced by 454-GS FLX technology; Polymorphic loci discovery by alignment of Illumina resequencing to the transcriptome reference; Identifying a subset of loci that are polymorphic in the entire germplasm collection for downstream diversity analysis by genotyping with Fluidigm technology.

Note:

Article no. e1910

Related Files :
Diversity
Genetics
Mangifera indica
mango
Marker-assisted selection
SNP
SSR
Show More
Related Content
More details
DOI :
10.21769/BioProtoc.1910
Article number:
0
Affiliations:
Database:
Google Scholar
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
44960
Last updated date:
02/03/2022 17:27
Creation date:
12/11/2019 11:35
Scientific Publication
Experimental Pipeline for SNP and SSR Discovery and Genotyping Analysis of Mango (Mangifera indica L.)
6 (issue 16 - August 20)
Experimental Pipeline for SNP and SSR Discovery and Genotyping Analysis of Mango (Mangifera indica L.)

Establishing a reservoir of polymorphic markers is an important key for marker-assisted breeding. Many crops are still lack of such genomic infrastructure. Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are useful as markers because they are widespread over the genome and many technologies were developed for high throughput genotyping. We present here a pipeline for developing a reservoir of SNP and SSR markers for Mangifera indica L. as an example for fruit tree crops having no genomic information available. Our pipeline includes de novo assembly of reference transcriptome with MIRA and CAP3 based on reads produced by 454-GS FLX technology; Polymorphic loci discovery by alignment of Illumina resequencing to the transcriptome reference; Identifying a subset of loci that are polymorphic in the entire germplasm collection for downstream diversity analysis by genotyping with Fluidigm technology.

Article no. e1910

Scientific Publication
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